SMTL ID : 1aqe.1

CRYSTAL STRUCTURE OF THE Y73E MUTANT OF CYTOCHROME C OF CLASS III (AMBLER) 26 KD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: T.79, R.91, R.95 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.95, A:R.95 Salt bridges: A:R.91, A:R.95 SO4.6: 3 residues within 4Å: Chain B: T.79, R.91, R.95 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.95, B:R.95 Salt bridges: B:R.91, B:R.95

8 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 22 residues within 4Å: Chain A: F.3, I.5, P.6, V.9, M.11, F.28, H.30, H.33, M.34, I.36, A.37, C.38, C.41, H.42, I.51, S.53, C.54, M.55 Chain B: Q.39, V.45 Ligands: HEM.3, HEM.4 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.3, A:F.3, A:I.5, A:I.5, A:P.6, A:V.9, A:F.28, A:F.28, A:H.33, A:I.36, A:I.51, B:V.45 Hydrogen bonds: A:S.53, A:C.54, A:M.55 Water bridges: A:I.51 Metal complexes: A:H.30, A:H.42 HEM.3: 18 residues within 4Å: Chain A: C.41, H.42, H.43, T.44, E.52, S.53, C.54, C.59, H.60, I.69, R.74, T.75, F.76, T.78, D.81, K.84, S.85 Ligands: HEM.2 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:T.44, A:E.52, A:I.69, A:T.75, A:F.76, A:K.84 Water bridges: A:H.43 Salt bridges: A:H.43, A:R.74, A:K.84 pi-Cation interactions: A:K.84 Metal complexes: A:H.43, A:H.60 HEM.4: 21 residues within 4Å: Chain A: V.26, T.27, F.28, N.29, S.32, H.33, I.36, Q.40, E.83, K.84, S.85, C.86, C.89, H.90, L.93, D.100, A.101, P.102, C.108 Ligands: HEM.2, HEM.5 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:V.26, A:I.36, A:L.93, A:P.102 Hydrogen bonds: A:N.29, A:S.32 Water bridges: A:D.100 pi-Stacking: A:F.28, A:H.33 Metal complexes: A:H.33, A:H.90 HEM.5: 22 residues within 4Å: Chain A: M.11, P.13, Y.19, P.21, K.22, K.23, V.26, M.55, V.72, E.73, F.76, H.77, C.86, V.87, H.90, P.102, L.103, A.104, C.105, C.108, H.109 Ligands: HEM.4 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:M.11, A:P.13, A:Y.19, A:V.72, A:E.73, A:F.76, A:F.76, A:F.76, A:V.87 Hydrogen bonds: A:Y.19, A:Y.19, A:K.22, A:K.23 Water bridges: A:H.109 Salt bridges: A:H.109 pi-Stacking: A:H.77, A:H.109 Metal complexes: A:H.77, A:H.109 HEM.7: 22 residues within 4Å: Chain A: Q.39, V.45 Chain B: F.3, I.5, P.6, V.9, M.11, F.28, H.30, H.33, M.34, I.36, A.37, C.38, C.41, H.42, I.51, S.53, C.54, M.55 Ligands: HEM.8, HEM.9 18 PLIP interactions: 17 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:F.3, B:F.3, B:I.5, B:I.5, B:P.6, B:V.9, B:F.28, B:F.28, B:H.33, B:I.36, B:I.51, A:V.45 Hydrogen bonds: B:S.53, B:C.54, B:M.55 Water bridges: B:I.51 Metal complexes: B:H.30, B:H.42 HEM.8: 18 residues within 4Å: Chain B: C.41, H.42, H.43, T.44, E.52, S.53, C.54, C.59, H.60, I.69, R.74, T.75, F.76, T.78, D.81, K.84, S.85 Ligands: HEM.7 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:T.44, B:E.52, B:I.69, B:T.75, B:F.76, B:K.84 Water bridges: B:H.43, B:D.81 Salt bridges: B:H.43, B:R.74, B:K.84 pi-Cation interactions: B:K.84 Metal complexes: B:H.43, B:H.60 HEM.9: 21 residues within 4Å: Chain B: V.26, T.27, F.28, N.29, S.32, H.33, I.36, Q.40, E.83, K.84, S.85, C.86, C.89, H.90, L.93, D.100, A.101, P.102, C.108 Ligands: HEM.7, HEM.10 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:V.26, B:I.36, B:L.93, B:P.102 Hydrogen bonds: B:N.29, B:S.32 Water bridges: B:D.100 pi-Stacking: B:F.28, B:H.33 Metal complexes: B:H.33, B:H.90 HEM.10: 22 residues within 4Å: Chain B: M.11, P.13, Y.19, P.21, K.22, K.23, V.26, M.55, V.72, E.73, F.76, H.77, C.86, V.87, H.90, P.102, L.103, A.104, C.105, C.108, H.109 Ligands: HEM.9 19 PLIP interactions: 19 interactions with chain B, Hydrophobic interactions: B:M.11, B:P.13, B:Y.19, B:V.72, B:E.73, B:F.76, B:F.76, B:F.76, B:V.87 Hydrogen bonds: B:Y.19, B:Y.19, B:K.22, B:K.23 Water bridges: B:H.109 Salt bridges: B:H.109 pi-Stacking: B:H.77, B:H.109 Metal complexes: B:H.77, B:H.109

Links

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Citation

Aubert, C. et al., Structural and kinetic studies of the Y73E mutant of octaheme cytochrome c3 (Mr = 26 000) from Desulfovibrio desulfuricans Norway. Biochemistry (1998)

Release Date

1998-02-04

Peptides

CYTOCHROME C3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CYTOCHROME C3