Structure of PDB 3g0r Chain A Binding Site BS02

Receptor Information

>3g0r Chain A (length=255) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H)

VLKIISWNVNGLRAVHRKGFLKWFMEEKPDILCLQEIKAAPEQLPRKLRH
VEGYRSFFTPAERKGYSGVAMYTKVPPSSLREGFGVERFDTEGRIQIADF
DDFLLYNIYFPNGKMSEERLKYKLEFYDAFLEDVNRERDSGRNVIICGNF
NTAHREIDLARPKENSNVSGFLPVERAWIDKFIENGYVDTFRMFNSDPGQ
YTWWSYRTRARERNVGWRLDYFFVNEEFKGKVKRSWILSDVMGSDHCPIG
LEIEL

Ligand information

>3g0r Chain K (length=11)

ccctgugcagc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3g0r Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): N12 G13 R15 A16 R19 K20 K40 Q45 K66 G67 S207 Y208 R209 T210
• Binding residue (residue number reindexed from 1): N10 G11 R13 A14 R17 K18 K38 Q43 K64 G65 S205 Y206 R207 T208

Enzymatic activity

• Catalytic site (original residue number in PDB): N10 N12 E38 Y111 N151 N153 D222 D247 H248
• Catalytic site (residue number reindexed from 1): N8 N10 E36 Y109 N149 N151 D220 D245 H246
• Enzyme Commision number: 3.1.11.2: exodeoxyribonuclease III.
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003824 catalytic activity
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0004518 nuclease activity
• GO:0004519 endonuclease activity
• GO:0008081 phosphoric diester hydrolase activity
• GO:0008311 double-stranded DNA 3'-5' DNA exonuclease activity
• GO:0016787 hydrolase activity
• GO:0016829 lyase activity
• GO:0046872 metal ion binding
• GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

External links

• PDB: RCSB:3g0r, PDBe:3g0r, PDBj:3g0r
• PDBsum: 3g0r
• PubMed: 20434457
• UniProt: O26314|UREND_METTH DNA uridine endonuclease (Gene Name=MTH_212)