SMTL ID : 7a0c.1 (1 other biounit)

X-ray structure of NikA from Escherichia coli in complex with Fe-6-Me2-BPMCN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x FE: FE (III) ION(Non-functional Binders)

FE.1: 1 residues within 4Å: Ligands: QTT.2 No protein-ligand interaction detected (PLIP)

1 x QTT: 2-[[(1~{S},2~{S})-2-[methyl-[(6-methylpyridin-2-yl)methyl]amino]cyclohexyl]-[(6-methylpyridin-2-yl)methyl]amino]ethanoic acid(Non-covalent)

QTT.2: 9 residues within 4Å: Chain A: Y.22, M.27, W.100, R.137, W.398, Y.402, H.416, T.490 Ligands: FE.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.22, A:W.100, A:W.398, A:W.398, A:W.398, A:Y.402, A:T.490 Water bridges: A:R.137, A:R.137 Salt bridges: A:R.137 pi-Stacking: A:W.100, A:W.100

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

ACT.3: 3 residues within 4Å: Chain A: T.23, P.24, Q.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.26 ACT.4: 1 residues within 4Å: Chain A: R.384 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.384 ACT.5: 4 residues within 4Å: Chain A: K.330, D.331, I.332, R.365 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.331, A:I.332 Salt bridges: A:R.365 ACT.6: 2 residues within 4Å: Chain A: A.322, K.335 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.335 Salt bridges: A:K.335 ACT.7: 3 residues within 4Å: Chain A: N.261, E.262, L.263 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.261, A:L.263 Water bridges: A:A.264, A:R.266 ACT.8: 1 residues within 4Å: Chain A: K.192 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.180, A:K.192 ACT.9: 1 residues within 4Å: Chain A: R.457 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.457 ACT.10: 1 residues within 4Å: Chain A: R.68 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.68 Salt bridges: A:R.68 ACT.11: 2 residues within 4Å: Chain A: K.257, A.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.258 Salt bridges: A:K.257

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 6 residues within 4Å: Chain A: V.273, N.274, K.275, K.276, Q.309, Y.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.274, A:K.275, A:Y.310 GOL.13: 5 residues within 4Å: Chain A: R.386, D.387, P.414, S.415, Q.420 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.420 Water bridges: A:R.386, A:R.386 GOL.14: 8 residues within 4Å: Chain A: W.10, N.220, I.246, E.247, R.396, M.472, A.489, T.490 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.220, A:E.247, A:R.396 Water bridges: A:N.220, A:A.489, A:T.490, A:T.490 GOL.15: 5 residues within 4Å: Chain A: V.249, S.353, F.394, H.395, R.396 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.353, A:H.395, A:R.396 Water bridges: A:R.396 GOL.16: 6 residues within 4Å: Chain A: W.10, N.25, Q.26, M.27, F.28, T.490 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.25, A:M.27, A:F.28, A:T.490 Water bridges: A:R.137

1 x MG: MAGNESIUM ION(Non-covalent)

MG.17: 4 residues within 4Å: Chain A: K.275, A.290, D.291, S.308 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.291, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez, S. et al., A Selective Sulfide Oxidation Catalyzed by Heterogeneous Artificial Metalloenzymes Iron@NikA. Chemistry (2020)

Release Date

2020-11-04

Peptides

Nickel-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Nickel-binding periplasmic protein

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