SMTL ID : 4qom.1

Bacillus pumilus catalase with pyrogallol bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 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.54, V.55, V.56, H.57, R.94, G.113, F.114, A.115, V.128, G.129, N.130, F.135, A.140, F.143, G.198, V.199, H.200, F.316, L.332, R.336, S.339, Y.340, T.343, Q.344, R.347 Chain D: D.47 Ligands: HEM.2, PYG.4 26 PLIP interactions: 26 interactions with chain A, Hydrophobic interactions: A:V.55, A:H.57, A:V.128, A:F.135, A:F.135, A:F.135, A:A.140, A:F.143, A:F.143, A:F.143, A:V.199, A:L.332, A:R.336, A:Y.340, A:Y.340 Hydrogen bonds: A:Q.344 Water bridges: A:V.55, A:A.314, A:R.347 Salt bridges: A:R.54, A:R.54, A:R.94, A:R.347 pi-Stacking: A:H.57 pi-Cation interactions: A:R.336 Metal complexes: A:Y.340 HEM.2: 27 residues within 4Å: Chain A: R.54, V.55, V.56, H.57, R.94, G.113, V.128, G.129, N.130, F.135, A.140, F.143, V.199, H.200, F.316, L.332, G.335, R.336, S.339, Y.340, T.343, Q.344, R.347 Chain D: L.43, D.47 Ligands: HEM.1, PYG.4 33 PLIP interactions: 32 interactions with chain A, 1 interactions with chain D, Hydrophobic interactions: A:V.55, A:H.57, A:V.128, A:N.130, A:F.135, A:F.135, A:A.140, A:F.143, A:F.143, A:F.143, A:F.143, A:V.199, A:L.332, A:L.332, A:R.336, A:Y.340, A:Y.340, A:Y.340, A:T.343, D:L.43 Hydrogen bonds: A:Q.344 Water bridges: A:S.96, A:T.343, A:R.347 Salt bridges: A:R.54, A:R.54, A:R.94, A:R.347 pi-Stacking: A:H.57, A:F.143 pi-Cation interactions: A:R.336, A:R.336 Metal complexes: A:Y.340 HEM.8: 27 residues within 4Å: Chain B: R.54, V.55, V.56, H.57, R.94, G.113, F.114, V.128, G.129, N.130, F.135, A.140, F.143, G.198, V.199, H.200, F.316, L.332, R.336, S.339, Y.340, T.343, Q.344, R.347 Chain C: D.47 Ligands: HEM.9, PYG.11 28 PLIP interactions: 28 interactions with chain B, Hydrophobic interactions: B:V.55, B:V.56, B:H.57, B:V.128, B:F.135, B:F.135, B:F.135, B:A.140, B:F.143, B:F.143, B:F.143, B:F.143, B:F.143, B:V.199, B:L.332, B:R.336, B:Y.340, B:Y.340 Hydrogen bonds: B:Q.344 Water bridges: B:A.314 Salt bridges: B:R.54, B:R.54, B:R.94, B:R.347 pi-Stacking: B:H.57, B:F.143 pi-Cation interactions: B:R.336 Metal complexes: B:Y.340 HEM.9: 29 residues within 4Å: Chain B: R.54, V.55, V.56, H.57, R.94, G.113, F.114, A.115, V.128, G.129, N.130, F.135, A.140, F.143, V.199, H.200, F.316, L.332, G.335, R.336, S.339, Y.340, T.343, Q.344, R.347 Chain C: L.43, D.47 Ligands: HEM.8, PYG.11 31 PLIP interactions: 30 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:V.55, B:V.56, B:H.57, B:V.128, B:N.130, B:F.135, B:F.135, B:A.140, B:F.143, B:F.143, B:F.143, B:F.143, B:V.199, B:V.199, B:L.332, B:L.332, B:R.336, B:Y.340, B:Y.340, B:Y.340, C:L.43 Hydrogen bonds: B:Q.344 Water bridges: B:V.55, B:R.94 Salt bridges: B:R.54, B:R.54, B:R.94, B:R.347 