SMTL ID : 6gt2.1

Reduced copper nitrite reductase from Achromobacter cycloclastes determined by serial femtosecond rotation crystallography

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 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: I.295, H.344 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.138, A:H.173, C:H.344 CU.11: 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.12: 5 residues within 4Å: Chain A: I.295, H.344 Chain B: D.136, H.138, H.173 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.138, B:H.173, A:H.344 CU.21: 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.22: 5 residues within 4Å: Chain B: I.295, H.344 Chain C: D.136, H.138, H.173 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Metal complexes: B:H.344, C:H.138, C:H.173

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

MLI.3: 11 residues within 4Å: Chain A: R.288, R.291, N.345, E.348 Chain B: R.288, D.289, R.291 Ligands: MLI.4, MLI.13, MLI.14, MLI.23 Ligand excluded by PLIP MLI.4: 9 residues within 4Å: Chain A: L.251, R.288 Chain C: L.251, T.252, R.288 Ligands: MLI.3, MLI.14, MLI.23, MLI.24 Ligand excluded by PLIP MLI.5: 5 residues within 4Å: Chain A: E.115, T.165, K.166, R.309 Chain C: D.315 Ligand excluded by PLIP MLI.6: 8 residues within 4Å: Chain A: L.144, A.175, E.177, V.180 Chain C: I.295, A.340, F.350 Ligands: MLI.29 Ligand excluded by PLIP MLI.7: 3 residues within 4Å: Chain A: V.275, G.362, E.363 Ligand excluded by PLIP MLI.8: 6 residues within 4Å: Chain A: T.266, G.267, A.270, V.338, H.357, K.359 Ligand excluded by PLIP MLI.9: 6 residues within 4Å: Chain A: G.263, T.266, F.350, A.355, H.357 Ligands: MLI.16 Ligand excluded by PLIP MLI.10: 2 residues within 4Å: Chain A: Y.241, E.242 Ligand excluded by PLIP MLI.13: 11 residues within 4Å: Chain B: R.288, R.291, N.345, E.348 Chain C: R.288, D.289, R.291 Ligands: MLI.3, MLI.14, MLI.23, MLI.24 Ligand excluded by PLIP MLI.14: 9 residues within 4Å: Chain A: L.251, T.252, R.288 Chain B: L.251, R.288 Ligands: MLI.3, MLI.4, MLI.13, MLI.24 Ligand excluded by PLIP MLI.15: 5 residues within 4Å: Chain A: D.315 Chain B: E.115, T.165, K.166, R.309 Ligand excluded by PLIP MLI.16: 8 residues within 4Å: Chain A: I.295, A.340, F.350 Chain B: L.144, A.175, E.177, V.180 Ligands: MLI.9 Ligand excluded by PLIP MLI.17: 3 residues within 4Å: Chain B: V.275, G.362, E.363 Ligand excluded by PLIP MLI.18: 6 residues within 4Å: Chain B: T.266, G.267, A.270, V.338, H.357, K.359 Ligand excluded by PLIP MLI.19: 6 residues within 4Å: Chain B: G.263, T.266, F.350, A.355, H.357 Ligands: MLI.26 Ligand excluded by PLIP MLI.20: 2 residues within 4Å: Chain B: Y.241, E.242 Ligand excluded by PLIP MLI.23: 11 residues within 4Å: Chain A: R.288, D.289, R.291 Chain C: R.288, R.291, N.345, E.348 Ligands: MLI.3, MLI.4, MLI.13, MLI.24 Ligand excluded by PLIP MLI.24: 9 residues within 4Å: Chain B: L.251, T.252, R.288 Chain C: L.251, R.288 Ligands: MLI.4, MLI.13, MLI.14, MLI.23 Ligand excluded by PLIP MLI.25: 5 residues within 4Å: Chain B: D.315 Chain C: E.115, T.165, K.166, R.309 Ligand excluded by PLIP MLI.26: 8 residues within 4Å: Chain B: I.295, A.340, F.350 Chain C: L.144, A.175, E.177, V.180 Ligands: MLI.19 Ligand excluded by PLIP MLI.27: 3 residues within 4Å: Chain C: V.275, G.362, E.363 Ligand excluded by PLIP MLI.28: 6 residues within 4Å: Chain C: T.266, G.267, A.270, V.338, H.357, K.359 Ligand excluded by PLIP MLI.29: 6 residues within 4Å: Chain C: G.263, T.266, F.350, A.355, H.357 Ligands: MLI.6 Ligand excluded by PLIP MLI.30: 2 residues within 4Å: Chain C: Y.241, E.242 Ligand excluded by PLIP

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

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