SMTL ID : 1ycg.1 (8 other biounits)

X-ray Structures of Moorella thermoacetica FprA. Novel Diiron Site Structure and Mechanistic Insights into a Scavenging Nitric Oxide Reductase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: S.1, E.59 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.1, A:E.59 ZN.2: 2 residues within 4Å: Chain A: H.270, D.274 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.270 ZN.3: 1 residues within 4Å: Chain A: H.117 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.117, H2O.2 ZN.4: 2 residues within 4Å: Chain A: E.54, E.58 No protein-ligand interaction detected (PLIP) ZN.8: 2 residues within 4Å: Chain B: S.1, E.59 No protein-ligand interaction detected (PLIP) ZN.9: 2 residues within 4Å: Chain B: H.270, D.274 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.270, B:D.274, B:D.274 ZN.10: 1 residues within 4Å: Chain B: D.119 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.119, H2O.2, H2O.2, H2O.3, H2O.3 ZN.11: 2 residues within 4Å: Chain B: E.54, E.58 No protein-ligand interaction detected (PLIP)

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

FEO.5: 9 residues within 4Å: Chain A: H.80, E.82, D.84, H.85, H.147, D.166, S.226, H.227 Ligands: EDO.6 8 PLIP interactions: 8 interactions with chain A, Metal complexes: A:H.80, A:E.82, A:D.84, A:H.85, A:H.147, A:D.166, A:D.166, A:H.227 FEO.12: 9 residues within 4Å: Chain B: H.80, E.82, D.84, H.85, H.147, D.166, S.226, H.227 Ligands: EDO.13 8 PLIP interactions: 8 interactions with chain B, Metal complexes: B:H.80, B:E.82, B:D.84, B:H.85, B:H.147, B:D.166, B:D.166, B:H.227

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 8 residues within 4Å: Chain A: F.23, H.24, E.82, D.84, H.147, D.166, H.227 Ligands: FEO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.166 EDO.13: 8 residues within 4Å: Chain B: F.23, H.24, E.82, D.84, H.147, D.166, H.227 Ligands: FEO.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.166

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.7: 22 residues within 4Å: Chain A: T.260, M.261, W.262, L.263, S.264, T.265, P.311, T.312, I.313, N.314, N.315, A.343, Y.344, G.345, W.346, G.347, G.348, W.375 Chain B: H.24, E.82, H.147, W.148 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.313, B:W.148 Hydrogen bonds: A:M.261, A:W.262, A:L.263, A:S.264, A:S.264, A:T.265, A:T.312, A:T.312, A:T.312, A:N.314, A:N.315, A:Y.344, A:G.345, A:W.346, A:G.347, A:G.348 Water bridges: A:S.264, A:S.264 pi-Stacking: A:W.346, A:W.346, B:W.148 FMN.14: 22 residues within 4Å: Chain A: H.24, E.82, H.147, W.148 Chain B: T.260, M.261, W.262, L.263, S.264, T.265, P.311, T.312, I.313, N.314, N.315, A.343, Y.344, G.345, W.346, G.347, G.348, W.375 25 PLIP interactions: 23 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.313, A:W.148 Hydrogen bonds: B:M.261, B:W.262, B:L.263, B:S.264, B:S.264, B:S.264, B:T.265, B:T.265, B:T.312, B:T.312, B:T.312, B:N.314, B:N.315, B:N.315, B:Y.344, B:G.345, B:W.346, B:G.347, B:G.348, B:W.375 pi-Stacking: B:W.346, B:W.346, A:W.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silaghi-Dumitrescu, R. et al., X-ray crystal structures of Moorella thermoacetica FprA. Novel diiron site structure and mechanistic insights into a scavenging nitric oxide reductase. Biochemistry (2005)

Release Date

2005-04-19

Peptides

Nitric oxide reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nitric oxide reductase

Related Entries With Identical Sequence