Structure of PDB 2dy4 Chain B Binding Site BS02

Receptor Information
>2dy4 Chain B (length=888) Species: 12353 (Escherichia phage RB69) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYF
DIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYE
IKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFD
LLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLME
YLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRV
KVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNV
GKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYY
AKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPI
PNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERP
SDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIK
DVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLIN
SLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGE
AFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAID
RGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWD
MEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYF
KEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRA
IKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLH
WMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFD
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2dy4 A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		N284 D621 K706 Y708 M728 G729 K734 S735 S784 N786 N787 K800 H804
Binding residue
(residue number reindexed from 1)		N284 D607 K692 Y694 M714 G715 K720 S721 S770 N772 N773 K786 H790
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0004527 exonuclease activity
GO:0008408 3'-5' exonuclease activity
GO:0046872 metal ion binding
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0039686 bidirectional double-stranded viral DNA replication
GO:0039693 viral DNA genome replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2dy4, PDBe:2dy4, PDBj:2dy4
PDBsum2dy4
PubMed17210917
UniProtQ38087|DPOL_BPR69 DNA-directed DNA polymerase (Gene Name=43)

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