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(-) Description

Title :  CRYSTAL STRUCTURE OF DNA2 IN COMPLEX WITH A 5' OVERHANG DNA
 
Authors :  C. Zhou, S. Pourmal, N. P. Pavletich
Date :  16 Oct 15  (Deposition) - 18 Nov 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Dna Binding Protein, Hydrolase-Dna Complex (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
    Chains: A
    EC Number: 3.1.-.-, 3.6.4.12
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: DNA2, DNA2L, KIAA0083
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: DNA REPLICATION ATP-DEPENDENT HELICASE-LIKE HOMOLOG
 
Molecule 2 - DNA (5'-D(P*AP*CP*TP*CP*TP*GP*CP*CP*AP*AP*GP*AP*GP*GP*A)- 3')
    Chains: B
    Engineered: YES
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA2Ligand/IonCALCIUM ION
3SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3SF42Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:137 , ARG A:140 , CYS A:394 , CYS A:397 , CYS A:403binding site for residue SF4 A 1101
2AC2SOFTWAREHIS A:164 , ASP A:278 , GLU A:299 , LEU A:300 , DA B:12 , HOH B:201binding site for residue CA A 1102
3AC3SOFTWAREGLY A:626 , LEU A:627 , ASN A:628 , GLN A:631 , GLY A:654 , THR A:656 , THR A:657 , LYS A:689 , TYR A:828binding site for residue ADP A 1103
4AC4SOFTWARELYS A:301 , HOH A:1202 , DG B:11 , DA B:12 , DG B:13 , HOH B:201 , HOH B:202binding site for residue CA B 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EAN)

(-) 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:1051
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh.....hhhhhhhhhhhhhh............eeeeeeeeee.....eeeeeeee........eeeee.hhhhhh......eeeee......eeee.....eeee.....eehhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.ee............eeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee..eeeeeeeeeeee......hhhhhhhhhhhhhhhh.......eeeeee.....eeeee.hhhhhhhhhhhhhhhhhhhhh.eee......eee........hhhhhhh..hhhhhhhhhhhh.........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhh...eeeee......eeee..eeeeeee...............eeeeee.hhhhh..eeeeeeee...eeeeee............eeeee......hhhhhhhhhhhh..hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh....ee..hhhhh...hhhhhhhhhhhhh...hhhhhhhhhh...eeeee.hhh.hhhhhh..eeeeee.hhhhhhhhhhhhhhh.eeeeeeee..........hhhhhhh....hhhhhhhhhhh.eeee.ee...hhhhhhhhhhhh.....ee.hhhhhhh.....hhhhhhhhhh.......hhhhhhhhh....eeeee........eee..eeehhhhhhhhhhhhhhhhhh..hhh.eeee..hhhhhhhhhhhhhhh.....eeehhhhhh...eeeeeee...........hhhhhhhhhhhhhh.eeeeeeeeehhhhhh.hhhhhhhhhhhhh...eee.....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ean A   -2 GGHMEPLDELDLLLLEAVPRVELLRKKADALFPETVLSRGVDNRYLVLAVETSQNERGAEEKRLHVTASQDREHEVLCILRNGWSSVPVEPGDIVHLEGDCTSEPWIIDDDFGYFILYPDMMISGTSVASSIRCLRRAVLSETFRGSDPATRQMLIGTILHEVFQKAISESFAPERLQELALQTLREVRHLKEMYRLNLSQDEILCEVEEYLPSFSKWAEDFMRKGPSSEFPQMQLSLPSDGRSSPCNIEVVKSLDIEESIWSPRFGLKGKIDVTVGVKIHRDCKMKYKVMPLELKTGKESNSIEHRSQVVLYTLLSQERREDPEAGWLLYLKTGQMYPVPANHLDKRELLKLRNWLAASLLHRVSRAAPGEEARLSALPQIIEEEKTCKYCSQIGNCALYSRAVEEQGDDASIPEAMLSKIQEETRHLQLAHLKYFSLWCLMLTLESQSKDNRKTHQSIWLTPASELEESGNCVGNLVRTEPVSRVCDGQYLHNFQRKNGPMPATNLMAGDRIILSGEERKLFALSKGYVKKMNKAAVTCLLDRNLSTLPATTVFRLDREERHGDISTPLGNLSKLMESTDPSKRLRELIIDFREPQFIAYLSSVLPHDAKDTVANILKGLNKPQRQAMKRVLLSKDYTLIVGMPGTGKTTTICALVRILSACGFSVLLTSYTHSAVDNILLKLAKFKVGFLRLGQSHKVHPDIQKFTEEEICRSRSIASLAHLEELYNSHPIVATTCMGINHPIFSRKTFDFCIVDEASQISQPVCLGPLFFSRRFVLVGDHQQLPPLVVNREARALGMSESLFKRLERNESAVVQLTVQYRMNRKIMSLSNKLTYAGKLECGSDRVANAVLALPNLKDARLSLQLYADYSDSPWLAGVLEPDNPVCFLNTDKVPAPEQVENGGVSNVTEARLIVFLTSTFIKAGCSPSDIGVIAPYRQQLRIISDLLARSSVGMVEVNTVDKYQGRDKSLILVSFVRSNEDGTLGELLKDWRRLNVALTRAKHKLILLGSVSSLKRFPPLGTLFDHLNAEQLILDLPSREHESLSHIL 1056
                                     7     || 23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243 ||    255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055 
                                          13|                                                                                                                                                                                                                              245|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                           20                                                                                                                                                                                                                               248                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:DNA  Length:15
                                                
                5ean B    1 ACTCTGCCAAGAGGA   15
                                    10
   Legend:   → Mismatch (orange background)
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  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 5EAN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 38)

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  DNA2_MOUSE | Q6ZQJ5
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DNA2_MOUSE | Q6ZQJ5: 5eaw 5eax

(-) Related Entries Specified in the PDB File

5eaw 5eax 5eay