SMTL ID : 5ogf.1

Cu nitrite reductase serial data at varying temperatures RT 0.27MGy

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.88, C.129, H.138, M.143 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.88, A:C.129, A:H.138 CU.2: 5 residues within 4Å: Chain A: D.91, H.93, H.128 Chain C: H.299 Ligands: NO.9 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: A:H.93, A:H.128, C:H.299, NO.9 CU.10: 4 residues within 4Å: Chain B: H.88, C.129, H.138, M.143 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.88, B:C.129, B:H.138 CU.11: 5 residues within 4Å: Chain A: H.299 Chain B: D.91, H.93, H.128 Ligands: NO.18 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.93, B:H.128, A:H.299 CU.19: 4 residues within 4Å: Chain C: H.88, C.129, H.138, M.143 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.88, C:C.129, C:H.138 CU.20: 5 residues within 4Å: Chain B: H.299 Chain C: D.91, H.93, H.128 Ligands: NO.27 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: C:H.93, C:H.128, B:H.299, NO.27

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

ACT.3: 3 residues within 4Å: Chain A: G.222, H.312, K.314 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.222 Salt bridges: A:H.312, A:K.314 ACT.12: 3 residues within 4Å: Chain B: G.222, H.312, K.314 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.222 Salt bridges: B:H.312, B:K.314 ACT.21: 3 residues within 4Å: Chain C: G.222, H.312, K.314 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.222 Salt bridges: C:H.312, C:K.314

15 x NO2: NITRITE ION(Non-covalent)

NO2.4: 6 residues within 4Å: Chain A: N.242, R.243, D.244 Chain C: R.246, N.300 Ligands: NO2.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:D.244, C:N.300 Water bridges: C:R.246 NO2.5: 5 residues within 4Å: Chain A: R.243, D.244, R.246, E.303 Ligands: NO2.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.244, A:D.244, A:R.246 Water bridges: A:R.246 NO2.6: 5 residues within 4Å: Chain A: I.79, G.110, E.111, E.112 Chain C: S.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.112 NO2.7: 6 residues within 4Å: Chain A: W.258, T.260, G.261, K.262, N.265 Chain C: Q.271 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:T.260, A:K.262, A:N.265, C:Q.271 Water bridges: A:A.259 NO2.8: 4 residues within 4Å: Chain A: E.40, K.41, K.42, H.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.53 Water bridges: A:E.40, A:K.42 NO2.13: 6 residues within 4Å: Chain A: R.246, N.300 Chain B: N.242, R.243, D.244 Ligands: NO2.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.300, B:D.244 Water bridges: A:R.246 NO2.14: 5 residues within 4Å: Chain B: R.243, D.244, R.246, E.303 Ligands: NO2.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.244, B:D.244, B:R.246 Water bridges: B:R.246 NO2.15: 5 residues within 4Å: Chain A: S.332 Chain B: I.79, G.110, E.111, E.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.112 NO2.16: 6 residues within 4Å: Chain A: Q.271 Chain B: W.258, T.260, G.261, K.262, N.265 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.260, B:T.260, B:K.262, B:N.265, A:Q.271 Water bridges: B:A.259 NO2.17: 4 residues within 4Å: Chain B: E.40, K.41, K.42, H.53 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.40, B:K.42 NO2.22: 6 residues within 4Å: Chain B: R.246, N.300 Chain C: N.242, R.243, D.244 Ligands: NO2.23 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.300, C:D.244 Water bridges: B:R.246 NO2.23: 5 residues within 4Å: Chain C: R.243, D.244, R.246, E.303 Ligands: NO2.22 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.244, C:D.244, C:R.246 Water bridges: C:R.246 NO2.24: 5 residues within 4Å: Chain B: S.332 Chain C: I.79, G.110, E.111, E.112 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.112 NO2.25: 6 residues within 4Å: Chain B: Q.271 Chain C: W.258, T.260, G.261, K.262, N.265 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:T.260, C:T.260, C:K.262, C:N.265, B:Q.271 Water bridges: C:A.259 NO2.26: 4 residues within 4Å: Chain C: E.40, K.41, K.42, H.53 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.40, C:K.42

3 x NO: NITRIC OXIDE(Non-covalent)

NO.9: 7 residues within 4Å: Chain A: D.91, H.93, H.128 Chain C: I.250, H.299, L.301 Ligands: CU.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.91 NO.18: 7 residues within 4Å: Chain A: I.250, H.299, L.301 Chain B: D.91, H.93, H.128 Ligands: CU.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.128 NO.27: 7 residues within 4Å: Chain B: I.250, H.299, L.301 Chain C: D.91, H.93, H.128 Ligands: CU.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horrell, S. et al., Enzyme catalysis captured using multiple structures from one crystal at varying temperatures. IUCrJ (2018)

Release Date

2018-05-23

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Copper-containing nitrite reductase

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