SMTL ID : 6r4q.2 (1 other biounit)

Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)CO H2O Cl

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x RU: RUTHENIUM ION(Non-covalent)

RU.1: 4 residues within 4Å: Chain A: R.137 Ligands: 6RP.2, CL.3, CMO.4 No protein-ligand interaction detected (PLIP)

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

6RP.2: 10 residues within 4Å: Chain A: Y.22, M.27, W.100, R.137, W.398, Y.402, H.416 Ligands: RU.1, CL.3, CMO.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.398 Salt bridges: A:R.137 pi-Stacking: A:W.100, A:W.100, A:W.398, A:W.398, A:W.398, A:W.398, A:Y.402

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

CL.3: 4 residues within 4Å: Chain A: R.137 Ligands: RU.1, 6RP.2, CMO.4 Ligand excluded by PLIP

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

CMO.4: 5 residues within 4Å: Chain A: R.137 Ligands: RU.1, 6RP.2, CL.3, GOL.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.137

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: W.10, P.11, G.219, N.220, G.222, L.223 Ligands: GOL.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.220, A:N.220, A:G.222, A:G.222 Water bridges: A:R.205 GOL.6: 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:R.396 Water bridges: A:S.353 GOL.7: 3 residues within 4Å: Chain A: D.427, L.430, R.457 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.457, A:R.457 GOL.8: 3 residues within 4Å: Chain A: I.374, E.376, R.384 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.384 Water bridges: A:G.375 GOL.9: 8 residues within 4Å: Chain A: W.10, N.25, Q.26, M.27, F.28, R.137, T.490 Ligands: CMO.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.25, A:M.27, A:F.28, A:R.137, A:R.137, A:T.490 Water bridges: A:Q.26 GOL.10: 6 residues within 4Å: Chain A: N.220, E.247, R.396, A.489, T.490 Ligands: GOL.5 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.13: 4 residues within 4Å: Chain A: Q.241, N.482, P.484, Y.485 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.482, A:N.482, A:Y.485 Water bridges: A:Q.241 GOL.14: 6 residues within 4Å: Chain A: F.209, E.210, G.212, I.214, Y.238, K.477 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.209, A:G.212

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

ACT.11: 1 residues within 4Å: Chain A: R.68 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.68 ACT.12: 3 residues within 4Å: Chain A: Y.300, L.303, Q.448 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.300, A:L.303, A:Q.448 Hydrogen bonds: A:Q.448 Water bridges: A:R.452

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cavazza, C. et al., Crystal structure of the periplasmic nickel-binding protein NikA from Escherichia coli in complex with Ru(bpza)CO H2O Cl. To Be Published

Release Date

2020-04-08

Peptides

Nickel-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Nickel-binding periplasmic protein

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