SMTL ID : 3ayf.2 (1 other biounit)

Crystal structure of nitric oxide reductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 31 residues within 4Å: Chain A: S.92, Y.93, M.94, F.316, Q.319, T.320, G.323, A.324, L.326, A.327, Y.330, F.348, K.352, H.355, L.356, A.359, W.362, I.363, E.429, Y.430, T.648, P.649, H.653, M.656, M.657, M.700, R.742, D.746, F.749 Ligands: HEM.2, CA.4 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:F.316, A:T.320, A:L.326, A:Y.330, A:L.356, A:A.359, A:W.362, A:I.363, A:M.657, A:F.749, A:F.749 Hydrogen bonds: A:Y.93, A:Y.93, A:M.94, A:E.429 Water bridges: A:Y.330 Salt bridges: A:K.352, A:K.352 Metal complexes: A:H.355, A:H.653 HEM.2: 26 residues within 4Å: Chain A: E.429, Y.430, W.504, E.512, H.559, H.560, E.581, L.585, N.622, A.626, G.630, F.631, I.633, N.634, E.642, H.643, G.644, T.648, H.651, G.652, A.655, M.656, V.659, Y.660 Ligands: HEM.1, CA.4 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:Y.430, A:W.504, A:L.585, A:A.626, A:F.631, A:I.633, A:N.634, A:A.655, A:V.659 Hydrogen bonds: A:Y.93, A:Y.430, A:G.644 Water bridges: A:E.429, A:H.643 Salt bridges: A:H.643 pi-Stacking: A:H.560 Metal complexes: A:H.651, H2O.3 HEM.11: 31 residues within 4Å: Chain B: S.92, Y.93, M.94, F.316, Q.319, T.320, G.323, A.324, L.326, A.327, Y.330, F.348, K.352, H.355, L.356, A.359, W.362, I.363, E.429, Y.430, T.648, P.649, H.653, M.656, M.657, M.700, R.742, D.746, F.749 Ligands: HEM.12, CA.14 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:F.316, B:T.320, B:L.326, B:Y.330, B:L.356, B:A.359, B:W.362, B:I.363, B:M.657, B:F.749, B:F.749 Hydrogen bonds: B:Y.93, B:M.94, B:Y.330, B:E.429 Salt bridges: B:K.352, B:K.352 Metal complexes: B:H.355, B:H.653 HEM.12: 26 residues within 4Å: Chain B: E.429, Y.430, W.504, E.512, H.559, H.560, E.581, L.585, N.622, A.626, G.630, F.631, I.633, N.634, E.642, H.643, G.644, T.648, H.651, G.652, A.655, M.656, V.659, Y.660 Ligands: HEM.11, CA.14 22 PLIP interactions: 21 interactions with chain B, 1 Ligand-Water interactions, Hydrophobic interactions: B:Y.430, B:W.504, B:L.585, B:A.626, B:F.631, B:I.633, B:N.634, B:A.655, B:V.659 Hydrogen bonds: B:Y.430, B:Y.430, B:G.644, B:T.648 Water bridges: B:G.91, B:Y.93, B:Y.93, B:Y.93, B:H.643 Salt bridges: B:H.643 pi-Stacking: B:H.560 Metal complexes: B:H.651, H2O.8

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.508, H.559, H.560 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.508, A:H.559, A:H.560, H2O.2, H2O.3 ZN.13: 3 residues within 4Å: Chain B: H.508, H.559, H.560 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.508, B:H.559, B:H.560, H2O.6, H2O.8

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 5 residues within 4Å: Chain A: G.91, Y.93, E.429 Ligands: HEM.1, HEM.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.91, A:Y.93, A:E.429, A:E.429, H2O.4 CA.14: 5 residues within 4Å: Chain B: G.91, Y.93, E.429 Ligands: HEM.11, HEM.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:G.91, B:Y.93, B:E.429, B:E.429, H2O.8

