SMTL ID : 5c53.1

Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.57 Å

Oligo State

hetero-1-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.1101 Ligands: 4Y3.3, DOC.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.1101 MG.2: 4 residues within 4Å: Chain A: D.856, V.857, D.1101 Ligands: 4Y3.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.856, A:V.857, A:D.1101

1 x 4Y3: [[(2~{S},5~{R})-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3$l^{4}-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

4Y3.3: 17 residues within 4Å: Chain A: D.856, V.857, D.858, S.859, Q.860, E.861, H.898, R.909, K.913, I.914, Y.917, D.1101 Chain D: G.4, A.5 Ligands: MG.1, MG.2, DOC.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.856, A:Q.860, A:Y.917 Salt bridges: A:H.898, A:R.909, A:K.913, A:K.913, A:K.913

1 x DOC: 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

DOC.4: 8 residues within 4Å: Chain A: R.819, N.830, H.1100 Chain D: A.5, T.6 Chain E: A.21 Ligands: MG.1, 4Y3.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.819, A:N.830

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sohl, C.D. et al., Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2016-01-27

Peptides

DNA polymerase subunit gamma-1: A
Pol gamma B: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA polymerase subunit gamma-1

Pol gamma B

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