SMTL ID : 4i8c.3 (2 other biounits)

X-ray structure of NikA in complex with Ni-(L-His)2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

2 x HIS: HISTIDINE(Non-covalent)

HIS.1: 9 residues within 4Å: Chain A: Y.22, M.27, W.100, R.137, W.398, Y.402, H.416 Ligands: HIS.2, NI.3 11 PLIP interactions: 8 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:W.100, A:W.398, A:Y.402 Hydrogen bonds: A:S.415 Salt bridges: A:R.137, H.1, H.2 pi-Stacking: A:W.398, A:W.398, A:Y.402 Water bridges: H.2 HIS.2: 11 residues within 4Å: Chain A: Y.22, T.23, M.27, R.97, R.137, Y.382, R.386, S.415, H.416 Ligands: HIS.1, NI.3 11 PLIP interactions: 8 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.382 Hydrogen bonds: A:T.23, A:R.137, A:S.415, H.2 Water bridges: A:R.97, H.1, H.1 Salt bridges: A:R.97, A:R.386 pi-Cation interactions: A:R.137

1 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 3 residues within 4Å: Chain A: H.416 Ligands: HIS.1, HIS.2 3 PLIP interactions: 2 Ligand-Ligand interactions, 1 interactions with chain A Metal complexes: HIS.1, HIS.2, A:H.416

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 5 residues within 4Å: Chain A: V.273, K.275, K.276, S.308, Y.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.275, A:K.276 Salt bridges: A:K.276 ACT.5: 3 residues within 4Å: Chain A: T.441, H.442, D.443 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.442, A:D.443 ACT.6: 6 residues within 4Å: Chain A: Y.382, Q.385, F.394, H.395, R.396, H.416 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.396 Hydrogen bonds: A:Y.382, A:Y.382, A:Q.385, A:R.396 Salt bridges: A:H.395, A:H.416

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: Q.361, D.370, V.371, S.372, L.373 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.370, A:L.373 GOL.8: 2 residues within 4Å: Chain A: N.261, E.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.261

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

SO4.9: 1 residues within 4Å: Chain A: R.341 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.341 Salt bridges: A:R.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lebrette, H. et al., The binding mode of Ni-((L)-His)(2) in NikA revealed by X-ray crystallography. J.Inorg.Biochem. (2012)

Release Date

2013-01-30

Peptides

Nickel-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Nickel-binding periplasmic protein

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