SMTL ID : 2oz0.2 (1 other biounit)

Mechanistic and Structural Studies of H373Q Flavocytochrome b2: Effects of Mutating the Active Site Base

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.1: 15 residues within 4Å: Chain A: F.39, H.43, P.44, G.45, V.49, I.50, F.62, H.66, V.70, Y.74, Y.97, Q.139, Y.143, L.199, L.230 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:F.39, A:P.44, A:V.49, A:I.50, A:F.62, A:V.70, A:Y.74, A:Y.97, A:L.199, A:L.199, A:L.230 Hydrogen bonds: A:Q.139 Salt bridges: A:K.296 pi-Stacking: A:F.62 Metal complexes: A:H.43 HEM.5: 15 residues within 4Å: Chain C: F.39, H.43, P.44, G.45, V.49, I.50, F.62, H.66, V.70, Y.74, Y.97, Q.139, Y.143, L.199, L.230 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:F.39, C:P.44, C:V.49, C:I.50, C:F.62, C:V.70, C:Y.74, C:Y.97, C:L.199, C:L.199, C:L.230 Hydrogen bonds: C:Q.139, C:Y.143 Salt bridges: C:K.296 pi-Stacking: C:F.62 Metal complexes: C:H.43

4 x FMN: FLAVIN MONONUCLEOTIDE(Covalent)(Non-covalent)

FMN.2: 23 residues within 4Å: Chain A: Y.143, Y.144, S.195, A.196, T.197, A.198, S.228, Q.252, Y.254, T.280, K.349, S.371, Q.373, G.374, R.376, D.409, G.410, G.411, R.413, L.431, G.432, R.433, L.436 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.143, A:Y.144, A:A.198, A:R.433, A:L.436 Hydrogen bonds: A:S.195, A:A.196, A:A.196, A:S.228, A:K.349, A:K.349, A:S.371, A:G.410, A:G.411, A:G.432, A:R.433 Salt bridges: A:R.413, A:R.433 pi-Cation interactions: A:R.376 FMN.3: 24 residues within 4Å: Chain B: Y.144, S.195, A.196, T.197, A.198, S.228, Q.252, Y.254, T.280, K.349, S.371, Q.373, G.374, R.376, D.409, G.410, G.411, R.413, L.431, G.432, R.433, P.434, L.436 Ligands: PYR.4 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.144, B:R.433, B:L.436 Hydrogen bonds: B:A.196, B:A.196, B:A.198, B:S.228, B:Q.252, B:Y.254, B:K.349, B:K.349, B:S.371, B:G.410, B:G.411, B:G.432, B:R.433 Salt bridges: B:R.413, B:R.433 pi-Cation interactions: B:R.376 FMN.6: 23 residues within 4Å: Chain C: Y.143, Y.144, S.195, A.196, T.197, A.198, S.228, Q.252, Y.254, T.280, K.349, S.371, Q.373, G.374, R.376, D.409, G.410, G.411, R.413, L.431, G.432, R.433, L.436 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:Y.143, C:Y.144, C:A.198, C:R.433, C:L.436 Hydrogen bonds: C:S.195, C:A.196, C:A.196, C:S.228, C:T.280, C:K.349, C:K.349, C:S.371, C:G.410, C:G.411, C:G.432, C:R.433 Salt bridges: C:R.413, C:R.433 pi-Cation interactions: C:R.376 FMN.7: 24 residues within 4Å: Chain D: Y.144, S.195, A.196, T.197, A.198, S.228, Q.252, Y.254, T.280, K.349, S.371, Q.373, G.374, R.376, D.409, G.410, G.411, R.413, L.431, G.432, R.433, P.434, L.436 Ligands: PYR.8 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:Y.144, D:R.433, D:L.436 Hydrogen bonds: D:A.196, D:A.196, D:A.198, D:S.228, D:Q.252, D:T.280, D:K.349, D:K.349, D:S.371, D:G.410, D:G.411, D:G.432, D:R.433 Salt bridges: D:R.413, D:R.433 pi-Cation interactions: D:R.376

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.4: 7 residues within 4Å: Chain B: Y.143, A.198, Y.254, R.289, Q.373, R.376 Ligands: FMN.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.198 Hydrogen bonds: B:Y.143, B:Y.254, B:Q.373 Salt bridges: B:R.289, B:R.376 PYR.8: 7 residues within 4Å: Chain D: Y.143, A.198, Y.254, R.289, Q.373, R.376 Ligands: FMN.7 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:A.198 Hydrogen bonds: D:Y.143, D:Q.373 Salt bridges: D:R.289, D:R.376

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsai, C.L. et al., Mechanistic and structural studies of H373Q flavocytochrome b2: effects of mutating the active site base. Biochemistry (2007)

Release Date

2007-09-11

Peptides

Cytochrome b2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Cytochrome b2

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