SMTL ID : 5lmc.2 (1 other biounit)

Oxidized flavodiiron core of Escherichia coli flavorubredoxin, including the Fe-4SG atoms from its rubredoxin domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x FEO: MU-OXO-DIIRON(Non-covalent)

FEO.1: 8 residues within 4Å: Chain A: H.79, E.81, D.83, H.84, H.147, D.166, H.227 Ligands: PO4.3 8 PLIP interactions: 8 interactions with chain A, Metal complexes: A:H.79, A:E.81, A:D.83, A:H.84, A:H.147, A:D.166, A:D.166, A:H.227 FEO.9: 8 residues within 4Å: Chain B: H.79, E.81, D.83, H.84, H.147, D.166, H.227 Ligands: PO4.11 8 PLIP interactions: 8 interactions with chain B, Metal complexes: B:H.79, B:E.81, B:D.83, B:H.84, B:H.147, B:D.166, B:D.166, B:H.227

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 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 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:T.260, A:M.261, 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:S.349, A:G.350, A:W.375 Water bridges: A:S.262, A:S.262, A:N.317, A:N.317, A:S.349 pi-Stacking: A:W.348, A:W.348 FMN.10: 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 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:M.261, 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:S.349, B:G.350, B:W.375 Water bridges: B:S.262, B:S.262, B:N.317, B:N.317, B:S.349 pi-Stacking: B:W.348, B:W.348

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

PO4.3: 11 residues within 4Å: Chain A: F.22, H.23, E.81, D.83, H.147, D.166, H.171, Y.194, I.198, H.227 Ligands: FEO.1 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 PO4.4: 3 residues within 4Å: Chain A: R.64, N.65, E.66 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.67 PO4.11: 11 residues within 4Å: Chain B: F.22, H.23, E.81, D.83, H.147, D.166, H.171, Y.194, I.198, H.227 Ligands: FEO.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.194, B:Y.194 Salt bridges: B:H.23, B:H.147, B:H.171, B:H.227 PO4.12: 3 residues within 4Å: Chain B: R.64, N.65, E.66 1 PLIP interactions: 1 interactions with chain B Water bridges: B:I.67

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.5: 2 residues within 4Å: Chain A: A.70, D.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.73 CAC.13: 2 residues within 4Å: Chain B: A.70, D.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.73, B:D.73

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.6: 3 residues within 4Å: Chain A: H.53, S.56, G.86 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.53 Water bridges: A:S.56, A:E.90 ACY.14: 3 residues within 4Å: Chain B: H.53, S.56, G.86 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:H.53 Water bridges: B:S.56, B:E.90

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: S.357, Q.361, M.367, S.368, S.370 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.357 Water bridges: A:S.370, A:S.370, A:S.370 GOL.15: 5 residues within 4Å: Chain B: S.357, Q.361, M.367, S.368, S.370 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.357 Water bridges: B:T.358, B:S.370, B:S.370, B:S.370

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

FE.8: 4 residues within 4Å: Chain A: C.428, C.431, C.461, C.464 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.428, A:C.431, A:C.461, A:C.464 FE.16: 4 residues within 4Å: Chain B: C.428, C.431, C.461, C.464 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.428, B:C.431, B:C.461, B:C.464

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

2016-10-19

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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