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(-) Description

Title :  SNAPSHOT OF THE LARGE FRAGMENT OF DNA POLYMERASE I FROM THERMUS AQUATICUS PROCESSING MODIFIED PYRIMIDINES
 
Authors :  A. Marx, K. Diederichs, S. Obeid
Date :  11 Apr 12  (Deposition) - 27 Mar 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Dna Polymerase, Modified Nucleotides, A Family, Dna Synthesis, Rigid Linker, Non-Natural Nucleotide, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Obeid, H. Busskamp, W. Welte, K. Diederichs, A. Marx
Interactions Of Non-Polar And "Click-Able" Nucleotides In The Confines Of A Dna Polymerase Active Site.
Chem. Commun. (Camb. ) V. 48 8320 2012
PubMed-ID: 22766607  |  Reference-DOI: 10.1039/C2CC34181F

(-) Compounds

Molecule 1 - DNA POLYMERASE I, THERMOSTABLE
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: POLA, POL1
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: TAQ POLYMERASE 1
 
Molecule 2 - DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SYNTHETIC DNA
    Organism Taxid: 32630
    Other Details: DNA PRIMER
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*AP*AP*AP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)- 3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC DNA
    Organism Taxid: 32630
    Other Details: DNA TEMPLATE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric/Biological Unit (6, 18)
No.NameCountTypeFull Name
10R51Ligand/Ion2'-DEOXY-5-[(4-ETHYNYLPHENYL)ETHYNYL]URIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)
2ACT3Ligand/IonACETATE ION
3DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4EDO1Ligand/Ion1,2-ETHANEDIOL
5GOL9Ligand/IonGLYCEROL
6MG3Ligand/IonMAGNESIUM ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:573 , ARG A:587 , ASP A:610 , TYR A:611 , SER A:612 , GLN A:613 , ILE A:614 , GLU A:615 , HIS A:639 , ARG A:659 , ARG A:660 , LYS A:663 , THR A:664 , PHE A:667 , ASP A:785 , MG A:902 , MG A:903 , HOH A:1002 , HOH A:1006 , HOH A:1056 , HOH A:1066 , HOH A:1067 , HOH A:1084 , HOH A:1115 , DOC B:112 , DA C:204 , DG C:205BINDING SITE FOR RESIDUE 0R5 A 901
02AC2SOFTWAREASP A:610 , TYR A:611 , ASP A:785 , 0R5 A:901 , MG A:903BINDING SITE FOR RESIDUE MG A 902
03AC3SOFTWAREASP A:610 , ASP A:785 , 0R5 A:901 , MG A:902 , HOH A:1001 , HOH A:1002 , DOC B:112BINDING SITE FOR RESIDUE MG A 903
04AC4SOFTWAREARG A:660 , LYS A:663 , LYS A:831 , HOH A:1067 , HOH A:1115 , DOC B:112BINDING SITE FOR RESIDUE GOL A 904
05AC5SOFTWAREASP A:452 , TYR A:455 , ARG A:596 , ASP A:826BINDING SITE FOR RESIDUE ACT A 905
06AC6SOFTWAREGLY A:672 , GLU A:745 , ARG A:746 , DA C:203BINDING SITE FOR RESIDUE GOL A 906
07AC7SOFTWARETHR A:544 , TYR A:545 , PRO A:579 , ASN A:580 , ASN A:583 , GOL A:910 , HOH A:1136 , DC C:209 , DC C:210BINDING SITE FOR RESIDUE GOL A 907
08AC8SOFTWAREARG A:313 , TRP A:318 , ASP A:551BINDING SITE FOR RESIDUE ACT A 908
09AC9SOFTWARELYS A:354 , ASP A:355 , ARG A:563 , GLN A:566 , HOH A:1009 , HOH A:1073 , HOH A:1128BINDING SITE FOR RESIDUE GOL A 909
10BC1SOFTWARELEU A:552 , ASP A:578 , PRO A:579 , GOL A:907 , HOH A:1018 , DC C:209 , DC C:210BINDING SITE FOR RESIDUE GOL A 910
11BC2SOFTWARELYS A:508 , THR A:509 , ARG A:715 , LEU A:733 , GLU A:734 , ARG A:736 , HOH A:1134BINDING SITE FOR RESIDUE GOL A 911
12BC3SOFTWARESER A:460 , LYS A:542BINDING SITE FOR RESIDUE ACT A 912
13BC4SOFTWAREARG A:728 , TYR A:729 , HOH A:1013 , HOH A:1173BINDING SITE FOR RESIDUE GOL A 913
14BC5SOFTWAREGLU A:347 , ARG A:349 , GLY A:370 , ASP A:371BINDING SITE FOR RESIDUE EDO A 914
15BC6SOFTWAREDG B:107 , DG B:108 , HOH B:313 , HOH B:315 , HOH B:323 , DG C:208 , DC C:209 , HOH C:416BINDING SITE FOR RESIDUE GOL B 201
16BC7SOFTWAREARG A:728 , HOH A:1173 , DG C:206 , DC C:207BINDING SITE FOR RESIDUE GOL C 301
17BC8SOFTWAREHOH C:432 , HOH C:433 , HOH C:434 , HOH C:435BINDING SITE FOR RESIDUE MG C 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ELT)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:299 -Pro A:300
2Asp A:578 -Pro A:579

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ELT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ELT)

(-) Exons   (0, 0)

(no "Exon" information available for 4ELT)

(-) 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:539
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........eeeeee.........eeeeeee...eeee..hhhhhhhhh......hhhhhhhhhhhh........hhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh..................hhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhh.........eee.........eee..........hhhhhhhhh.ee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4elt A 294 LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE 832
                                   303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823         


Chain B from PDB  Type:DNA  Length:12
                                            
                 4elt B 101 GACCACGGCGCc 112
                                   110 |
                                     112-DOC


Chain C from PDB  Type:DNA  Length:16
                                                
                 4elt C 201 AAAAGGCGCCGTGGTC 216
                                   210
   Legend:   → Mismatch (orange background)
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    → 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 4ELT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ELT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ELT)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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        DPO1_THEAQ | P19821: 1bgx 1jxe 1ktq 1qss 1qsy 1qtm 1taq 1tau 2ktq 3ktq 3lwl 3lwm 3m8r 3m8s 3ojs 3oju 3po4 3po5 3py8 3rr7 3rr8 3rrg 3rrh 3rtv 3sv3 3sv4 3syz 3sz2 3t3f 4bwj 4bwm 4c8k 4c8l 4c8m 4c8n 4c8o 4cch 4df4 4df8 4dfj 4dfk 4dfm 4dfp 4dle 4dlg 4elu 4elv 4ktq 4n56 4n5s 4xiu 5e41 5ktq 5nkl 5szt

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3ojs 3oju 4elu 4elv