Structure of PDB 1yqk Chain A Binding Site BS03

Receptor Information
>1yqk Chain A (length=312) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEFGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGV
LADQVWTLTQTEEQLHCTVYRSQASRPTPDELEAVRKYFQLDVTLAQLYH
HWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSCNNIARITGMVER
LCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSAS
ARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDK
PQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYA
GWAQAVLFSADL
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain1yqk Chain A Residue 328 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1yqk Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		C241 L243 V246
Binding residue
(residue number reindexed from 1)		C230 L232 V235
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.2.-
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003824 catalytic activity
GO:0004519 endonuclease activity
GO:0005515 protein binding
GO:0008017 microtubule binding
GO:0008534 oxidized purine nucleobase lesion DNA N-glycosylase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016829 lyase activity
GO:0019104 DNA N-glycosylase activity
GO:0019899 enzyme binding
GO:0032357 oxidized purine DNA binding
GO:0034039 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0140097 catalytic activity, acting on DNA
Biological Process
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006285 base-excision repair, AP site formation
GO:0006289 nucleotide-excision repair
GO:0006355 regulation of DNA-templated transcription
GO:0006974 DNA damage response
GO:0006979 response to oxidative stress
GO:0009314 response to radiation
GO:0009410 response to xenobiotic stimulus
GO:0009416 response to light stimulus
GO:0032355 response to estradiol
GO:0034614 cellular response to reactive oxygen species
GO:0043066 negative regulation of apoptotic process
GO:0044029 positive regulation of gene expression via chromosomal CpG island demethylation
GO:0045007 depurination
GO:0045008 depyrimidination
GO:0045471 response to ethanol
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0051593 response to folic acid
GO:0071276 cellular response to cadmium ion
GO:1901291 negative regulation of double-strand break repair via single-strand annealing
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:0016363 nuclear matrix
GO:0016607 nuclear speck
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1yqk, PDBe:1yqk, PDBj:1yqk
PDBsum1yqk
PubMed15800616
UniProtO15527|OGG1_HUMAN N-glycosylase/DNA lyase (Gene Name=OGG1)

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