SMTL ID : 3p9p.1

Structure of I274V variant of E. coli KatE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 28 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, F.214, V.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain D: I.114, D.118 Ligands: HDE.2, HEM.3, HDD.4 24 PLIP interactions: 22 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: A:H.128, A:A.186, A:V.199, A:F.206, A:F.214, A:F.214, A:F.214, A:V.274, A:L.407, A:L.407, A:R.411, A:Y.415, D:I.114 Hydrogen bonds: A:Q.419 Water bridges: 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, H2O.23 HEM.3: 27 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, A.211, F.214, G.273, V.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain D: D.118 Ligands: HEM.1, HDE.2, HDD.4 25 PLIP interactions: 24 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:V.127, A:H.128, A:A.186, A:V.199, A:A.211, A:F.214, A:F.214, A:F.214, A:V.274, A:L.407, A:R.411, A:Y.415 Hydrogen bonds: A:Q.419 Water bridges: A:I.126, A:A.186, A:A.389, A:R.422 Salt bridges: A:R.125, A:R.125, A:R.165, A:R.422 pi-Stacking: A:H.128 pi-Cation interactions: A:R.411 Metal complexes: A:Y.415, H2O.23 HEM.5: 27 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, F.214, V.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: HDE.6, HEM.7, HDD.8 27 PLIP interactions: 26 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:H.128, B:A.186, B:V.199, B:F.206, B:F.206, B:F.214, B:F.214, B:F.214, B:V.274, B:L.407, B:L.407, B:R.411, B:Y.415 Hydrogen bonds: B:T.418, B:T.418, B:Q.419 Water bridges: B:R.125, B:I.126, B:F.391 Salt bridges: 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, H2O.62 HEM.7: 26 residues within 4Å: Chain B: R.125, V.127, H.128, R.165, G.184, F.185, V.199, G.200, N.201, A.211, F.214, G.273, V.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain C: D.118 Ligands: HEM.5, HDE.6, HDD.8 27 PLIP interactions: 26 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:H.128, B:V.199, B:A.211, B:F.214, B:F.214, B:F.214, B:F.214, B:F.214, B:V.274, B:L.407, B:L.407, B:R.411, B:Y.415, B:Y.415 Hydrogen bonds: B:Q.419 Water bridges: B:I.126, B:T.418 Salt bridges: B:R.125, 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.62 HEM.9: 26 residues within 4Å: Chain B: D.118 Chain C: R.125, V.127, H.128, R.165, G.184, F.185, V.199, G.200, N.201, F.206, F.214, V.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HDE.10, HEM.11, HDD.12 27 PLIP interactions: 26 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:R.125, C:V.127, C:H.128, C:V.199, C:F.206, C:F.206, C:F.214, C:F.214, C:F.214, C:F.214, C:V.274, C:L.407, C:L.407, C:R.411, C:Y.415, C:Y.415 Hydrogen bonds: C:Q.419 Water bridges: C:I.126, C:A.389, C:R.422 Salt bridges: C:R.125, C:R.165, C:R.422 pi-Stacking: C:H.128, C:F.214 Metal complexes: C:Y.415, H2O.92 HEM.11: 28 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, G.273, V.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HEM.9, HDE.10, HDD.12 30 PLIP interactions: 29 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:V.127, C:H.128, C:A.186, C:V.199, C:N.201, C:F.206, C:A.211, C:F.214, C:F.214, C:F.214, C:F.214, C:F.214, C:V.274, C:L.407, C:L.407, C:R.411, C:Y.415, C:Y.415 Hydrogen bonds: C:Q.419 Water bridges: C:I.126, C:A.186 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, H2O.92 HEM.13: 27 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, F.214, V.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HDE.14, HEM.15, HDD.16 25 PLIP interactions: 25 interactions with chain D, Hydrophobic interactions: D:V.127, D:H.128, D:V.199, D:F.206, D:F.214, D:F.214, D:F.214, D:F.214, D:V.274, D:L.407, D:L.407, D:R.411, D:Y.415, D:Y.415 Hydrogen bonds: D:Q.419 Water bridges: D:R.125, D:I.126, D:T.418, D:R.422 Salt bridges: D:R.125, D:R.165, D:R.422 pi-Stacking: D:H.128, D:F.214 Metal complexes: D:Y.415 HEM.15: 26 residues within 4Å: Chain A: D.118 Chain D: R.125, V.127, H.128, R.165, G.184, F.185, V.199, G.200, N.201, F.206, A.211, F.214, G.273, V.274, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HEM.13, HDE.14, HDD.16 30 PLIP interactions: 30 interactions with chain D, Hydrophobic interactions: D:V.127, D:H.128, D:V.199, D:N.201, D:F.206, D:A.211, D:F.214, D:F.214, D:F.214, D:F.214, D:V.274, D:L.407, D:L.407, D:R.411, D:Y.415, D:Y.415, D:Y.415 Hydrogen bonds: D:Q.419 Water bridges: D:I.126, D:A.389, D:T.418 Salt bridges: D:R.125, 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 HDE: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE 17R, 18S(Non-covalent)

