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

X-ray structure of the diatomic oxo-intermediate NikA/1-Int', prior hydroxylation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

ACT.1: 3 residues within 4Å: Chain A: K.52, R.68, D.69 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.52 Hydrogen bonds: A:D.69 Water bridges: A:K.52, A:L.67 Salt bridges: A:K.52, A:R.68 ACT.2: 3 residues within 4Å: Chain A: N.261, E.262, L.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.263 Water bridges: A:A.264, A:R.266 ACT.3: 2 residues within 4Å: Chain A: N.235, A.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.235 ACT.15: 6 residues within 4Å: Chain A: R.89, L.92, R.95, V.108, D.109, V.110 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.89, A:L.92 Hydrogen bonds: A:R.95, A:D.109, A:V.110

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

SO4.4: 2 residues within 4Å: Chain A: R.384, R.389 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.384, A:R.389

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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.6: 4 residues within 4Å: Chain A: F.147, K.148, N.149, K.157 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.147, A:N.149, A:K.157, A:K.157 GOL.7: 4 residues within 4Å: Chain A: E.358, Q.361, S.372, L.373 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.358, A:Q.361, A:L.373, A:L.373 GOL.13: 8 residues within 4Å: Chain A: N.220, I.246, E.247, R.396, M.472, A.489, T.490 Ligands: GOL.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.220, A:E.247, A:R.396 Water bridges: A:E.247 GOL.14: 7 residues within 4Å: Chain A: W.10, P.11, G.219, N.220, G.222, L.223 Ligands: GOL.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.220, A:G.222, A:G.222 GOL.16: 7 residues within 4Å: Chain A: F.28, S.31, K.39, R.140, E.491, I.492, E.495 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.28, A:K.39, A:R.140, A:I.492 Water bridges: A:K.39, A:R.140

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

FE.8: 2 residues within 4Å: Ligands: BHZ.9, PER.10 No protein-ligand interaction detected (PLIP)

1 x BHZ: 2-[2-[carboxymethyl(phenylmethyl)amino]ethyl-[(2-hydroxyphenyl)methyl]amino]ethanoic acid(Non-covalent)

BHZ.9: 11 residues within 4Å: Chain A: Y.22, M.27, R.97, W.100, R.137, W.398, Y.402, H.416, T.490 Ligands: FE.8, PER.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.398, A:T.490 Water bridges: A:T.23, A:R.137 Salt bridges: A:R.97, A:R.137, A:R.137 pi-Stacking: A:W.398, A:W.398, A:Y.402

1 x PER: PEROXIDE ION(Non-covalent)

PER.10: 3 residues within 4Å: Chain A: R.137 Ligands: FE.8, BHZ.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.137

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

CL.11: 2 residues within 4Å: Chain A: H.442, D.443 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: R.68 Ligand excluded by PLIP

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

Related Entries With Identical Sequence