6 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.5: 4 residues within 4Å: Chain A: L.757, I.761, K.762, F.765 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.757, A:I.761, A:K.762 Salt bridges: A:K.762 BOG.6: 8 residues within 4Å: Chain A: L.22, I.25, V.271, Y.275, L.277, R.540, F.544, T.547 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.22, A:I.25, A:Y.275, A:L.277, A:F.544 Hydrogen bonds: A:Y.275, A:R.540 Salt bridges: A:R.540 BOG.7: 5 residues within 4Å: Chain A: W.43, K.46, E.47, W.253, V.569 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.253, A:V.569 Hydrogen bonds: A:K.46, A:E.47 BOG.15: 4 residues within 4Å: Chain B: L.757, I.761, K.762, F.765 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.757, B:I.761, B:K.762 Salt bridges: B:K.762 BOG.16: 8 residues within 4Å: Chain B: L.22, I.25, V.271, Y.275, L.277, R.540, F.544, T.547 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.22, B:I.25, B:Y.275, B:L.277, B:F.544 Hydrogen bonds: B:Y.275, B:R.540 Salt bridges: B:R.540 BOG.17: 5 residues within 4Å: Chain B: W.43, K.46, E.47, W.253, V.569 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.253, B:V.569 Hydrogen bonds: B:K.46, B:E.47

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.8: 9 residues within 4Å: Chain A: M.321, A.324, H.328, T.331, F.337, L.740, A.743, T.747, L.750 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.331 Water bridges: A:A.327 Salt bridges: A:H.328 EPE.18: 9 residues within 4Å: Chain B: M.321, A.324, H.328, T.331, F.337, L.740, A.743, T.747, L.750 2 PLIP interactions: 2 interactions with chain B Water bridges: B:A.327 Salt bridges: B:H.328

4 x LOP: (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE(Non-covalent)

LOP.9: 15 residues within 4Å: Chain A: K.23, L.26, I.27, I.30, S.34, D.465, K.466, G.467, L.472, Y.475, I.478, F.482, F.483, V.517, Y.543 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.26, A:I.27, A:I.30, A:L.472, A:Y.475, A:I.478, A:F.482, A:F.483, A:F.483, A:V.517 Hydrogen bonds: A:T.17, A:D.465, A:K.466 Salt bridges: A:K.23, A:K.23, A:K.466 LOP.10: 16 residues within 4Å: Chain A: Y.596, M.599, R.600, W.613, I.616, S.617, I.620, W.621, V.624, F.629, K.687, C.690, W.691, N.694, A.698, V.702 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.596, A:Y.596, A:W.613, A:W.613, A:I.616, A:I.616, A:I.620, A:I.620, A:W.621, A:W.621, A:V.624, A:F.629, A:W.691, A:W.691, A:N.694, A:A.698, A:V.702 Hydrogen bonds: A:R.600 LOP.19: 15 residues within 4Å: Chain B: K.23, L.26, I.27, I.30, S.34, D.465, K.466, G.467, L.472, Y.475, I.478, F.482, F.483, V.517, Y.543 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.26, B:I.27, B:I.30, B:L.472, B:Y.475, B:I.478, B:F.482, B:F.483, B:F.483, B:V.517 Hydrogen bonds: B:K.466, B:Y.543 Salt bridges: B:K.23, B:K.23, B:K.466 LOP.20: 16 residues within 4Å: Chain B: Y.596, M.599, R.600, W.613, I.616, S.617, I.620, W.621, V.624, F.629, K.687, C.690, W.691, N.694, A.698, V.702 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.596, B:Y.596, B:W.613, B:W.613, B:I.616, B:I.616, B:I.620, B:I.620, B:W.621, B:W.621, B:V.624, B:F.629, B:W.691, B:W.691, B:N.694, B:A.698, B:V.702 Hydrogen bonds: B:Y.596, B:R.600

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsumoto, Y. et al., Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus. Nat.Struct.Mol.Biol. (2012)

Release Date

2012-01-25

Peptides

Nitric oxide reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

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

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