HDE.2: 26 residues within 4Å: Chain A: R.125, V.127, H.128, R.165, G.184, F.185, V.199, G.200, N.201, F.206, A.211, F.214, G.273, V.274, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain D: D.118 Ligands: HEM.1, HEM.3, HDD.4 26 PLIP interactions: 25 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:R.125, A:H.128, A:V.199, A:F.206, A:A.211, A:F.214, A:F.214, A:F.214, A:V.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.165, A:A.186, A:R.422 Salt bridges: A:R.125, A:R.165, A:R.422 pi-Stacking: A:H.128, A:F.206 pi-Cation interactions: A:R.411 Metal complexes: A:Y.415, H2O.23 HDE.6: 29 residues within 4Å: Chain B: R.125, I.126, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, A.211, F.214, G.273, V.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain C: D.118 Ligands: HEM.5, HEM.7, HDD.8 24 PLIP interactions: 23 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:R.125, B:H.128, B:A.186, B:V.199, B:F.206, B:A.211, B:F.214, B:F.214, B:F.214, B:V.274, B:L.407, B:L.407, B:R.411, B:Y.415, B:Y.415 Hydrogen bonds: B:Q.419, B:R.422 Water bridges: B:A.186 Salt bridges: B:R.125, B:R.165 pi-Stacking: B:H.128 pi-Cation interactions: B:R.411 Metal complexes: B:Y.415, H2O.62 HDE.10: 29 residues within 4Å: Chain B: D.118 Chain C: R.125, I.126, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, A.211, F.214, G.273, V.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HEM.9, HEM.11, HDD.12 25 PLIP interactions: 24 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:R.125, C:H.128, C:V.199, C:F.206, C:A.211, C:F.214, C:F.214, C:F.214, C:V.274, C:F.391, C:L.407, C:L.407, C:R.411, C:Y.415, C:Y.415, C:T.418 Hydrogen bonds: C:Q.419 Water bridges: C:R.422 Salt bridges: C:R.125, C:R.165, C:R.422 pi-Stacking: C:H.128 pi-Cation interactions: C:R.411 Metal complexes: C:Y.415, H2O.92 HDE.14: 27 residues within 4Å: Chain A: D.118 Chain D: R.125, I.126, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, A.211, F.214, G.273, V.274, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419 Ligands: HEM.13, HEM.15, HDD.16 27 PLIP interactions: 27 interactions with chain D, Hydrophobic interactions: D:R.125, D:H.128, D:A.186, D:V.199, D:F.206, D:A.211, D:F.214, D:F.214, D:F.214, D:F.214, D:V.274, D:L.407, D:L.407, D:R.411, D:Y.415, D:Y.415, D:T.418 Hydrogen bonds: D:Q.419 Water bridges: D:A.186, D:R.422 Salt bridges: D:R.125, D:R.165, D:R.422 pi-Stacking: D:H.128, D:F.206 pi-Cation interactions: D:R.411 Metal complexes: D:Y.415

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

HDD.4: 28 residues within 4Å: Chain A: R.125, I.126, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, A.211, F.214, V.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419 Chain D: F.117, D.118 Ligands: HEM.1, HDE.2, HEM.3 29 PLIP interactions: 27 interactions with chain A, 1 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: 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:V.274, A:L.407, A:L.407, A:R.411, A:Y.415, A:Y.415, A:T.418, D:F.117 Hydrogen bonds: A:Q.419 Water bridges: A:R.165, A:R.422 Salt bridges: A:R.125, A:R.165 pi-Stacking: A:H.128, A:F.214 Metal complexes: A:Y.415, H2O.23 HDD.8: 27 residues within 4Å: Chain B: R.125, I.126, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, F.214, V.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain C: D.118 Ligands: HEM.5, HDE.6, HEM.7 26 PLIP interactions: 25 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:R.125, B:I.126, B:V.127, B:H.128, B:A.186, B:V.199, B:N.201, B:F.206, B:F.214, B:F.214, B:F.214, B:V.274, B:L.407, B:L.407, B:R.411, B:Y.415, B:Y.415 Hydrogen bonds: B:Q.419 Salt bridges: 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, H2O.62 HDD.12: 27 residues within 4Å: Chain B: 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, A.211, F.214, V.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HEM.9, HDE.10, HEM.11 25 PLIP interactions: 24 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:R.125, C:H.128, 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:V.274, C:L.407, C:L.407, C:R.411, C:Y.415, C:Y.415 Hydrogen bonds: C:Q.419 Water bridges: C:R.422 Salt bridges: C:R.125, C:R.165, C:R.422 pi-Stacking: C:H.128, C:F.214 Metal complexes: C:Y.415, H2O.92 HDD.16: 26 residues within 4Å: Chain D: R.125, I.126, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, F.206, F.214, V.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HEM.13, HDE.14, HEM.15 27 PLIP interactions: 27 interactions with chain D, Hydrophobic interactions: D:R.125, D:I.126, D:H.128, D:A.186, D:V.199, D:N.201, D:F.206, D:F.206, D:F.214, D:F.214, D:F.214, D:V.274, D:L.407, D:L.407, D:R.411, D:Y.415, D:Y.415, D:T.418 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.214 Metal complexes: D:Y.415

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jha, V. et al., Modulation of heme orientation and binding by a single residue in catalase HPII of Escherichia coli. Biochemistry (2011)

Release Date

2010-12-22

Peptides

Catalase HPII: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase HPII