SMTL ID : 1h7k.1

Formation of a tyrosyl radical intermediate in Proteus mirabilis catalase by directed mutagenesis and consequences for nucleotide reactivity

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 26 residues within 4Å: Chain A: R.50, M.52, H.53, R.90, G.109, F.110, A.111, V.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, S.335, Y.336, A.339, H.340, R.343 Chain C: L.39, D.43 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:H.53, A:V.124, A:P.136, A:F.139, A:F.139, A:F.139, A:L.277, A:R.332, A:Y.336, A:A.339, C:L.39 Water bridges: A:A.310, A:R.343 Salt bridges: A:R.50, A:R.50, A:R.90, A:H.340, A:R.343 pi-Stacking: A:F.131 pi-Cation interactions: A:R.332 Metal complexes: A:Y.336 HEM.4: 26 residues within 4Å: Chain B: R.50, M.52, H.53, R.90, G.109, F.110, A.111, V.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, S.335, Y.336, A.339, H.340, R.343 Chain D: L.39, D.43 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:H.53, B:V.124, B:P.136, B:F.139, B:F.139, B:F.139, B:L.277, B:R.332, B:Y.336, B:A.339, D:L.39 Water bridges: B:A.310, B:R.343 Salt bridges: B:R.50, B:R.50, B:R.90, B:H.340, B:R.343 pi-Stacking: B:F.131 pi-Cation interactions: B:R.332 Metal complexes: B:Y.336 HEM.7: 26 residues within 4Å: Chain A: L.39, D.43 Chain C: R.50, M.52, H.53, R.90, G.109, F.110, A.111, V.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, S.335, Y.336, A.339, H.340, R.343 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:H.53, C:V.124, C:P.136, C:F.139, C:F.139, C:F.139, C:L.277, C:R.332, C:Y.336, C:A.339, A:L.39 Water bridges: C:A.310, C:R.343 Salt bridges: C:R.50, C:R.50, C:R.90, C:H.340, C:R.343 pi-Stacking: C:F.131 pi-Cation interactions: C:R.332 Metal complexes: C:Y.336 HEM.10: 26 residues within 4Å: Chain B: L.39, D.43 Chain D: R.50, M.52, H.53, R.90, G.109, F.110, A.111, V.124, G.125, N.126, P.136, F.139, G.194, S.195, H.196, L.277, F.312, M.328, R.332, S.335, Y.336, A.339, H.340, R.343 21 PLIP interactions: 20 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:H.53, D:V.124, D:P.136, D:F.139, D:F.139, D:F.139, D:L.277, D:R.332, D:Y.336, D:A.339, B:L.39 Water bridges: D:A.310, D:R.343 Salt bridges: D:R.50, D:R.50, D:R.90, D:H.340, D:R.343 pi-Stacking: D:F.131 pi-Cation interactions: D:R.332 Metal complexes: D:Y.336

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: R.341, H.348 Chain D: A.8, E.37, H.41 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:E.37 Water bridges: D:A.8 Salt bridges: D:H.41, A:R.341, A:H.348 ACT.5: 5 residues within 4Å: Chain B: R.341, H.348 Chain C: A.8, E.37, H.41 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Salt bridges: B:R.341, B:H.348, C:H.41 Hydrogen bonds: C:E.37 Water bridges: C:A.8 ACT.8: 5 residues within 4Å: Chain B: A.8, E.37, H.41 Chain C: R.341, H.348 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:E.37 Water bridges: B:A.8 Salt bridges: B:H.41, C:R.341, C:H.348 ACT.11: 5 residues within 4Å: Chain A: A.8, E.37, H.41 Chain D: R.341, H.348 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Salt bridges: D:R.341, D:H.348, A:H.41 Hydrogen bonds: A:E.37 Water bridges: A:A.8

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

SO4.3: 3 residues within 4Å: Chain A: F.418, S.419, R.422 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.419 Salt bridges: A:R.422 SO4.6: 3 residues within 4Å: Chain B: F.418, S.419, R.422 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.419 Salt bridges: B:R.422 SO4.9: 3 residues within 4Å: Chain C: F.418, S.419, R.422 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.419 Salt bridges: C:R.422 SO4.12: 3 residues within 4Å: Chain D: F.418, S.419, R.422 2 PLIP interactions: 2 interactions with chain D Water bridges: D:S.419 Salt bridges: D:R.422

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andreoletti, P. et al., Formation of a Tyrosyl Radical Intermediate in Proteus Mirabilis Catalase by Directed Mutagenesis and Consequences for Nucleotide Reactivity. Biochemistry (2001)

Release Date

2004-02-25

Peptides

CATALASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

CATALASE