SMTL ID : 6tpo.1

Conformation of cd1 nitrite reductase NirS without bound heme d1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.1: 8 residues within 4Å: Chain A: H.291, E.293, N.308, T.316, T.318, K.354, D.355, R.356 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.356, A:R.356 Water bridges: A:N.308, A:T.316 1PE.4: 8 residues within 4Å: Chain B: H.291, E.293, N.308, T.316, T.318, K.354, D.355, R.356 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.356, B:R.356 Water bridges: B:N.308, B:T.316

2 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.2: 5 residues within 4Å: Chain A: V.264, S.265, L.305, V.317, S.319 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.317 BU3.5: 5 residues within 4Å: Chain B: V.264, S.265, L.305, V.317, S.319 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.317

2 x HEC: HEME C(Covalent)

HEC.3: 28 residues within 4Å: Chain A: I.42, Y.43, R.46, C.47, C.50, H.51, T.59, G.60, K.61, L.63, I.67, R.71, Y.75, L.76, L.79, I.80, T.84, L.86, G.87, M.88, P.89, W.91, L.97, M.105, I.109, Y.179, A.180 Chain B: P.85 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:K.61, A:K.61, A:L.63, A:L.63, A:L.76, A:I.80, A:I.80, A:M.88, A:W.91, A:L.97, A:I.109, A:A.180 Hydrogen bonds: A:Y.75, A:T.84, A:T.84 Salt bridges: A:K.61, A:R.71 Metal complexes: A:H.51 HEC.6: 28 residues within 4Å: Chain A: P.85 Chain B: I.42, Y.43, R.46, C.47, C.50, H.51, T.59, G.60, K.61, L.63, I.67, R.71, Y.75, L.76, L.79, I.80, T.84, L.86, G.87, M.88, P.89, W.91, L.97, M.105, I.109, Y.179, A.180 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:K.61, B:K.61, B:L.63, B:L.63, B:L.76, B:I.80, B:I.80, B:M.88, B:W.91, B:L.97, B:I.109, B:A.180 Hydrogen bonds: B:Y.75, B:T.84, B:T.84 Salt bridges: B:K.61, B:R.71 Metal complexes: B:H.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klunemann, T. et al., Structure of heme d 1 -free cd 1 nitrite reductase NirS. Acta Crystallogr.,Sect.F (2020)

Release Date

2020-11-18

Peptides

Nitrite reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Nitrite reductase

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