Structure of PDB 5vzb Chain A

Receptor sequence

>5vzbA (length=327) Species: 9606 (Homo sapiens)

MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLK
ALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTM
KLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLS
TPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITH
PKEGQEAGLLPRVMCRLQDQGLILYHQHAFERSFCIFRLPQPGSWKAVRV
DLVVAPVSQFPFALLSWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQK
TFFQAASEEDIFRHLGLEYLPPEQRNA

3D structure

• PDB: 5vzb Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu.
• Chain: A
• Resolution: 1.5 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D330 D332 D418
• Catalytic site (residue number reindexed from 1): D193 D195 D251
• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	L177 F385 E386 R387 R442 R445 R449 K450 N457 H459	L40 F230 E231 R232 R275 R278 R282 K283 N290 H292
BS02	dna	A	T241 G245 V246 G247 T250 H329 R416	T104 G108 V109 G110 T113 H192 R249
BS03	dna	A	G174 R175 T178 F179 P203 H204 G206 H208 S209	G37 R38 T41 F42 P66 H67 G69 H71 S72
BS04	MG	A	D330 D332 D418	D193 D195 D251
BS05	MG	A	D330 D332	D193 D195
BS06	UTP	A	G320 R323 K325 H329 D330 D332 S433 W434 G436 K438	G183 R186 K188 H192 D193 D195 S266 W267 G269 K271

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0034061 DNA polymerase activity

Biological Process

• GO:0006281 DNA repair

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:5vzb, PDBe:5vzb, PDBj:5vzb
• PDBsum: 5vzb
• PubMed: 28911097
• UniProt: Q9NP87|DPOLM_HUMAN DNA-directed DNA/RNA polymerase mu (Gene Name=POLM)