SMTL ID : 7omg.1

Crystal structure of KOD DNA Polymerase in a ternary complex with an Uracil containing template

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 19 residues within 4Å: Chain A: D.404, F.405, R.406, S.407, L.408, Y.409, P.410, R.460, K.487, N.491, Y.494, T.541, D.542 Chain B: T.9, G.10 Chain C: C.12 Ligands: MG.2, MG.3, MN.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.409 Hydrogen bonds: A:S.407, A:L.408, A:Y.409, A:N.491 Water bridges: A:D.404, A:R.460, A:R.460, A:R.460, A:K.464, A:K.464, A:K.464, A:E.578 Salt bridges: A:R.460, A:K.464, A:K.487, A:K.487, A:K.487

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.404, F.405, E.580 Ligands: DTP.1, MN.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.404, A:E.580, H2O.2, H2O.3, H2O.3 MG.3: 6 residues within 4Å: Chain A: Y.402, D.404, D.542 Chain C: C.12 Ligands: DTP.1, MN.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.404, A:D.542, H2O.1, H2O.3

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 6 residues within 4Å: Chain A: D.404, F.405, D.542 Ligands: DTP.1, MG.2, MG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.404, A:F.405, A:D.542

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

EDO.5: 9 residues within 4Å: Chain A: D.113, I.114, E.354, W.355, L.358, K.371, R.503 Chain B: C.5, A.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.113, A:E.354, A:E.354, A:K.371, A:R.503 EDO.6: 3 residues within 4Å: Chain A: V.433, W.516, E.519 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.433 Water bridges: A:Y.520

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 2 residues within 4Å: Chain A: E.10, R.32 No protein-ligand interaction detected (PLIP) CA.8: 2 residues within 4Å: Chain A: N.568, L.571 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.568, A:L.571, H2O.1, H2O.2, H2O.4

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 3 residues within 4Å: Chain A: K.371 Chain B: C.5, A.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kropp, H.M. et al., Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase. Chembiochem (2021)

Release Date

2021-10-13

Peptides

DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase

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