SMTL ID : 5l8d.1 (1 other biounit)

X-ray structure of NikA from Escherichia coli in complex with Ru(bis(pyrzol-1-yl)acetate scorpionate)(CO)2Cl

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

ACT.1: 4 residues within 4Å: Chain A: K.52, R.68, D.69, D.70 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.69 Salt bridges: A:K.52, A:R.68 ACT.2: 3 residues within 4Å: Chain A: N.261, E.262, L.263 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.261, A:L.263 Water bridges: A:A.264, A:R.266, 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.10: 3 residues within 4Å: Chain A: Q.361, S.372, L.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.361, A:L.373, A:L.373 ACT.11: 3 residues within 4Å: Chain A: K.148, N.149, K.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.149 Water bridges: A:H.150 Salt bridges: A:K.157 ACT.12: 1 residues within 4Å: Chain A: K.335 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.335 ACT.17: 2 residues within 4Å: Chain A: T.23, Q.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.26

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

SO4.4: 3 residues within 4Å: Chain A: E.343, R.384, R.389 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.343 Water bridges: A:R.384, A:R.384 Salt bridges: A:R.384, A:R.389

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: W.10, N.220, I.246, E.247, R.396, M.472, T.490 Ligands: GOL.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.220, A:N.220, A:E.247, A:R.396 Water bridges: A:E.247 GOL.6: 7 residues within 4Å: Chain A: W.10, P.11, G.219, N.220, G.222, L.223 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.220, A:N.220, A:G.222 Water bridges: A:R.205, A:N.220 GOL.7: 3 residues within 4Å: Chain A: D.227, T.228, R.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.231, A:R.231, A:R.231 GOL.13: 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:Q.168 GOL.14: 2 residues within 4Å: Chain A: P.327, A.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.328 GOL.15: 1 residues within 4Å: Chain A: K.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.316 Water bridges: A:R.333 GOL.16: 1 residues within 4Å: Chain A: N.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.281

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

FE.8: 1 residues within 4Å: Ligands: EDT.9 No protein-ligand interaction detected (PLIP)

1 x EDT: {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID(Non-covalent)

EDT.9: 9 residues within 4Å: Chain A: Y.22, M.27, R.97, W.100, R.137, W.398, Y.402, T.490 Ligands: FE.8 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.97, A:R.97, A:R.137, A:Y.402 Salt bridges: A:R.97, A:R.137, A:R.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez, S. et al., Efficient conversion of alkenes to chlorohydrins by a Ru-based artificial enzyme. Chem. Commun. (Camb.) (2017)

Release Date

2017-03-29

Peptides

Nickel-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Nickel-binding periplasmic protein

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