SMTL ID : 4i9d.2 (1 other biounit)

X-ray structure of NikA in complex with Fe-N,N'-Bis(2-pyridylmethyl)-N-carboxymethyl-N'-methyl

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: W.10, P.11, G.219, N.220, G.222, L.223 Ligands: GOL.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.220, A:G.222, A:G.222 Water bridges: A:R.205, A:Y.218, A:N.220 GOL.2: 8 residues within 4Å: Chain A: V.273, N.274, K.275, K.276, D.291, S.308, Q.309, Y.310 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.275, A:K.275, A:K.276, A:Y.310 Water bridges: A:V.273, A:S.308 GOL.4: 7 residues within 4Å: Chain A: E.221, V.249, S.353, M.356, F.394, H.395, R.396 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.221, A:E.221, A:R.396 Water bridges: A:F.394, A:R.396 GOL.6: 7 residues within 4Å: Chain A: N.220, I.246, E.247, R.396, A.489, T.490 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.220, A:N.220, A:E.247, A:R.396 GOL.10: 2 residues within 4Å: Chain A: D.4, E.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.4, A:D.4, A:E.5, A:E.5 GOL.11: 4 residues within 4Å: Chain A: W.63, A.125, Y.126, Y.127 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.127 GOL.14: 3 residues within 4Å: Chain A: K.52, S.53, W.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.52, A:W.54, A:W.54 GOL.16: 7 residues within 4Å: Chain A: K.257, E.343, R.384, R.389, F.390, G.391 Ligands: ACT.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.257, A:K.257 Water bridges: A:K.257, A:S.345, A:R.384, A:G.391

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

ACT.3: 2 residues within 4Å: Chain A: R.389 Ligands: GOL.16 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.389 Water bridges: A:K.257, A:R.384, A:R.384 Salt bridges: A:K.257, A:R.384, A:R.389 ACT.5: 1 residues within 4Å: Chain A: H.150 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.150 ACT.7: 2 residues within 4Å: Chain A: L.430, R.457 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.430 Salt bridges: A:R.457 ACT.8: 1 residues within 4Å: Chain A: R.341 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.341 ACT.9: 2 residues within 4Å: Chain A: K.306, K.314 5 PLIP interactions: 5 interactions with chain A Water bridges: A:K.306, A:Q.309, A:D.311 Salt bridges: A:K.306, A:K.314 ACT.12: 4 residues within 4Å: Chain A: T.23, P.24, Q.26, E.378 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.23, A:T.23, A:Q.26 ACT.15: 4 residues within 4Å: Chain A: Q.385, H.416, A.417 Ligands: L4D.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:H.416 Hydrogen bonds: A:Q.385, A:S.415, A:A.417 Salt bridges: A:H.416

1 x L4D: {(S)-N-(2-{methyl[(pyridin-2-yl-kappaN)methyl]amino-kappaN}ethyl)-N-[(pyridin-2-yl-kappaN)methyl]glycinato-kappa~2~N,O}iron(2+)(Non-covalent)

L4D.13: 7 residues within 4Å: Chain A: Y.22, M.27, W.100, R.137, W.398, T.490 Ligands: ACT.15 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Water interactions Hydrophobic interactions: A:T.490 Salt bridges: A:R.137 pi-Cation interactions: A:W.100, A:W.100, A:W.100, A:W.398 Metal complexes: H2O.21, H2O.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esmieu, C. et al., An artificial oxygenase built from scratch: substrate binding site identified using a docking approach. Angew.Chem.Int.Ed.Engl. (2013)

Release Date

2013-04-17

Peptides

Nickel-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Nickel-binding periplasmic protein

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