SMTL ID : 6gti.1

Achromobacter cycloclastes copper nitrite reductase at pH 5.0

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

6 x CU: COPPER (II) ION(Non-covalent)

CU.1: 4 residues within 4Å: Chain A: H.133, C.174, H.183, M.188 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.133, A:C.174, A:H.183 CU.2: 5 residues within 4Å: Chain A: D.136, H.138, H.173 Chain C: H.344 Ligands: NO2.3 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Metal complexes: C:H.344, A:H.138, A:H.173 CU.7: 4 residues within 4Å: Chain B: H.133, C.174, H.183, M.188 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.133, B:C.174, B:H.183 CU.8: 5 residues within 4Å: Chain A: H.344 Chain B: D.136, H.138, H.173 Ligands: NO2.9 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.344, B:H.138, B:H.173 CU.13: 4 residues within 4Å: Chain C: H.133, C.174, H.183, M.188 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.133, C:C.174, C:H.183 CU.14: 5 residues within 4Å: Chain B: H.344 Chain C: D.136, H.138, H.173 Ligands: NO2.15 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Metal complexes: B:H.344, C:H.138, C:H.173

3 x NO2: NITRITE ION(Non-covalent)

NO2.3: 8 residues within 4Å: Chain A: D.136, H.138, H.173 Chain C: H.293, I.295, H.344, L.346 Ligands: CU.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.136 NO2.9: 8 residues within 4Å: Chain A: H.293, I.295, H.344, L.346 Chain B: D.136, H.138, H.173 Ligands: CU.8 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.136 NO2.15: 8 residues within 4Å: Chain B: H.293, I.295, H.344, L.346 Chain C: D.136, H.138, H.173 Ligands: CU.14 1 PLIP interactions: 1 interactions with chain C Water bridges: C:D.136

9 x MLI: MALONATE ION(Non-functional Binders)

MLI.4: 5 residues within 4Å: Chain A: G.263, T.266, F.350, A.355, H.357 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.355 Water bridges: A:R.92, A:R.92, A:R.92, A:G.263, A:H.357 Salt bridges: A:H.357, A:H.357 MLI.5: 9 residues within 4Å: Chain A: R.288, R.291, N.345, E.348 Chain B: R.288, D.289, R.291 Ligands: MLI.11, MLI.17 18 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A, 9 interactions with chain B Water bridges: C:D.289, C:D.289, C:D.289, A:R.288, A:E.348, B:R.288, B:R.288, B:D.289, B:D.289, B:D.289 Hydrogen bonds: A:N.345, B:D.289, B:R.291 Salt bridges: A:R.288, A:R.291, A:R.291, B:R.288, B:R.288 MLI.6: 5 residues within 4Å: Chain A: T.266, G.267, A.270, V.338, H.357 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.338 Hydrogen bonds: A:G.267 Water bridges: A:H.357 Salt bridges: A:H.357, A:H.357 MLI.10: 5 residues within 4Å: Chain B: G.263, T.266, F.350, A.355, H.357 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.355 Water bridges: B:R.92, B:R.92, B:R.92, B:G.263, B:T.266, B:H.357 Salt bridges: B:H.357, B:H.357 MLI.11: 9 residues within 4Å: Chain B: R.288, R.291, N.345, E.348 Chain C: R.288, D.289, R.291 Ligands: MLI.5, MLI.17 18 PLIP interactions: 7 interactions with chain C, 6 interactions with chain A, 5 interactions with chain B Hydrogen bonds: C:D.289, C:R.291, B:N.345 Water bridges: C:R.288, C:R.288, C:R.288, A:D.289, A:D.289, A:D.289, A:D.289, A:D.289, A:D.289, B:R.288 Salt bridges: C:R.288, C:R.288, B:R.288, B:R.291, B:R.291 MLI.12: 5 residues within 4Å: Chain B: T.266, G.267, A.270, V.338, H.357 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.338 Hydrogen bonds: B:G.267 Water bridges: B:H.357, B:H.357 Salt bridges: B:H.357, B:H.357 MLI.16: 5 residues within 4Å: Chain C: G.263, T.266, F.350, A.355, H.357 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.355 Water bridges: C:R.92, C:R.92, C:R.92, C:G.263, C:T.266, C:H.357 Salt bridges: C:H.357, C:H.357 MLI.17: 9 residues within 4Å: Chain A: R.288, D.289, R.291 Chain C: R.288, R.291, N.345, E.348 Ligands: MLI.5, MLI.11 19 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B, 5 interactions with chain C Hydrogen bonds: A:D.289, A:D.289, A:R.291, C:N.345 Water bridges: A:R.288, A:R.288, A:R.288, A:D.289, A:D.289, A:D.289, B:D.289, B:D.289, B:D.289, C:R.288 Salt bridges: A:R.288, A:R.288, C:R.288, C:R.291, C:R.291 MLI.18: 5 residues within 4Å: Chain C: T.266, G.267, A.270, V.338, H.357 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.338 Hydrogen bonds: C:G.267 Water bridges: C:H.357 Salt bridges: C:H.357, C:H.357

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halsted, T.P. et al., Catalytically important damage-free structures of a copper nitrite reductase obtained by femtosecond X-ray laser and room-temperature neutron crystallography. Iucrj (2019)

Release Date

2019-07-03

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Copper-containing nitrite reductase

Related Entries With Identical Sequence