SMTL ID : 7r2p.1 (1 other biounit)

Crystal structure of a flavodiiron protein D52K/S262Y mutant in the oxidized state from Escherichia coli

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 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, Y.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: 21 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.260, A:M.261, A:Y.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:S.349, A:G.350, A:W.375 pi-Stacking: A:W.348, A:W.348 Hydrophobic interactions: B:W.148 FMN.7: 21 residues within 4Å: Chain A: H.23, E.81, W.148 Chain B: T.260, M.261, Y.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: 21 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.261, B:Y.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:S.349, B:G.350, B:W.375 pi-Stacking: B:W.348, B:W.348 Hydrophobic interactions: A:W.148

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, OXY.5, O.6 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.6 FE.3: 7 residues within 4Å: Chain A: H.79, E.81, H.147, D.166 Ligands: FE.2, OXY.5, O.6 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.6 FE.8: 7 residues within 4Å: Chain B: D.83, H.84, D.166, H.227 Ligands: FE.9, OXY.11, O.12 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.12 FE.9: 7 residues within 4Å: Chain B: H.79, E.81, H.147, D.166 Ligands: FE.8, OXY.11, O.12 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.12

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 6 residues within 4Å: Chain A: I.3, E.175, H.176, L.177, F.178, E.181 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.3, A:L.177 IPA.10: 6 residues within 4Å: Chain B: I.3, E.175, H.176, L.177, F.178, E.181 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.3, B:L.177

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.5: 9 residues within 4Å: Chain A: H.23, E.81, D.83, H.147, D.166, Y.194 Ligands: FE.2, FE.3, O.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.194 OXY.11: 9 residues within 4Å: Chain B: H.23, E.81, D.83, H.147, D.166, Y.194 Ligands: FE.8, FE.9, O.12 No protein-ligand interaction detected (PLIP)

2 x O: OXYGEN ATOM(Non-covalent)

O.6: 8 residues within 4Å: Chain A: H.79, E.81, D.83, H.84, D.166 Ligands: FE.2, FE.3, OXY.5 No protein-ligand interaction detected (PLIP) O.12: 8 residues within 4Å: Chain B: H.79, E.81, D.83, H.84, D.166 Ligands: FE.8, FE.9, OXY.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borges, P.T. et al., Crystal structure of a flavodiiron protein D52K/S262Y mutant in the oxidized state from Escherichia coli. To Be Published

Release Date

2023-02-15

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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