SMTL ID : 4qcl.1

Crystal structure of the catalytic core of human DNA polymerase alpha in ternary complex with an RNA-primed DNA template and dCTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.1: 19 residues within 4Å: Chain A: D.525, F.526, N.527, S.528, L.529, Y.530, P.531, R.587, K.615, L.616, N.619, Y.622, T.668, D.669 Chain B: C.11 Chain C: G.10, G.11 Ligands: MG.2, ZN.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.530 Hydrogen bonds: A:S.528, A:S.528, A:L.529, A:Y.530, A:N.619 Water bridges: A:R.587, A:K.591, A:K.591, A:K.615, A:K.615, A:K.615 Salt bridges: A:R.587, A:K.615, A:K.615, A:K.615

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.525, F.526, D.669 Ligands: DCP.1, ZN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.525, A:F.526, A:D.669

3 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.3: 5 residues within 4Å: Chain A: D.525, D.669 Chain B: C.11 Ligands: DCP.1, MG.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.525, A:D.669, H2O.5, H2O.8 ZN.4: 2 residues within 4Å: Chain A: H.7, E.165 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.7, A:E.165 ZN.8: 1 residues within 4Å: Chain B: G.6 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.5: 4 residues within 4Å: Chain A: C.889, E.890, I.892, I.895 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.892, A:I.895, H2O.5

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.6: 8 residues within 4Å: Chain A: Q.4, V.5, F.6, I.32, P.169, A.181, E.182, A.183 No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: Y.53, K.102, Y.462, Y.466, I.467, V.468 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.102, A:V.468

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baranovskiy, A.G. et al., Activity and fidelity of human DNA polymerase alpha depend on primer structure. J.Biol.Chem. (2018)

Release Date

2014-11-26

Peptides

DNA polymerase alpha catalytic subunit: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase alpha catalytic subunit

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