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(-) Description

Title :  CRYSTAL STRUCTURE OF DNA2 NUCLEASE-HELICASE
 
Authors :  C. Zhou, S. Pourmal, N. P. Pavletich
Date :  17 Oct 15  (Deposition) - 18 Nov 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dna Binding Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Zhou, S. Pourmal, N. P. Pavletich
Dna2 Nuclease-Helicase Structure, Mechanism And Regulation By Rpa.
Elife V. 4 2015
PubMed-ID: 26491943  |  Reference-DOI: 10.7554/ELIFE.09832

(-) Compounds

Molecule 1 - DNA REPLICATION ATP-DEPENDENT HELICASE/NUCLEASE DNA2
    ChainsA, B
    EC Number3.1.-.-, 3.6.4.12
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    GeneDNA2, DNA2L, KIAA0083
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymDNA REPLICATION ATP-DEPENDENT HELICASE-LIKE HOMOLOG

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:137 , ARG A:140 , ILE A:387 , CYS A:394 , CYS A:397 , CYS A:403binding site for residue SF4 A 1101
2AC2SOFTWAREGLY A:626 , LEU A:627 , ASN A:628 , GLN A:631 , GLY A:654 , LYS A:655 , THR A:656 , THR A:657 , LYS A:689 , TYR A:828binding site for residue ADP A 1102
3AC3SOFTWARECYS B:137 , ARG B:140 , ILE B:387 , CYS B:394 , CYS B:397 , CYS B:403 , MET B:423binding site for residue SF4 B 1101
4AC4SOFTWAREGLY B:626 , LEU B:627 , ASN B:628 , GLN B:631 , GLY B:654 , THR B:656 , THR B:657 , LYS B:689 , TYR B:828binding site for residue ADP B 1102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EAW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5EAW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EAW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EAW)

(-) Exons   (0, 0)

