SMTL ID : 5c52.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.64 Å

Oligo State

hetero-1-2-mer

Ligands

1 x 1RY: [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

1RY.1: 16 residues within 4Å: Chain A: R.819, V.857, D.858, S.859, Q.860, E.861, R.909, K.913, Y.917, Q.1068, D.1101 Chain D: G.4, A.5 Chain E: C.22 Ligands: MG.2, MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.860 Salt bridges: A:H.898, A:R.909, A:K.913, A:K.913, A:K.913 pi-Stacking: A:Y.917

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.856, D.1101 Chain E: C.22 Ligands: 1RY.1 No protein-ligand interaction detected (PLIP) MG.3: 5 residues within 4Å: Chain A: D.856, V.857, D.858, D.1101 Ligands: 1RY.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.856, A:V.857

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

2016-05-11

Peptides

DNA polymerase subunit gamma-1: A
DNA polymerase subunit gamma-2, mitochondrial: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA polymerase subunit gamma-1

DNA polymerase subunit gamma-2, mitochondrial

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