SMTL ID : 5l8d.2 (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

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

ACT.1: 3 residues within 4Å: Chain A: T.203, P.225, D.227 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.203, A:P.225 ACT.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.13: 3 residues within 4Å: Chain A: T.23, Q.26 Ligands: CMO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.23, A:Q.26

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: S.243, Q.244, I.246, Y.485, A.486, A.489 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.244, A:Q.244, A:A.486 Water bridges: A:A.486, A:A.486 GOL.3: 8 residues within 4Å: Chain A: W.10, P.11, R.205, G.219, N.220, G.222, L.223 Ligands: GOL.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.220, A:N.220, A:G.222 Water bridges: A:R.205, A:N.220, A:N.220, A:G.222 GOL.4: 8 residues within 4Å: Chain A: W.10, N.220, I.246, E.247, R.396, A.489, T.490 Ligands: GOL.3 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.9: 7 residues within 4Å: Chain A: V.273, N.274, K.275, K.276, S.308, Q.309, Y.310 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.274, A:K.275, A:K.275, A:K.276, A:Y.310 GOL.14: 1 residues within 4Å: Chain A: K.314 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.314

1 x RU: RUTHENIUM ION(Non-functional Binders)

RU.6: 4 residues within 4Å: Ligands: CL.7, 6RP.8, CMO.11, CMO.12 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: CMO.12

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

CL.7: 5 residues within 4Å: Chain A: R.137 Ligands: RU.6, 6RP.8, CMO.11, CMO.12 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: M.27, F.28, T.490 Ligand excluded by PLIP

1 x 6RP: bis(pyrzol-1-yl)acetate scorpionate(Non-covalent)

6RP.8: 12 residues within 4Å: Chain A: Y.22, M.27, W.100, R.137, W.398, Y.402, H.416, T.490 Ligands: RU.6, CL.7, CMO.11, CMO.12 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.398, A:T.490 Salt bridges: A:R.137 pi-Stacking: A:W.100, A:W.100, A:W.398, A:W.398, A:Y.402

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.11: 6 residues within 4Å: Chain A: R.137 Ligands: RU.6, CL.7, 6RP.8, CMO.12, ACT.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.137 Water bridges: A:Q.26 CMO.12: 4 residues within 4Å: Ligands: RU.6, CL.7, 6RP.8, CMO.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.398

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
B

Nickel-binding periplasmic protein

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