(no "Exon" information available for 5EAW)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:1046
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...hhhhhhhhhhhhhhh......hhhhh.eeeeeeeeeee...eeeeeeeee........eeeeee.hhhhh......eeee........eee......eee.....eehhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.ee............eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee..eeeeeeeeee........hhhhhhhhhhhhhhhhh......eeee........eeee.hhhhhhhhhhhhhhhhhhhhh.ee........ee........hhhhhhh..hhhhhhhhhhhh.........hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee............eeeeeee..............eeeeee.hhhhh..eeeee.......eeeee............eeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...............hhhhhhhhhhhhhh.hhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh....ee..........hhhhhhhhhhhhh...hhhhhhhhhhhh.eee........hhhhhh.eeeeee......hhhhhhhhhh.eeeeeeee..........hhhhhhh....hhhhhhhhhhh.eeee.ee...hhhhhhhhhhhh.....ee.hhhhhhh.....hhhhhhhhh.......hhhhhhhhhh....eeeee........eee..eeehhhhhhhhhhhhhhhhhh..hhh.eeee..hhhhhhhhhhhhhhh.....eeehhhhhh...eeeeeee...............hhhhhhhhh..eeeeeeeeehhhhhh.hhhhhhhhhhhhhh..eee.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5eaw A    1 MEPLDELDLLLLEAVPRVELLRKKADALFPETVLSRGVDNRYLVLAVETSQNERGAEEKRLHVTASQDREHEVLCILRNGWSSVPVEPGDIVHLEGDCTSEPWIIDDDFGYFILYPDMMISGTSVASSIRCLRRAVLSETFRGSDPATRQMLIGTILHEVFQKAISESFAPERLQELALQTLREVRHLKEMYRLNLSQDEILCEVEEYLPSFSKWAEDFMRKGPSSEFPQMQLSLPSDGRSSPCNIEVVKSLDIEESIWSPRFGLKGKIDVTVGVKIHRDCKMKYKVMPLELKTGKESNSIEHRSQVVLYTLLSQERREDPEAGWLLYLKTGQMYPVPANHLDKRELLKLRNWLAASLLHRVSRAAPGEEARLSALPQIIEEEKTCKYCSQIGNCALYSRAVEEDDASIPEAMLSKIQEETRHLQLAHLKYFSLWCLMLTLESQSKDNRKTHQSIWLTPASELEESGNCVGNLVRTEPVSRVCDGQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTVFRLDREERHGDISTPLGNLSKLMESTDPSKRLRELIIDFREPQFIAYLSSVLPHDAKDTVANILKGLNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHKVHPDIQKFTEEEICRSRSIASLAHLEELYNSHPIVATTCMGINHPIFSRKTFDFCIVDEASQISQPVCLGPLFFSRRFVLVGDHQQLPPLVVNREARALGMSESLFKRLERNESAVVQLTVQYRMNRKIMSLSNKLTYAGKLECGSDRVANAVLALPNLKDARLSLQLYADYSDSPWLAGVLEPDNPVCFLNTDKVPAPEQVENGGVSNVTEARLIVFLTSTFIKAGCSPSDIGVIAPYRQQLRIISDLLARSSVGMVEVNTVDKYQGRDKSLILVSFVRSNEDGTLGELLKDWRRLNVALTRAKHKLILLGSVSSLKRFPPLGTLFDHLNAEQLILDLPSREHESLSHIL 1056
                                    10  ||    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408   ||  420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      
                                       13|                                                                                                                                                                                                                              245|                                                                                                                                                                 412|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                        20                                                                                                                                                                                                                               248                                                                                                                                                                  415                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:1046
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...hhhhhhhhhhhhhhh......hhhhh.eeeeeeeeeee...eeeeeeeee........eeeeee.hhhhh......eeee........eee......eee.....eehhhhhhhh.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.ee............eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee..eeeeeeeeee........hhhhhhhhhhhhhhhhh......eeee........eeee.hhhhhhhhhhhhhhhhhhhhh.ee........ee........hhhhhhh..hhhhhhhhhhhh.........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......ee............eeeeeee..............eeeeee.hhhhh..eeeee.......eeeee............eeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhh...............hhhhhhhhhhhhhh.hhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh....ee..........hhhhhhhhhhhhh...hhhhhhhhhhhh.eeeee.....hhhhhh..eeeeee......hhhhhhhhhh.eeeeeeee..........hhhhhhh....hhhhhhhhhhh.eeee.ee...hhhhhhhhhhhh.....ee.hhhhhhh.....hhhhhhhhh.......hhhhhhhhhh....eeeee........eee..eeehhhhhhhhhhhhhhhhhh..hhh.eeee..hhhhhhhhhhhhhhh.....eeehhhhhh...eeeeeee...............hhhhhhhhh..eeeeeeeeehhhhhh.hhhhhhhhhhhhhh..eee.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5eaw B    1 MEPLDELDLLLLEAVPRVELLRKKADALFPETVLSRGVDNRYLVLAVETSQNERGAEEKRLHVTASQDREHEVLCILRNGWSSVPVEPGDIVHLEGDCTSEPWIIDDDFGYFILYPDMMISGTSVASSIRCLRRAVLSETFRGSDPATRQMLIGTILHEVFQKAISESFAPERLQELALQTLREVRHLKEMYRLNLSQDEILCEVEEYLPSFSKWAEDFMRKGPSSEFPQMQLSLPSDGRSSPCNIEVVKSLDIEESIWSPRFGLKGKIDVTVGVKIHRDCKMKYKVMPLELKTGKESNSIEHRSQVVLYTLLSQERREDPEAGWLLYLKTGQMYPVPANHLDKRELLKLRNWLAASLLHRVSRAAPGEEARLSALPQIIEEEKTCKYCSQIGNCALYSRAVEEDDASIPEAMLSKIQEETRHLQLAHLKYFSLWCLMLTLESQSKDNRKTHQSIWLTPASELEESGNCVGNLVRTEPVSRVCDGQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTVFRLDREERHGDISTPLGNLSKLMESTDPSKRLRELIIDFREPQFIAYLSSVLPHDAKDTVANILKGLNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHKVHPDIQKFTEEEICRSRSIASLAHLEELYNSHPIVATTCMGINHPIFSRKTFDFCIVDEASQISQPVCLGPLFFSRRFVLVGDHQQLPPLVVNREARALGMSESLFKRLERNESAVVQLTVQYRMNRKIMSLSNKLTYAGKLECGSDRVANAVLALPNLKDARLSLQLYADYSDSPWLAGVLEPDNPVCFLNTDKVPAPEQVENGGVSNVTEARLIVFLTSTFIKAGCSPSDIGVIAPYRQQLRIISDLLARSSVGMVEVNTVDKYQGRDKSLILVSFVRSNEDGTLGELLKDWRRLNVALTRAKHKLILLGSVSSLKRFPPLGTLFDHLNAEQLILDLPSREHESLSHIL 1056
                                    10  ||    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408   ||  420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      
                                       13|                                                                                                                                                                                                                              245|                                                                                                                                                                 412|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                        20                                                                                                                                                                                                                               248                                                                                                                                                                  415                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5EAW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EAW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EAW)

(-) Gene Ontology  (38, 38)

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        DNA2_MOUSE | Q6ZQJ55ean 5eax

(-) Related Entries Specified in the PDB File

5ean 5eax 5eay