SMTL ID : 3pq6.1

Structure of I274C variant of E. coli KatE[] - Images 25-30

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

HDD.1: 26 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, C.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419 Chain D: F.117 Ligands: HDE.2, H2S.3 25 PLIP interactions: 23 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:A.211, 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, D:F.117 Hydrogen bonds: A:Q.419 Water bridges: A:A.186 Salt bridges: A:R.125, A:R.165 pi-Stacking: A:H.128, A:F.214 pi-Cation interactions: A:R.411 Metal complexes: A:Y.415, H2O.35 HDD.4: 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, A.211, F.214, C.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HDE.5, H2S.6 27 PLIP interactions: 26 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:R.125, B:V.127, B:H.128, 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:L.407, B:R.411, B:Y.415, B:Y.415, B:T.418 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.65 HDD.7: 26 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, F.214, C.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HDE.8, H2S.9 26 PLIP interactions: 25 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:R.125, C:V.127, C:H.128, C:V.199, C:N.201, 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 Hydrogen bonds: C:Q.419 Water bridges: C:R.165 Salt bridges: 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.94 HDD.10: 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, F.214, C.274, H.275, F.391, L.407, G.410, R.411, S.414, Y.415, T.418, Q.419, R.422 Ligands: HDE.11, H2S.12 26 PLIP interactions: 25 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:R.125, D:V.127, D:H.128, D:V.199, D:N.201, D:F.206, D:F.214, D:F.214, D:F.214, D:F.214, 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:A.186 Salt bridges: 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, H2O.129

4 x HDE: CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE 17R, 18S(Covalent)

HDE.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, C.274, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419, R.422 Chain D: D.118 Ligands: HDD.1, H2S.3 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:R.125, A:V.127, A:H.128, A:V.199, A:F.206, A:A.211, A:F.214, A:F.214, A:F.214, A:F.214, A:F.391, A:L.407, A:L.407, A:R.411, A:Y.415, A:Y.415 Hydrogen bonds: A:Q.419 Salt bridges: A:R.125, A:R.165, A:R.422 pi-Stacking: A:H.128, A:F.214 pi-Cation interactions: A:R.411 Metal complexes: A:Y.415 HDE.5: 24 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, A.211, F.214, C.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419 Chain C: F.117 Ligands: HDD.4, H2S.6 24 PLIP interactions: 22 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: B:R.125, B:H.128, B:A.186, B:V.199, B:A.211, B:F.214, B:F.214, B:F.214, B:F.214, B:F.391, B:L.407, B:R.411, B:Y.415, B:Y.415, C:F.117 Hydrogen bonds: B:Q.419 Water bridges: B:A.186 Salt bridges: B:R.125, B:R.165 pi-Stacking: B:H.128, B:F.214 pi-Cation interactions: B:R.411 Metal complexes: B:Y.415, H2O.65 HDE.8: 23 residues within 4Å: Chain C: R.125, V.127, H.128, R.165, G.184, F.185, A.186, V.199, G.200, N.201, A.211, F.214, C.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419 Ligands: HDD.7, H2S.9 25 PLIP interactions: 24 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:R.125, C:H.128, C:V.199, C:A.211, C:F.214, C:F.214, C:F.214, C:F.214, C:F.214, C:F.391, 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:F.391 Salt bridges: C:R.125, C:R.165 pi-Stacking: C:H.128, C:F.214 pi-Cation interactions: C:R.411 Metal complexes: C:Y.415, H2O.94 HDE.11: 25 residues within 4Å: Chain A: F.117 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, C.274, H.275, F.391, L.407, R.411, S.414, Y.415, T.418, Q.419 Ligands: HDD.10, H2S.12 24 PLIP interactions: 22 interactions with chain D, 1 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: D:R.125, D:H.128, D:V.199, 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, A:F.117 Hydrogen bonds: D:Q.419 Water bridges: D:R.165 Salt bridges: D:R.125, D:R.165 pi-Stacking: D:H.128, D:F.214 pi-Cation interactions: D:R.411 Metal complexes: D:Y.415, H2O.129

4 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.3: 5 residues within 4Å: Chain A: I.205, F.206, C.274 Ligands: HDD.1, HDE.2 No protein-ligand interaction detected (PLIP) H2S.6: 5 residues within 4Å: Chain B: I.205, F.206, C.274 Ligands: HDD.4, HDE.5 No protein-ligand interaction detected (PLIP) H2S.9: 6 residues within 4Å: Chain C: I.205, F.206, C.274, H.275 Ligands: HDD.7, HDE.8 No protein-ligand interaction detected (PLIP) H2S.12: 5 residues within 4Å: Chain D: I.205, F.206, C.274 Ligands: HDD.10, HDE.11 No protein-ligand interaction detected (PLIP)

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

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