SMTL ID : 3mzb.1 (1 other biounit)

X-ray structure of NikA in complex with the doubly hydroxylated iron complex, 1-O2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

ACT.1: 5 residues within 4Å: Chain A: N.270, D.291, H.459, A.462, Y.464 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.464 Water bridges: A:V.463 Salt bridges: A:H.459 ACT.2: 4 residues within 4Å: Chain A: K.52, R.68, D.69, D.70 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.69 Water bridges: A:K.52, A:L.67, A:R.68, A:D.70 Salt bridges: A:K.52, A:R.68 ACT.3: 2 residues within 4Å: Chain A: N.302, G.304 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.304 ACT.4: 4 residues within 4Å: Chain A: N.261, E.262, L.263 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.263 Water bridges: A:A.264, A:A.264 ACT.5: 2 residues within 4Å: Chain A: N.235, A.237 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.237 Hydrogen bonds: A:N.235 ACT.6: 2 residues within 4Å: Chain A: N.482, Q.496 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.482 ACT.7: 4 residues within 4Å: Chain A: Q.385, F.394, H.395, R.396 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.396 Water bridges: A:Q.385, A:H.395 Salt bridges: A:H.395

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

SO4.8: 3 residues within 4Å: Chain A: E.343, R.384, R.389 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.343 Water bridges: A:R.384 Salt bridges: A:R.384, A:R.389

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain A: A.158, P.159, L.167, Q.168 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.167 GOL.10: 4 residues within 4Å: Chain A: F.147, K.148, N.149, K.157 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.149, A:K.157 Water bridges: A:F.147, A:F.147, A:H.150, A:K.157 GOL.11: 7 residues within 4Å: Chain A: S.243, Q.244, I.246, M.472, Y.485, A.486, A.489 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.243, A:Q.244, A:A.486 Water bridges: A:A.486 GOL.12: 2 residues within 4Å: Chain A: N.281, I.359 No protein-ligand interaction detected (PLIP) GOL.13: 7 residues within 4Å: Chain A: R.68, D.69, P.78, F.79, D.80, K.115, T.116 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.68, A:D.80 Water bridges: A:D.69, A:F.79 GOL.14: 5 residues within 4Å: Chain A: E.86, R.89, P.144, F.147, H.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.86, A:R.89 Water bridges: A:E.82, A:E.82, A:S.145 GOL.15: 9 residues within 4Å: Chain A: T.255, N.261, L.263, R.266, G.424, L.425, A.426, E.461 Ligands: ACT.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.255, A:N.261, A:L.263, A:R.266, A:R.266, A:A.426 Water bridges: A:N.261, A:D.427, A:E.461 GOL.23: 2 residues within 4Å: Chain A: E.210, T.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.210 GOL.24: 4 residues within 4Å: Chain A: D.453, T.456, R.457, D.460 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.460 GOL.25: 5 residues within 4Å: Chain A: F.229, A.230, S.233, L.242, T.286 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.285

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.16: 2 residues within 4Å: Chain A: T.23, Q.26 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: K.330, D.331, R.365 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain A: R.97 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain A: S.53, W.54 Ligand excluded by PLIP

1 x BHR: 2-[2-[carboxymethyl-[(2-hydroxyphenyl)methyl]amino]ethyl-[(2,3-dihydroxyphenyl)methyl]amino]ethanoic acid(Non-covalent)

BHR.19: 10 residues within 4Å: Chain A: Y.22, T.23, M.27, R.97, W.100, R.137, W.398, Y.402, T.490 Ligands: FE.20 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.22, A:Y.22, A:T.23, A:T.490 Hydrogen bonds: A:R.137 Water bridges: A:Y.402 Salt bridges: A:R.137

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

FE.20: 1 residues within 4Å: Ligands: BHR.19 No protein-ligand interaction detected (PLIP)

1 x DTD: DITHIANE DIOL(Non-covalent)

DTD.21: 8 residues within 4Å: Chain A: W.10, P.11, R.205, Y.218, G.219, N.220, G.222, L.223 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.220, A:N.220, A:N.220, A:G.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cavazza, C. et al., Crystallographic snapshots of the reaction of aromatic C-H with O(2) catalysed by a protein-bound iron complex. NAT.CHEM. (2010)

Release Date

2011-02-09

Peptides

Nickel-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Nickel-binding periplasmic protein

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