SMTL ID : 6etb.1

Aerobic S262Y mutation of E. coli FLRD core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-tetramer

Ligands

4 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 C: H.23, E.81, W.148 23 PLIP interactions: 22 interactions with chain A, 1 interactions with chain C 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:G.350, A:W.375 Water bridges: A:N.317, A:N.317, A:W.348 pi-Stacking: A:W.348 Hydrophobic interactions: C:W.148 FMN.6: 21 residues within 4Å: 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 Chain D: H.23, E.81, W.148 24 PLIP interactions: 22 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:Y.262, D:W.148 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:G.350, B:W.375 Water bridges: B:N.317, B:S.349 pi-Stacking: B:W.348, D:W.148 FMN.11: 21 residues within 4Å: Chain A: H.23, E.81, W.148 Chain C: 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 23 PLIP interactions: 22 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:M.261, C:Y.262, C:N.264, C:N.264, C:T.265, C:T.265, C:S.313, C:S.313, C:T.314, C:T.314, C:N.316, C:N.317, C:H.346, C:G.347, C:W.348, C:S.349, C:G.350, C:W.375 Water bridges: C:N.317, C:N.317, C:W.348 pi-Stacking: C:W.348 Hydrophobic interactions: A:W.148 FMN.16: 21 residues within 4Å: Chain B: H.23, E.81, W.148 Chain D: 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 24 PLIP interactions: 22 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:Y.262, B:W.148 Hydrogen bonds: D:T.260, D:M.261, D:Y.262, D:N.264, D:N.264, D:T.265, D:S.313, D:S.313, D:T.314, D:T.314, D:N.316, D:N.317, D:H.346, D:G.347, D:W.348, D:S.349, D:G.350, D:W.375 Water bridges: D:N.317, D:S.349 pi-Stacking: D:W.348, B:W.148

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

FE.2: 8 residues within 4Å: Chain A: E.81, D.83, H.84, D.166, H.227 Ligands: FE.3, OXY.4, O.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.5 FE.3: 7 residues within 4Å: Chain A: H.79, E.81, H.147, D.166 Ligands: FE.2, OXY.4, O.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.5 FE.7: 7 residues within 4Å: Chain B: D.83, H.84, D.166, H.227 Ligands: FE.8, OXY.9, O.10 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.10 FE.8: 7 residues within 4Å: Chain B: H.79, E.81, H.147, D.166 Ligands: FE.7, OXY.9, O.10 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.10 FE.12: 8 residues within 4Å: Chain C: E.81, D.83, H.84, D.166, H.227 Ligands: FE.13, OXY.14, O.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:D.83, C:H.84, C:D.166, C:H.227, O.15 FE.13: 7 residues within 4Å: Chain C: H.79, E.81, H.147, D.166 Ligands: FE.12, OXY.14, O.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.79, C:E.81, C:H.147, C:D.166, O.15 FE.17: 7 residues within 4Å: Chain D: D.83, H.84, D.166, H.227 Ligands: FE.18, OXY.19, O.20 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:D.83, D:H.84, D:D.166, D:H.227, O.20 FE.18: 7 residues within 4Å: Chain D: H.79, E.81, H.147, D.166 Ligands: FE.17, OXY.19, O.20 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:H.79, D:E.81, D:H.147, D:D.166, O.20

4 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 8 residues within 4Å: Chain A: D.83, H.147, D.166, Y.194, H.227 Ligands: FE.2, FE.3, O.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.194 OXY.9: 9 residues within 4Å: Chain B: D.83, H.147, D.166, H.171, Y.194, H.227 Ligands: FE.7, FE.8, O.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.194 OXY.14: 8 residues within 4Å: Chain C: D.83, H.147, D.166, Y.194, H.227 Ligands: FE.12, FE.13, O.15 No protein-ligand interaction detected (PLIP) OXY.19: 9 residues within 4Å: Chain D: D.83, H.147, D.166, H.171, Y.194, H.227 Ligands: FE.17, FE.18, O.20 No protein-ligand interaction detected (PLIP)

4 x O: OXYGEN ATOM(Non-covalent)

O.5: 9 residues within 4Å: Chain A: H.79, E.81, D.83, H.84, D.166, H.227 Ligands: FE.2, FE.3, OXY.4 No protein-ligand interaction detected (PLIP) O.10: 9 residues within 4Å: Chain B: H.79, E.81, D.83, H.84, D.166, H.227 Ligands: FE.7, FE.8, OXY.9 No protein-ligand interaction detected (PLIP) O.15: 9 residues within 4Å: Chain C: H.79, E.81, D.83, H.84, D.166, H.227 Ligands: FE.12, FE.13, OXY.14 No protein-ligand interaction detected (PLIP) O.20: 9 residues within 4Å: Chain D: H.79, E.81, D.83, H.84, D.166, H.227 Ligands: FE.17, FE.18, OXY.19 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borges, P.T. et al., A tyrosine mutation in E. coli flavodiiron protein increases radiation sensitivity in the crystal structure. To Be Published

Release Date

2018-11-07

Peptides

Anaerobic nitric oxide reductase flavorubredoxin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Anaerobic nitric oxide reductase flavorubredoxin