SMTL ID : 6q4t.1

KOD DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: D.404, F.405, L.408, D.542 Ligands: MG.2, HHZ.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.404, A:F.405, A:D.542

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 7 residues within 4Å: Chain A: Y.402, D.404, D.542, G.543 Chain C: C.12 Ligands: MN.1, HHZ.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.404, A:D.542, H2O.6, H2O.7 MG.14: 2 residues within 4Å: Chain B: G.8 Chain C: G.8 No protein-ligand interaction detected (PLIP)

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

EDO.3: 6 residues within 4Å: Chain A: D.6, Y.7, I.8, R.17, K.240, K.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.7, A:K.240, A:K.253 EDO.4: 9 residues within 4Å: Chain A: D.4, T.5, D.6, K.118, E.251, K.253, S.340, W.342, D.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.4, A:K.118 EDO.5: 7 residues within 4Å: Chain A: A.141, I.142, Y.209, N.210, F.214, D.215, D.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.142, A:I.142 EDO.6: 7 residues within 4Å: Chain A: R.266, L.333, T.349, L.352, A.485, I.488, L.489 No protein-ligand interaction detected (PLIP) EDO.7: 11 residues within 4Å: Chain A: P.36, Y.37, F.38, P.90, V.93, E.111, Y.112, D.113, I.114, F.116, R.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.37, A:Y.112, A:I.114 EDO.8: 9 residues within 4Å: Chain A: Y.402, F.545, Y.583, Y.594, V.596, T.604, R.606 Chain C: C.12 Ligands: HHZ.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.594, A:R.606, A:R.606 EDO.9: 4 residues within 4Å: Chain A: R.746, A.747, F.748, G.749 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.747

1 x HHZ: [[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[3-[2-(2-hydroxyethyloxy)ethanoylamino]prop-1-ynyl]pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

HHZ.10: 26 residues within 4Å: Chain A: D.404, F.405, R.406, S.407, L.408, Y.409, P.410, R.460, K.464, R.484, K.487, I.488, N.491, S.492, Y.494, G.495, T.541, D.542, R.606 Chain B: T.4, G.5 Chain C: A.11, C.12 Ligands: MN.1, MG.2, EDO.8 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:Y.409 Hydrogen bonds: A:S.407, A:S.407, A:L.408, A:Y.409, A:K.487, A:N.491 Water bridges: A:D.404, A:R.460, A:R.460, A:R.460, A:R.460, A:R.460, A:R.460, A:K.464, A:Q.483, A:E.578, A:R.606 Salt bridges: A:R.460, A:K.464, A:K.487, A:K.487, A:K.487

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.11: 4 residues within 4Å: Chain A: D.31, T.33, F.34, K.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.33, A:K.124 NO3.12: 5 residues within 4Å: Chain A: G.395, L.396, F.587, A.747, F.748 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.396 Water bridges: A:A.747

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.13: 6 residues within 4Å: Chain A: Y.7, P.90, Q.91, P.115, F.116, A.117 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.7, A:I.114, A:F.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kropp, H.M. et al., The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide. Angew.Chem.Int.Ed.Engl. (2019)

Release Date

2019-02-27

Peptides

DNA polymerase,DNA polymerase,DNA polymerase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase,DNA polymerase,DNA polymerase

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