pi-Stacking: B:H.57, B:F.143 Metal complexes: B:Y.340 HEM.14: 26 residues within 4Å: Chain B: D.47 Chain C: R.54, V.55, V.56, H.57, R.94, G.113, F.114, V.128, G.129, N.130, F.135, A.140, F.143, V.199, H.200, F.316, L.332, R.336, S.339, Y.340, T.343, Q.344, R.347 Ligands: HEM.15, PYG.17 30 PLIP interactions: 30 interactions with chain C, Hydrophobic interactions: C:V.55, C:V.56, C:H.57, C:V.128, C:N.130, C:F.135, C:F.135, C:F.135, C:A.140, C:F.143, C:F.143, C:F.143, C:F.143, C:F.143, C:V.199, C:L.332, C:R.336, C:Y.340, C:Y.340 Hydrogen bonds: C:Q.344 Water bridges: C:V.55, C:A.314, C:R.347 Salt bridges: C:R.54, C:R.54, C:R.94, C:R.347 pi-Stacking: C:F.143 pi-Cation interactions: C:R.336 Metal complexes: C:Y.340 HEM.15: 29 residues within 4Å: Chain B: L.43, D.47 Chain C: R.54, V.55, V.56, H.57, R.94, G.113, F.114, A.115, V.128, G.129, N.130, F.135, A.140, F.143, V.199, H.200, F.316, L.332, G.335, R.336, S.339, Y.340, T.343, Q.344, R.347 Ligands: HEM.14, PYG.17 31 PLIP interactions: 30 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:V.55, C:H.57, C:A.115, C:V.128, C:N.130, C:F.135, C:F.135, C:F.135, C:A.140, C:F.143, C:F.143, C:F.143, C:F.143, C:V.199, C:L.332, C:L.332, C:R.336, C:Y.340, C:Y.340, C:T.343, B:L.43 Hydrogen bonds: C:R.94, C:Q.344 Water bridges: C:R.347 Salt bridges: C:R.54, C:R.54, C:R.94, C:R.347 pi-Stacking: C:H.57, C:F.143 Metal complexes: C:Y.340 HEM.20: 27 residues within 4Å: Chain A: D.47 Chain D: R.54, V.55, V.56, H.57, R.94, G.113, F.114, A.115, V.128, G.129, N.130, F.135, A.140, F.143, V.199, H.200, F.316, L.332, R.336, S.339, Y.340, T.343, Q.344, R.347 Ligands: HEM.21, PYG.23 30 PLIP interactions: 30 interactions with chain D, Hydrophobic interactions: D:V.55, D:H.57, D:V.128, D:F.135, D:F.135, D:F.135, D:A.140, D:F.143, D:F.143, D:F.143, D:F.143, D:F.143, D:V.199, D:L.332, D:R.336, D:Y.340, D:Y.340, D:T.343 Hydrogen bonds: D:Q.344 Water bridges: D:V.55, D:A.314, D:R.347 Salt bridges: D:R.54, D:R.54, D:R.94, D:R.347 pi-Stacking: D:H.57, D:F.143 pi-Cation interactions: D:R.336 Metal complexes: D:Y.340 HEM.21: 29 residues within 4Å: Chain A: L.43, D.47 Chain D: R.54, V.55, V.56, H.57, R.94, G.113, F.114, A.115, V.128, G.129, N.130, F.135, A.140, F.143, V.199, H.200, F.316, L.332, G.335, R.336, S.339, Y.340, T.343, Q.344, R.347 Ligands: HEM.20, PYG.23 32 PLIP interactions: 31 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: D:V.55, D:V.56, D:H.57, D:A.115, D:V.128, D:N.130, D:F.135, D:F.135, D:A.140, D:F.143, D:F.143, D:F.143, D:F.143, D:V.199, D:F.316, D:L.332, D:L.332, D:R.336, D:Y.340, A:L.43 Hydrogen bonds: D:Q.344 Water bridges: D:V.55, D:R.94, D:R.347 Salt bridges: D:R.54, D:R.54, D:R.94, D:R.347 pi-Stacking: D:H.57, D:F.143 pi-Cation interactions: D:R.336 Metal complexes: D:Y.340

