SMTL ID : 1h6n.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: R.51, M.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, P.137, F.140, G.195, S.196, H.197, L.278, F.313, M.329, R.333, S.336, Y.337, A.340, H.341, R.344 Chain D: L.40, D.44 27 PLIP interactions: 1 interactions with chain D, 25 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: D:L.40, A:H.54, A:A.112, A:V.125, A:N.127, A:P.137, A:F.140, A:F.140, A:F.140, A:F.140, A:F.140, A:L.278, A:R.333, A:Y.337, A:A.340 Water bridges: A:A.311, A:R.344 Salt bridges: A:R.51, A:R.51, A:R.91, A:H.341, A:R.344 pi-Stacking: A:H.54, A:F.132 pi-Cation interactions: A:R.333 Metal complexes: A:Y.337, H2O.2 HEM.4: 26 residues within 4Å: Chain B: R.51, M.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, P.137, F.140, G.195, S.196, H.197, L.278, F.313, M.329, R.333, S.336, Y.337, A.340, H.341, R.344 Chain C: L.40, D.44 27 PLIP interactions: 25 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: B:H.54, B:A.112, B:V.125, B:N.127, B:P.137, B:F.140, B:F.140, B:F.140, B:F.140, B:F.140, B:L.278, B:R.333, B:Y.337, B:A.340, C:L.40 Water bridges: B:A.311, B:R.344 Salt bridges: B:R.51, B:R.51, B:R.91, B:H.341, B:R.344 pi-Stacking: B:H.54, B:F.132 pi-Cation interactions: B:R.333 Metal complexes: B:Y.337, H2O.15 HEM.7: 26 residues within 4Å: Chain B: L.40, D.44 Chain C: R.51, M.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, P.137, F.140, G.195, S.196, H.197, L.278, F.313, M.329, R.333, S.336, Y.337, A.340, H.341, R.344 27 PLIP interactions: 25 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: C:H.54, C:A.112, C:V.125, C:N.127, C:P.137, C:F.140, C:F.140, C:F.140, C:F.140, C:F.140, C:L.278, C:R.333, C:Y.337, C:A.340, B:L.40 Water bridges: C:A.311, C:R.344 Salt bridges: C:R.51, C:R.51, C:R.91, C:H.341, C:R.344 pi-Stacking: C:H.54, C:F.132 pi-Cation interactions: C:R.333 Metal complexes: C:Y.337, H2O.27 HEM.10: 26 residues within 4Å: Chain A: L.40, D.44 Chain D: R.51, M.53, H.54, R.91, G.110, F.111, A.112, V.125, G.126, N.127, P.137, F.140, G.195, S.196, H.197, L.278, F.313, M.329, R.333, S.336, Y.337, A.340, H.341, R.344 27 PLIP interactions: 25 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: D:H.54, D:A.112, D:V.125, D:N.127, D:P.137, D:F.140, D:F.140, D:F.140, D:F.140, D:F.140, D:L.278, D:R.333, D:Y.337, D:A.340, A:L.40 Water bridges: D:A.311, D:R.344 Salt bridges: D:R.51, D:R.51, D:R.91, D:H.341, D:R.344 pi-Stacking: D:H.54, D:F.132 pi-Cation interactions: D:R.333 Metal complexes: D:Y.337, H2O.40

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

ACT.2: 4 residues within 4Å: Chain A: R.342, H.349 Chain B: E.38, H.42 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:E.38 Salt bridges: B:H.42, A:R.342, A:H.349 ACT.5: 4 residues within 4Å: Chain A: E.38, H.42 Chain B: R.342, H.349 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.342, B:H.349, A:H.42 Hydrophobic interactions: A:E.38 ACT.8: 4 residues within 4Å: Chain C: R.342, H.349 Chain D: E.38, H.42 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:E.38 Salt bridges: D:H.42, C:R.342, C:H.349 ACT.11: 4 residues within 4Å: Chain C: E.38, H.42 Chain D: R.342, H.349 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Salt bridges: D:R.342, D:H.349, C:H.42 Hydrophobic interactions: C:E.38

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

SO4.3: 2 residues within 4Å: Chain A: F.419, R.423 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.420, A:S.420 Salt bridges: A:R.423 SO4.6: 2 residues within 4Å: Chain B: F.419, R.423 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.417, B:S.420 Salt bridges: B:R.423 SO4.9: 2 residues within 4Å: Chain C: F.419, R.423 3 PLIP interactions: 3 interactions with chain C Water bridges: C:S.420, C:S.420 Salt bridges: C:R.423 SO4.12: 2 residues within 4Å: Chain D: F.419, R.423 3 PLIP interactions: 3 interactions with chain D Water bridges: D:D.417, D:S.420 Salt bridges: D:R.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andreoletti, P. et al., High Resolution Structure and Biochemical Properties of a Recombinant Proteus Mirabilis Catalase Depleted in Iron. Proteins: Struct.,Funct., Genet. (2003)

Release Date

2003-10-03

Peptides

CATALASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

CATALASE