SMTL ID : 4xyd.1

Nitric oxide reductase from Roseobacter denitrificans (RdNOR)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-1-1-mer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)(Non-covalent)

HEM.1: 26 residues within 4Å: Chain A: Q.23, V.24, G.27, L.28, L.30, Y.34, R.50, H.53, T.54, L.57, E.122, F.123, H.336, F.339, V.344, M.380, M.383, R.419, V.426, V.427 Chain B: G.72, A.73, Y.74, F.75 Ligands: CA.3, HEM.4 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:V.24, A:L.30, A:L.30, A:Y.34, A:T.54, A:L.57, A:F.339, A:F.339, A:V.344, A:V.426, A:V.427 Hydrogen bonds: A:Y.34, B:Y.74 Salt bridges: A:R.50, A:R.50 Metal complexes: A:H.53, A:H.336 HEM.4: 29 residues within 4Å: Chain A: E.122, F.123, W.190, V.197, E.198, H.245, H.246, S.264, E.267, F.271, A.309, G.313, F.314, H.316, T.317, N.322, H.326, G.327, T.331, H.334, G.335, A.338, F.339, A.342, Y.343 Chain B: Y.74 Ligands: HEM.1, UNL.2, CA.3 22 PLIP interactions: 21 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:W.190, A:V.197, A:E.198, A:E.267, A:F.271, A:F.271, A:T.317, A:A.338, A:F.339, A:F.339, A:A.342, A:Y.343 Hydrogen bonds: A:N.322, A:G.327, A:T.331, A:T.331, B:Y.74 Water bridges: A:T.325 Salt bridges: A:H.316, A:H.326 pi-Stacking: A:H.246 Metal complexes: A:H.334

1 x UNL: UNKNOWN LIGAND

UNL.2: 7 residues within 4Å: Chain A: H.194, E.198, H.245, H.246, H.334 Ligands: HEM.4, FE.5 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: R.50, E.122 Chain B: G.72, Y.74 Ligands: HEM.1, HEM.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:G.72, B:Y.74, A:E.122

1 x FE: FE (III) ION(Non-covalent)

FE.5: 5 residues within 4Å: Chain A: H.194, E.198, H.245, H.246 Ligands: UNL.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.194, A:E.198, A:E.198, A:H.245, A:H.246

1 x HEC: HEME C(Covalent)

HEC.6: 25 residues within 4Å: Chain A: P.45, F.46, N.47, M.406 Chain B: H.60, G.61, C.62, C.65, H.66, A.76, P.77, L.79, V.82, R.85, W.86, L.99, W.102, M.103, T.108, R.113, R.114, Q.115, M.116, P.117, L.129 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:H.60, B:A.76, B:L.79, B:L.79, B:V.82, B:W.86, B:W.86, B:L.99, B:R.114, B:M.116, B:L.129, A:P.45, A:N.47 Salt bridges: B:R.85, B:R.113 pi-Stacking: B:H.66 pi-Cation interactions: B:H.66 Metal complexes: B:H.66

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

CU.7: 3 residues within 4Å: Chain B: E.49, H.52, E.124 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.49, B:H.52, B:E.124, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crow, A. et al., Structure of the Membrane-intrinsic Nitric Oxide Reductase from Roseobacter denitrificans. Biochemistry (2016)

Release Date

2016-05-25

Peptides

Nitric-oxide reductase subunit B: A
NorC-like protein: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Nitric-oxide reductase subunit B

NorC-like protein