Structure of PDB 5vzd Chain A

Receptor sequence

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

MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLK
ALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTM
KLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLS
TPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITH
PKEGQEAGLLPRVMCRLQDQGLILYHQHAFERSFCIFRLPQPGSWKAVRV
DLVVAPVSQFPFALLGATGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQK
TFFQAASEEDIFRHLGLEYLPPEQRNA

3D structure

• PDB: 5vzd Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu.
• Chain: A
• Resolution: 1.602 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 F389 R442 R445 R449 K450 N457 H459	L40 F230 E231 R232 F234 R275 R278 R282 K283 N290 H292
BS02	dna	A	G245 V246 G247 T250 F389 R416 D418	G108 V109 G110 T113 F234 R249 D251
BS03	dna	A	G174 R175 T178 F179 H204 G206 H208 S209	G37 R38 T41 F42 H67 G69 H71 S72
BS04	2KH	A	G319 G320 R323 K325 G328 H329 D330 D332 G433 A434 G436 K438	G182 G183 R186 K188 G191 H192 D193 D195 G266 A267 G269 K271
BS05	MG	A	D330 D332 D418	D193 D195 D251
BS06	MG	A	D330 D332	D193 D195

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