Structure of PDB 5vzi Chain A

Receptor sequence

>5vziA (length=326) Species: 9606 (Homo sapiens)

MPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLK
ALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTM
KLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLS
TPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITH
PKEGQEAGLLPRVMCRLQDQGLILYHQHFERSFCIFRLPQPGSWKAVRVD
LVVAPVSQFPFALLGHTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKT
FFQAASEEDIFRHLGLEYLPPEQRNA

3D structure

• PDB: 5vzi 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 D250
• 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 F229 E230 R231 F233 R274 R277 R281 K282 N289 H291
BS02	dna	A	G245 V246 G247 T250 H329 D330 D332 F389 R416 D418 G433 H434 T435 G436 K438	G108 V109 G110 T113 H192 D193 D195 F233 R248 D250 G265 H266 T267 G268 K270
BS03	dna	A	G174 R175 T178 F179 H204 G206 H208 S209	G37 R38 T41 F42 H67 G69 H71 S72
BS04	TTP	A	G319 G320 R323 H329	G182 G183 R186 H192
BS05	TTP	A	G319 G320 R323 H329 D330 D332 G433 H434 G436 K438	G182 G183 R186 H192 D193 D195 G265 H266 G268 K270
BS06	MG	A	D330 D332	D193 D195
BS07	MG	A	D330 D332 D418	D193 D195 D250

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