SMTL ID : 4xkp.1

Crystal structure of NikA from Staphylococcus aureus in complex with Ni(L-His)2 (co-crystallization with Ni(II) and BHI medium supernatant)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-functional Binders)

NI.1: 2 residues within 4Å: Ligands: HIS.2, HIS.3 3 PLIP interactions: 3 Ligand-Ligand interactions Metal complexes: HIS.2, HIS.2, HIS.3

2 x HIS: HISTIDINE(Non-covalent)

HIS.2: 10 residues within 4Å: Chain A: L.17, R.234, Y.322, R.325, I.354, E.355, Y.369, S.370 Ligands: NI.1, HIS.3 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:I.354, A:Y.369 Hydrogen bonds: A:Y.322, A:S.370 Water bridges: A:L.17 Salt bridges: A:R.234, A:R.325, H.2 HIS.3: 11 residues within 4Å: Chain A: F.134, R.234, R.325, E.355, Y.369, S.370, F.371, G.372, I.393 Ligands: NI.1, HIS.2 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.234, A:R.325, A:G.372 Water bridges: A:E.355, A:K.395 Salt bridges: A:R.234, H.3 pi-Stacking: A:F.371

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: K.54, K.69, D.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.70 Water bridges: A:E.67, A:E.67 GOL.5: 3 residues within 4Å: Chain A: E.83, A.110, K.111 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.110 GOL.7: 8 residues within 4Å: Chain A: D.256, R.261, T.277, P.290, K.291, T.293, S.431, V.434 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.256, A:T.277, A:T.293, A:S.431 Water bridges: A:R.261, A:T.293, A:T.293 GOL.8: 8 residues within 4Å: Chain A: K.32, T.209, Q.444, V.446, K.456, G.461, I.462, Y.463 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.32, A:T.458 Water bridges: A:K.32, A:T.209, A:T.209, A:D.210, A:Q.444, A:T.458, A:G.461, A:G.461, A:G.461 GOL.9: 6 residues within 4Å: Chain A: D.260, G.263, I.264, H.267, I.268, V.334 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.260, A:Q.295 GOL.10: 5 residues within 4Å: Chain A: T.109, A.110, K.114, L.115, T.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.114 GOL.11: 3 residues within 4Å: Chain A: K.318, K.349, Y.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.318, A:K.318, A:K.349 GOL.12: 4 residues within 4Å: Chain A: K.226, K.453, N.454, Y.455 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.226, A:N.454, A:Y.455, A:Y.455, A:Y.455 GOL.13: 4 residues within 4Å: Chain A: K.349, V.351, D.352, D.353 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.349, A:D.352, A:D.353, A:D.353 Water bridges: A:K.349

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

EPE.6: 4 residues within 4Å: Chain A: Y.101, K.389, D.390, D.404 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.101 Salt bridges: A:D.390, A:D.390

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lebrette, H. et al., Novel insights into nickel import in Staphylococcus aureus: the positive role of free histidine and structural characterization of a new thiazolidine-type nickel chelator. Metallomics (2015)

Release Date

2015-02-11

Peptides

Nickel ABC transporter substrate-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Nickel ABC transporter substrate-binding protein

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