SMTL ID : 4d02.1

The crystallographic structure of Flavorubredoxin from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 21 residues within 4Å: Chain A: T.260, M.261, S.262, N.263, N.264, T.265, S.313, T.314, M.315, N.316, N.317, S.345, H.346, G.347, W.348, S.349, G.350, W.375 Chain B: H.23, E.81, W.148 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:T.260, A:M.261, A:S.262, A:S.262, A:N.264, A:N.264, A:T.265, A:S.313, A:S.313, A:T.314, A:T.314, A:N.316, A:N.317, A:H.346, A:G.347, A:W.348, A:G.350, A:W.375 Water bridges: A:N.317, A:S.349 pi-Stacking: A:W.348, A:W.348 FMN.11: 21 residues within 4Å: Chain A: H.23, E.81, W.148 Chain B: T.260, M.261, S.262, N.263, N.264, T.265, S.313, T.314, M.315, N.316, N.317, S.345, H.346, G.347, W.348, S.349, G.350, W.375 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:M.261, B:S.262, B:S.262, B:N.264, B:N.264, B:T.265, B:T.265, B:S.313, B:S.313, B:T.314, B:T.314, B:N.316, B:N.317, B:H.346, B:G.347, B:W.348, B:G.350, B:W.375 Water bridges: B:N.317, B:S.349 pi-Stacking: B:W.348, B:W.348

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

FE.2: 7 residues within 4Å: Chain A: D.83, H.84, D.166, H.227 Ligands: FE.3, O.4, PO4.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.83, A:H.84, A:D.166, A:H.227, O.4 FE.3: 7 residues within 4Å: Chain A: H.79, E.81, H.147, D.166 Ligands: FE.2, O.4, PO4.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.79, A:E.81, A:H.147, A:D.166, O.4 FE.12: 7 residues within 4Å: Chain B: D.83, H.84, D.166, H.227 Ligands: FE.13, O.14, PO4.15 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.83, B:H.84, B:D.166, B:H.227, O.14 FE.13: 7 residues within 4Å: Chain B: H.79, E.81, H.147, D.166 Ligands: FE.12, O.14, PO4.15 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.79, B:E.81, B:H.147, B:D.166, O.14

2 x O: OXYGEN ATOM(Non-covalent)

O.4: 8 residues within 4Å: Chain A: H.79, E.81, D.83, H.84, D.166 Ligands: FE.2, FE.3, PO4.5 No protein-ligand interaction detected (PLIP) O.14: 8 residues within 4Å: Chain B: H.79, E.81, D.83, H.84, D.166 Ligands: FE.12, FE.13, PO4.15 No protein-ligand interaction detected (PLIP)

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

PO4.5: 12 residues within 4Å: Chain A: F.22, H.23, E.81, D.83, H.147, D.166, H.171, Y.194, H.227 Ligands: FE.2, FE.3, O.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.194 Salt bridges: A:H.23, A:H.147, A:H.171, A:H.227 PO4.6: 4 residues within 4Å: Chain A: A.70, D.71, I.72, D.73 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.71, A:I.72, A:D.73 PO4.15: 12 residues within 4Å: Chain B: F.22, H.23, E.81, D.83, H.147, D.166, H.171, Y.194, H.227 Ligands: FE.12, FE.13, O.14 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:H.23, B:H.147, B:H.171, B:H.227 PO4.16: 4 residues within 4Å: Chain B: A.70, D.71, I.72, D.73 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.73 Water bridges: B:D.71, B:D.71, B:I.72, B:D.73

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

CL.7: 4 residues within 4Å: Chain A: R.193, E.297, T.300 Ligands: GOL.10 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: G.350, G.351, V.353 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: R.193, E.297, T.300 Ligands: GOL.20 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: G.350, G.351, V.353 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain A: Q.184, L.187, F.188, W.231, Q.237, L.241 No protein-ligand interaction detected (PLIP) GOL.10: 5 residues within 4Å: Chain A: E.297, T.300, N.301, R.304 Ligands: CL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.304, A:R.304 Water bridges: A:K.286, A:N.301 GOL.19: 6 residues within 4Å: Chain B: Q.184, L.187, F.188, W.231, Q.237, L.241 No protein-ligand interaction detected (PLIP) GOL.20: 5 residues within 4Å: Chain B: E.297, T.300, N.301, R.304 Ligands: CL.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.304, B:R.304 Water bridges: B:K.286, B:N.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Romao, C.V. et al., Structure of Escherichia Coli Flavodiiron Nitric Oxide Reductase. J.Mol.Biol. (2016)

Release Date

2014-09-03

Peptides

ANAEROBIC NITRIC OXIDE REDUCTASE FLAVORUBREDOXIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ANAEROBIC NITRIC OXIDE REDUCTASE FLAVORUBREDOXIN

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