SMTL ID : 1nir.1

OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 3 residues within 4Å: Chain B: H.289, H.335, H.540 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.540 Salt bridges: B:H.289, B:H.335, B:H.540 PO4.6: 2 residues within 4Å: Chain A: H.335, H.540 7 PLIP interactions: 7 interactions with chain A Water bridges: A:H.289, A:H.289, A:Q.539, A:Q.539 Salt bridges: A:H.289, A:H.335, A:H.540

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

CL.2: 4 residues within 4Å: Chain A: V.264, S.265 Chain B: G.268, M.269 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: G.268, M.269 Chain B: V.264, S.265 Ligand excluded by PLIP

2 x OH: HYDROXIDE ION(Non-covalent)

OH.3: 4 residues within 4Å: Chain A: H.327, H.369 Chain B: Y.10 Ligands: DHE.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.10 OH.8: 4 residues within 4Å: Chain A: Y.10 Chain B: H.182, H.369 Ligands: DHE.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.10

2 x HEC: HEME C(Covalent)

HEC.4: 21 residues within 4Å: Chain A: R.46, C.47, C.50, H.51, T.59, K.61, L.63, I.67, R.71, L.76, L.79, I.80, T.84, L.86, G.87, M.88, P.89, W.91, L.97, I.109 Chain B: E.8 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:L.63, A:L.63, A:L.76, A:L.79, A:I.80, A:M.88, A:P.89, A:W.91, A:W.91, A:L.97, A:I.109, B:E.8 Water bridges: A:K.61, A:K.61 Salt bridges: A:R.71 Metal complexes: A:H.51 HEC.9: 19 residues within 4Å: Chain A: E.8 Chain B: R.46, C.47, C.50, H.51, A.58, T.59, K.61, L.63, R.71, L.79, I.80, T.84, L.86, G.87, M.88, P.89, W.91, I.109 15 PLIP interactions: 15 interactions with chain B, Hydrophobic interactions: B:A.58, B:L.63, B:L.63, B:L.79, B:L.79, B:I.80, B:M.88, B:P.89, B:I.109 Hydrogen bonds: B:T.84 Water bridges: B:T.59, B:K.61, B:Y.75 Salt bridges: B:R.71 Metal complexes: B:H.51

2 x DHE: HEME D(Non-covalent)

DHE.5: 23 residues within 4Å: Chain A: R.156, H.182, I.183, R.185, R.198, R.225, S.226, Y.245, A.283, A.284, I.285, H.327, R.372, F.425, F.441, Q.483, W.498, G.531, F.533 Chain B: Y.10, Q.11, A.13 Ligands: OH.3 35 PLIP interactions: 31 interactions with chain A, 3 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:I.183, A:R.225, A:R.225, A:A.283, A:A.284, A:F.425, A:F.425, A:W.498, A:F.533, B:Y.10, B:Y.10, B:Q.11 Hydrogen bonds: A:R.185, A:R.225, A:S.226, A:Y.245, A:I.285, A:Q.483 Water bridges: A:R.156, A:R.198, A:R.198, A:K.427, A:K.427, A:K.427 Salt bridges: A:R.156, A:H.182, A:H.182, A:R.185, A:R.198, A:R.198, A:R.225, A:R.372, A:K.427 Metal complexes: A:H.182, OH.3 DHE.10: 23 residues within 4Å: Chain A: Y.10, Q.11, A.13 Chain B: R.156, H.182, I.183, R.185, R.198, R.225, S.226, Y.245, A.283, A.284, I.285, H.327, R.372, F.425, F.441, Q.483, W.498, G.531, F.533 Ligands: OH.8 36 PLIP interactions: 4 interactions with chain A, 31 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.10, A:Y.10, A:Q.11, B:I.183, B:R.225, B:R.225, B:A.283, B:A.284, B:F.425, B:F.425, B:W.498, B:W.498, B:F.533 Water bridges: A:A.13, B:R.156, B:R.198, B:R.198, B:K.427, B:K.427, B:K.427 Hydrogen bonds: B:R.225, B:S.226, B:I.285, B:Q.483 Salt bridges: B:R.156, B:H.182, B:H.182, B:R.185, B:R.185, B:R.198, B:R.198, B:R.225, B:R.372, B:K.427 Metal complexes: B:H.182, OH.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nurizzo, D. et al., N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa. Structure (1997)

Release Date

1997-12-03

Peptides

NITRITE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NITRITE REDUCTASE

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