8 x PYG: BENZENE-1,2,3-TRIOL(Non-covalent)

PYG.3: 9 residues within 4Å: Chain A: I.99, R.109, D.110, P.111, L.150, Q.159, Y.164, L.181, F.182 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.150, A:Y.164, A:L.181, A:F.182 Hydrogen bonds: A:D.110, A:D.110, A:Q.159, A:Q.159 PYG.4: 12 residues within 4Å: Chain A: V.56, H.57, V.98, P.111, N.130, F.135, F.136, F.143, M.146, V.147 Ligands: HEM.1, HEM.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.98, A:F.136, A:F.143, A:F.143, A:V.147 Hydrogen bonds: A:H.57, A:H.57, A:N.130 pi-Stacking: A:F.135 PYG.10: 9 residues within 4Å: Chain B: I.99, R.109, D.110, P.111, L.150, Q.159, Y.164, L.181, F.182 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.150, B:Y.164, B:L.181, B:F.182 Hydrogen bonds: B:D.110, B:D.110, B:D.110, B:Q.159, B:Q.159 PYG.11: 11 residues within 4Å: Chain B: V.56, H.57, V.98, P.111, N.130, F.135, F.136, F.143, M.146 Ligands: HEM.8, HEM.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.98, B:F.136, B:F.143 Hydrogen bonds: B:H.57, B:N.130 pi-Stacking: B:F.135 PYG.16: 10 residues within 4Å: Chain C: I.99, R.109, D.110, P.111, F.136, L.150, Q.159, Y.164, L.181, F.182 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.136, C:L.150, C:Y.164, C:L.181, C:F.182 Hydrogen bonds: C:D.110, C:D.110, C:Q.159, C:Q.159 Water bridges: C:Y.164 PYG.17: 12 residues within 4Å: Chain C: V.56, H.57, V.98, P.111, N.130, F.135, F.136, F.143, M.146, V.147 Ligands: HEM.14, HEM.15 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.98, C:F.135, C:F.136, C:F.143, C:F.143, C:V.147 Hydrogen bonds: C:H.57, C:N.130, C:N.130 PYG.22: 9 residues within 4Å: Chain D: I.99, R.109, D.110, P.111, L.150, Q.159, Y.164, L.181, F.182 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.150, D:Y.164, D:L.181, D:F.182 Hydrogen bonds: D:D.110, D:D.110, D:D.110, D:Q.159, D:Q.159 Water bridges: D:Y.164 PYG.23: 12 residues within 4Å: Chain D: V.56, H.57, V.98, P.111, N.130, F.135, F.136, F.143, M.146, V.147 Ligands: HEM.20, HEM.21 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.98, D:F.136, D:F.143, D:F.143, D:V.147 Hydrogen bonds: D:H.57, D:N.130 pi-Stacking: D:F.135

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: R.48 Chain B: R.48 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: N.366, N.367 Chain C: K.42 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: N.366, N.367 Chain D: K.42 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: R.48 Chain D: R.48 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain A: K.42 Chain C: N.366, N.367 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain B: K.42 Chain D: N.366, N.367 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 2 residues within 4Å: Chain A: S.72, E.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.72, A:S.72 NA.13: 2 residues within 4Å: Chain B: S.72, E.85 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.72, B:E.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loewen, P.C. et al., Unprecedented access of phenolic substrates to the heme active site of a catalase: Substrate binding and peroxidase-like reactivity of Bacillus pumilus catalase monitored by X-ray crystallography and EPR spectroscopy. Proteins (2015)

Release Date

2015-02-25

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase

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