SMTL ID : 5lew.1

DNA polymerase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.8, E.67, H.101, C.152, D.220 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.67, A:H.101, A:C.152, H2O.3 ZN.2: 5 residues within 4Å: Chain A: H.8, H.10, E.67, D.220 Ligands: ZN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.8, A:H.10, A:E.67, A:D.220, H2O.3 ZN.3: 4 residues within 4Å: Chain A: D.17, H.42, H.222 Ligands: SO4.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.17, A:H.42, A:H.222, H2O.1

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

SO4.4: 5 residues within 4Å: Chain A: H.42, Y.69, Y.99, H.101 Ligands: ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.69, A:Y.99 Water bridges: A:H.101, A:S.154 Salt bridges: A:H.42, A:H.101 SO4.5: 4 residues within 4Å: Chain A: G.584, L.585, R.586, N.587 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.586, A:N.587 Salt bridges: A:R.586 SO4.6: 2 residues within 4Å: Chain A: H.537, Y.569 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.569 Salt bridges: A:H.537 SO4.7: 5 residues within 4Å: Chain A: V.441, Q.443, G.561, A.562, I.563 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.443, A:Q.443, A:I.563, A:I.563 SO4.8: 4 residues within 4Å: Chain A: D.191, H.192, G.256, K.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.192 Water bridges: A:G.193 Salt bridges: A:K.260 SO4.9: 4 residues within 4Å: Chain A: R.177, P.182, L.211, N.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.211, A:N.212 Salt bridges: A:R.177 SO4.10: 6 residues within 4Å: Chain A: P.332, D.333, G.334, Y.335, R.336, E.337 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.333, A:G.334, A:Y.335, A:R.336, A:E.337, A:E.337 SO4.11: 5 residues within 4Å: Chain A: F.46, S.123, Q.127, S.132, W.555 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.123, A:Q.127, A:S.132, A:S.132 SO4.12: 5 residues within 4Å: Chain A: N.587, I.590, G.629, F.631, D.634 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.634, A:Y.803

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.13: 10 residues within 4Å: Chain A: M.667, R.676, K.684, G.703, L.704, I.705, T.768, P.771, F.772, Y.775 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.684, A:K.684, A:I.705, A:F.772 Salt bridges: A:R.676

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banos-Mateos, S. et al., High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center. Nat Commun (2017)

Release Date

2017-10-25

Peptides

DNA polymerase III subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase III subunit alpha