SMTL ID : 4xkr.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

NI.1: 2 residues within 4Å: Ligands: HIS.2, 41K.3 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: HIS.2, HIS.2

1 x HIS: HISTIDINE(Non-covalent)

HIS.2: 11 residues within 4Å: Chain A: L.17, R.234, Y.322, R.325, I.354, E.355, Y.369, S.370 Ligands: NI.1, 41K.3, NA.23 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:I.354, A:Y.369 Hydrogen bonds: A:Y.322, A:E.355, A:S.370 Water bridges: A:L.17, A:L.17 Salt bridges: A:R.234, A:R.325, H.2

1 x 41K: (2R,4R)-2-methyl-1,3-thiazolidine-2,4-dicarboxylic acid(Non-covalent)

41K.3: 14 residues within 4Å: Chain A: D.28, F.134, R.234, R.325, Y.369, S.370, F.371, G.372, Y.381, I.393 Ligands: NI.1, HIS.2, GOL.22, NA.23 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.371, A:I.393 Hydrogen bonds: A:R.325, A:G.372 Salt bridges: A:R.234, A:R.234, H.2

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

EPE.4: 6 residues within 4Å: Chain A: Y.101, K.388, K.389, D.390, D.404 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.388, A:K.388, A:K.389, A:K.389 Salt bridges: A:D.390, A:D.390

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: K.318, K.349, Y.357 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: K.32, T.209, Q.444, K.456, G.461, I.462, Y.463 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: Q.295, I.297, D.338, K.341 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: Y.101, N.384, K.388, K.389, G.391 Ligands: EPE.4 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: D.260, G.263, I.264, H.267, I.268, V.334 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain A: E.90, M.93, I.105, S.106, S.107, I.108 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: R.252, Y.398, N.399, N.400, D.433 Ligands: GOL.18 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: D.256, R.261, T.277, P.290, K.291, T.293, S.431 Ligand excluded by PLIP GOL.13: 10 residues within 4Å: Chain A: Q.58, N.60, D.61, T.62, T.63, T.119, S.121, A.122, Y.123, L.126 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain A: Q.148, T.149, K.159, D.160 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain A: K.41, Y.463, I.465 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain A: K.226, K.453, N.454, Y.455 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain A: K.349, V.351, D.352, D.353, Y.357 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain A: H.242, N.244, K.245, M.247, T.248, K.249, R.252 Ligands: GOL.11 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain A: K.54, K.69, D.70, N.71 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain A: T.109, A.110, K.111, K.114, L.115, T.116 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain A: E.83, K.86, T.109, A.110 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain A: L.98, F.134, A.392, I.393, K.395 Ligands: 41K.3, NA.23 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.23: 5 residues within 4Å: Chain A: E.355, Y.369 Ligands: HIS.2, 41K.3, GOL.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.355, A:E.355

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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