SMTL ID : 5d4i.1

Intact nitrite complex of a copper nitrite reductase determined by serial femtosecond crystallography

Coordinates

PDB Format Compare

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.93, C.134, H.143, M.148 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.93, A:C.134, A:H.143 CU.2: 6 residues within 4Å: Chain A: D.96, H.98, H.133 Chain C: H.253, H.304 Ligands: NO2.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.98, A:H.133, C:H.304 CU.5: 4 residues within 4Å: Chain B: H.93, C.134, H.143, M.148 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.93, B:C.134, B:H.143 CU.6: 6 residues within 4Å: Chain A: H.253, H.304 Chain B: D.96, H.98, H.133 Ligands: NO2.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.98, B:H.133, A:H.304 CU.7: 4 residues within 4Å: Chain C: H.93, C.134, H.143, M.148 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.93, C:C.134, C:H.143 CU.8: 5 residues within 4Å: Chain B: H.304 Chain C: D.96, H.98, H.133 Ligands: NO2.9 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Metal complexes: B:H.304, C:H.98, C:H.133

3 x NO2: NITRITE ION(Non-covalent)

NO2.3: 8 residues within 4Å: Chain A: D.96, H.98, H.133 Chain C: H.253, I.255, H.304, L.306 Ligands: CU.2 No protein-ligand interaction detected (PLIP) NO2.4: 8 residues within 4Å: Chain A: H.253, I.255, H.304, L.306 Chain B: D.96, H.98, H.133 Ligands: CU.6 No protein-ligand interaction detected (PLIP) NO2.9: 8 residues within 4Å: Chain B: H.253, I.255, H.304, L.306 Chain C: D.96, H.98, H.133 Ligands: CU.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-03-09

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Copper-containing nitrite reductase

Related Entries With Identical Sequence