SMTL ID : 4ent.1

Structure of the S234A variant of E. coli KatE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x HDD: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE(Non-covalent)

HDD.1: 26 residues within 4Å: Chain A: R.125, I.126, V.127, H.128, R.165, G.184, F.185, V.199, G.200, N.201, F.206, A.211, F.214, I.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain D: D.118 Ligands: HEM.2 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:R.125, A:I.126, A:H.128, A:V.199, A:F.206, A:F.206, A:A.211, A:F.214, A:F.214, A:F.214, A:F.214, A:L.407, A:L.407, A:R.411, A:Y.415, A:Y.415, A:T.418 Hydrogen bonds: A:Q.419 Water bridges: A:R.422 Salt bridges: A:R.125, A:R.165, A:R.422 pi-Stacking: A:H.128, A:F.206, A:F.214 pi-Cation interactions: A:R.411 Metal complexes: A:Y.415 HDD.3: 25 residues within 4Å: Chain B: R.125, I.126, V.127, H.128, R.165, G.184, F.185, V.199, G.200, N.201, F.206, F.214, I.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain C: D.118 Ligands: HEM.4 25 PLIP interactions: 24 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:R.125, B:H.128, B:V.199, B:F.206, B:F.214, B:F.214, B:F.214, B:F.214, B:L.407, B:L.407, B:R.411, B:Y.415, B:Y.415, B:T.418 Hydrogen bonds: B:Q.419 Water bridges: B:R.422 Salt bridges: B:R.125, B:R.165, B:R.422 pi-Stacking: B:H.128, B:F.206, B:F.214 pi-Cation interactions: B:R.411 Metal complexes: B:Y.415, H2O.57 HDD.5: 26 residues within 4Å: Chain B: I.114, D.118 Chain C: R.125, I.126, V.127, H.128, R.165, G.184, F.185, V.199, G.200, N.201, F.206, F.214, I.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HEM.6 26 PLIP interactions: 25 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:R.125, C:H.128, C:V.199, C:F.206, C:F.214, C:F.214, C:F.214, C:F.214, C:L.407, C:L.407, C:R.411, C:Y.415, C:Y.415, C:T.418, B:I.114 Hydrogen bonds: C:Q.419 Water bridges: C:R.165, C:R.422 Salt bridges: C:R.125, C:R.165, C:R.422 pi-Stacking: C:H.128, C:F.206, C:F.214 pi-Cation interactions: C:R.411 Metal complexes: C:Y.415 HDD.7: 25 residues within 4Å: Chain A: I.114, D.118 Chain D: R.125, I.126, V.127, H.128, R.165, G.184, F.185, V.199, G.200, N.201, F.206, F.214, I.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HEM.8 27 PLIP interactions: 26 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: D:R.125, D:H.128, D:V.199, D:F.206, D:F.214, D:F.214, D:F.214, D:F.214, D:F.214, D:L.407, D:L.407, D:R.411, D:Y.415, D:Y.415, D:T.418, A:I.114 Hydrogen bonds: D:Q.419 Water bridges: D:R.165, D:R.422 Salt bridges: D:R.125, D:R.165, D:R.422 pi-Stacking: D:H.128, D:F.206, D:F.214 pi-Cation interactions: D:R.411 Metal complexes: D:Y.415

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.2: 25 residues within 4Å: Chain A: R.125, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, A.211, F.214, I.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain D: D.118 Ligands: HDD.1 31 PLIP interactions: 31 interactions with chain A, Hydrophobic interactions: A:V.127, A:H.128, A:A.186, A:V.199, A:N.201, A:F.206, A:F.206, A:A.211, A:F.214, A:F.214, A:F.214, A:F.214, A:F.214, A:I.274, A:L.407, A:L.407, A:R.411, A:Y.415, A:Y.415 Hydrogen bonds: A:Q.419 Water bridges: A:R.125, A:I.126, A:A.186, A:A.389 Salt bridges: A:R.125, A:R.125, A:R.165, A:R.422 pi-Stacking: A:H.128, A:F.214 Metal complexes: A:Y.415 HEM.4: 26 residues within 4Å: Chain B: R.125, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, A.211, F.214, I.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain C: I.114, D.118 Ligands: HDD.3 34 PLIP interactions: 33 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:V.127, B:H.128, B:A.186, B:V.199, B:N.201, B:F.206, B:F.206, B:A.211, B:F.214, B:F.214, B:F.214, B:F.214, B:F.214, B:I.274, B:F.391, B:L.407, B:L.407, B:R.411, B:Y.415, B:Y.415, C:I.114 Hydrogen bonds: B:Q.419 Water bridges: B:R.125, B:I.126, B:A.186, B:A.389 Salt bridges: B:R.125, B:R.125, B:R.165, B:R.422 pi-Stacking: B:H.128, B:F.214 pi-Cation interactions: B:R.411 Metal complexes: B:Y.415 HEM.6: 26 residues within 4Å: Chain B: D.118 Chain C: R.125, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, A.211, F.214, I.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HDD.5 31 PLIP interactions: 31 interactions with chain C, Hydrophobic interactions: C:V.127, C:H.128, C:A.186, C:V.199, C:N.201, C:F.206, C:F.206, C:A.211, C:F.214, C:F.214, C:F.214, C:F.214, C:I.274, C:L.407, C:L.407, C:R.411, C:Y.415, C:Y.415 Hydrogen bonds: C:R.165, C:Q.419 Water bridges: C:R.125, C:I.126, C:F.391 Salt bridges: C:R.125, C:R.125, C:R.165, C:R.422 pi-Stacking: C:H.128, C:F.214 pi-Cation interactions: C:R.411 Metal complexes: C:Y.415 HEM.8: 26 residues within 4Å: Chain A: D.118 Chain D: R.125, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, A.211, F.214, I.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HDD.7 32 PLIP interactions: 32 interactions with chain D, Hydrophobic interactions: D:V.127, D:H.128, D:A.186, D:V.199, D:N.201, D:F.206, D:F.206, D:F.206, D:A.211, D:F.214, D:F.214, D:F.214, D:F.214, D:L.407, D:L.407, D:R.411, D:Y.415, D:Y.415 Hydrogen bonds: D:R.165, D:S.167, D:Q.419 Water bridges: D:R.125, D:I.126, D:R.422 Salt bridges: D:R.125, D:R.125, D:R.165, D:R.422 pi-Stacking: D:H.128, D:F.214 pi-Cation interactions: D:R.411 Metal complexes: D:Y.415

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jha, V. et al., Influence of main channel structure on H(2)O(2) access to the heme cavity of catalase KatE of Escherichia coli. Arch.Biochem.Biophys. (2012)

Release Date

2012-05-02

Peptides

Catalase HPII: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase HPII