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(-) Description

Title :  HUMAN DNA POLYMERASE ETA-DNA TERNARY COMPLEX: REACTION FIRST WITH 1 MM MN2+ FOR 1800S THEN WITH 10 MM CA2+ FOR 60S
 
Authors :  Y. Gao, W. Yang
Date :  12 Jun 16  (Deposition) - 29 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  In Crystallo Reaction, Dna Polymerase, Metal Ion Dependent Catalysis, Replication, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Gao, W. Yang
Capture Of A Third Mg2+ Is Essential For Catalyzing Dna Synthesis.
Science V. 352 1334 2016
PubMed-ID: 27284197  |  Reference-DOI: 10.1126/SCIENCE.AAD9633

(-) Compounds

Molecule 1 - DNA POLYMERASE ETA
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: POLH, RAD30, RAD30A, XPV
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RAD30 HOMOLOG A,XERODERMA PIGMENTOSUM VARIANT TYPE PROTEIN
 
Molecule 2 - DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
    Chains: T
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*A)-3')
    Chains: P
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1DPO1Ligand/IonDIPHOSPHATE
2DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
3GOL3Ligand/IonGLYCEROL
4MN3Ligand/IonMANGANESE (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:13 , ASP A:115 , GLU A:116 , MN A:502 , DTP A:506 , HOH A:785 , DT P:8 , DA P:9binding site for residue MN A 501
2AC2SOFTWAREASP A:13 , MET A:14 , ASP A:115 , MN A:501 , DTP A:506 , DPO A:507 , DA P:9binding site for residue MN A 502
3AC3SOFTWAREARG A:24 , PRO A:244 , SER A:248 , GLY A:276 , HOH A:620 , HOH A:622 , HOH A:666 , HOH A:738binding site for residue GOL A 503
4AC4SOFTWAREGLU A:94 , ALA A:95 , GLU A:98 , ARG A:303 , HOH A:692 , HOH A:722 , HOH A:756binding site for residue GOL A 504
5AC5SOFTWAREASN A:26 , HIS A:28 , GLY A:271 , ILE A:272 , GLU A:273 , TYR A:274 , GLU A:277 , HOH A:601 , HOH A:604 , HOH A:727binding site for residue GOL A 505
6AC6SOFTWAREASP A:13 , MET A:14 , ASP A:15 , CYS A:16 , PHE A:17 , PHE A:18 , ILE A:48 , ALA A:49 , TYR A:52 , ARG A:55 , ARG A:61 , ASP A:115 , LYS A:231 , MN A:501 , MN A:502 , DPO A:507 , HOH A:625 , HOH A:631 , HOH A:656 , HOH A:688 , HOH A:785 , HOH A:806 , DT P:8 , DA P:9 , MN P:101 , HOH P:205 , HOH P:213 , HOH P:217 , HOH P:218 , DT T:3 , DT T:4 , DA T:5binding site for residue DTP A 506
7AC7SOFTWAREASP A:13 , MET A:14 , ASP A:15 , CYS A:16 , PHE A:17 , TYR A:52 , ARG A:55 , ARG A:61 , ASP A:115 , LYS A:231 , MN A:502 , DTP A:506 , HOH A:625 , HOH A:631 , HOH A:656 , HOH A:806 , DA P:9 , MN P:101binding site for residue DPO A 507
8AC8SOFTWAREARG A:61 , DTP A:506 , DPO A:507 , HOH A:631 , HOH A:688 , HOH A:806 , DA P:9 , HOH P:218binding site for residue MN P 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KG6)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:150 -Pro A:151
2Lys A:231 -Pro A:232
3Ser A:416 -Pro A:417

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KG6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KG6)

(-) Exons   (0, 0)

(no "Exon" information available for 5KG6)

(-) Sequences/Alignments

Asymmetric/Biological 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:431
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee.hhhhhhhhhhhhhhh...eeeee.......eeeeehhhhhh.......hhhhhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhhhh...eeeee..eeeeehhhhhhhhhhh......hhhhh..eee..........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh....eee....hhhhhhhhhhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeeee......eeehhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee........eeeeee....hhhhhhhhhhhhhhhhh......eeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kg6 A  -2 GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS 432
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      |161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431 
                                                                                                                                                                                      154|                                                                                                                                                                                                                                                                                 
                                                                                                                                                                                       159                                                                                                                                                                                                                                                                                 


Chain P from PDB  Type:DNA  Length:9
                                         
                 5kg6 P   1 AGCGTCATA   9


Chain T from PDB  Type:DNA  Length:12
                                            
                 5kg6 T   1 CATTATGACGCT  12
                                    10
   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 5KG6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KG6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KG6)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Leu A:150 - Pro A:151   [ RasMol ]  
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  5kg6
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  POLH_HUMAN | Q9Y253
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  2.7.7.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLH_HUMAN | Q9Y253: 2i5o 2lsk 3jaa 3mr2 3mr3 3mr5 3mr6 3si8 3tq1 3wup 4dl2 4dl3 4dl4 4dl5 4dl6 4dl7 4ecq 4ecr 4ecs 4ect 4ecu 4ecv 4ecw 4ecx 4ecy 4ecz 4ed0 4ed1 4ed2 4ed3 4ed6 4ed7 4ed8 4eey 4j9k 4j9l 4j9m 4j9n 4j9o 4j9p 4j9q 4j9r 4j9s 4o3n 4o3o 4o3p 4o3q 4o3r 4o3s 4q8e 4q8f 4rnm 4rnn 4rno 4ru9 4yp3 4yqw 4yr0 4yr2 4yr3 5dg7 5dg8 5dg9 5dga 5dgb 5dlf 5dlg 5dqg 5dqh 5dqi 5ewe 5ewf 5ewg 5f9l 5f9n 5jum 5kfa 5kfb 5kfc 5kfd 5kfe 5kff 5kfg 5kfh 5kfi 5kfj 5kfk 5kfl 5kfm 5kfn 5kfo 5kfp 5kfq 5kfr 5kfs 5kft 5kfu 5kfv 5kfw 5kfx 5kfy 5kfz 5kg0 5kg1 5kg2 5kg3 5kg4 5kg5 5kg7 5l1i 5l1j 5l1k 5l1l 5l9x

(-) Related Entries Specified in the PDB File

5kfa 5kfb 5kfc 5kfd 5kfe 5kff 5kfg 5kfh 5kfi 5kfj 5kfk 5kfl 5kfm 5kfn 5kfo 5kfp 5kfq 5kfr 5kfs 5kft 5kfu 5kfv 5kfw 5kfx 5kfy 5kfz 5kg0 5kg1 5kg2 5kg3 5kg4 5kg5 5kg7