SMTL ID : 5on1.2 (1 other biounit)

Crystal structure of NikA in complex with hydroxylated Fe-L1 (N-(2-hydroxybenzyl)-N'-(2-thiomethylbenzyl)-N,N'-ethylenediamine diacetic acid)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

FE.1: 1 residues within 4Å: Ligands: 9YK.2 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: 9YK.2, H2O.12

1 x 9YK: 2-[2-[[2,3-bis(oxidanyl)phenyl]methyl-(2-hydroxy-2-oxoethyl)amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid(Non-covalent)

9YK.2: 9 residues within 4Å: Chain A: Y.22, M.27, R.97, W.100, R.137, W.398, Y.402, T.490 Ligands: FE.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.22, 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:Y.22

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

ACT.3: 4 residues within 4Å: Chain A: T.203, P.225, D.227, T.228 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.203, A:P.225 Hydrogen bonds: A:D.227

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: I.246, M.472, Y.485, A.486 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.487 Water bridges: A:Y.218, A:Q.244, A:A.486 GOL.5: 8 residues within 4Å: Chain A: G.219, N.220, I.246, E.247, R.396, A.489, T.490 Ligands: DTD.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.220, A:N.220, A:E.247, A:R.396, A:A.489 GOL.8: 3 residues within 4Å: Chain A: E.343, R.384, R.389 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.343, A:R.384, A:R.389 Water bridges: A:R.384, A:R.384, A:R.384 GOL.9: 7 residues within 4Å: Chain A: E.221, V.249, S.353, M.356, F.394, H.395, R.396 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.221, A:S.353, A:H.395, A:R.396

1 x DTD: DITHIANE DIOL(Non-covalent)

DTD.6: 9 residues within 4Å: Chain A: W.10, P.11, R.205, Y.218, G.219, N.220, G.222, L.223 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.205

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

CL.7: 3 residues within 4Å: Chain A: L.21, Y.22, R.97 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: V.179, R.180, E.182 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez, S. et al., Cross-Linked Artificial Enzyme Crystals as Heterogeneous Catalysts for Oxidation Reactions. J. Am. Chem. Soc. (2017)

Release Date

2017-12-13

Peptides

Nickel-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Nickel-binding periplasmic protein

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