SMTL ID : 4qoq.1

Structure of Bacillus pumilus catalase with guaiacol bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: 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 D: D.47 Ligands: HEM.2 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:V.55, A:H.57, A:V.128, A:N.130, A:F.135, A:F.135, A:F.135, A:A.140, A:F.143, A:F.143, 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, A:F.143 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, F.114, 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 34 PLIP interactions: 33 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:V.199, A:F.316, A:L.332, A:L.332, A:R.336, A:Y.340, A:Y.340, A:T.343, D:L.43 Hydrogen bonds: A:S.96, A:S.96, A:Q.344 Water bridges: A:V.55, 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 Metal complexes: A:Y.340 HEM.7: 26 residues within 4Å: Chain B: R.54, V.55, V.56, H.57, R.94, G.113, 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 Chain C: L.43, D.47 Ligands: HEM.8 30 PLIP interactions: 28 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: B:V.55, B:H.57, B:V.128, B:N.130, 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, B:T.343, C:L.43 Hydrogen bonds: B:Q.344 Water bridges: B:A.314, B:R.347 Salt bridges: B:R.54, B:R.54, B:R.94, B:R.347 pi-Cation interactions: B:R.336 Metal complexes: B:Y.340, H2O.32 HEM.8: 28 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.7 32 PLIP interactions: 30 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: B:V.55, B:V.56, B:H.57, B:A.115, B:V.128, B:N.130, 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:V.199, B:L.332, B:L.332, B:R.336, B:Y.340, B:Y.340, C:L.43 Hydrogen bonds: B:Q.344 Water bridges: 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 pi-Cation interactions: B:R.336 Metal complexes: B:Y.340, H2O.32 HEM.13: 24 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, F.316, L.332, R.336, S.339, Y.340, T.343, Q.344, R.347 Ligands: HEM.14 32 PLIP interactions: 31 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:V.55, 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, C:T.343 Hydrogen bonds: C:Q.344 Water bridges: C:V.55, C:A.314, C:T.343 Salt bridges: C:R.54, C:R.54, C:R.94, C:R.347 pi-Stacking: C:H.57, C:F.143 pi-Cation interactions: C:R.336 Metal complexes: C:Y.340, H2O.49 HEM.14: 28 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.13 34 PLIP interactions: 33 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:V.55, C:V.56, C:H.57, C:A.115, C:V.128, C:N.130, C:F.135, C:F.135, C:A.140, C:F.143, C:F.143, C:F.143, C:V.199, C:V.199, C:F.316, C:L.332, C:L.332, C:R.336, C:Y.340, C:Y.340, B:L.43 Hydrogen bonds: C:Q.344 Water bridges: C:V.55, C:R.94, C:R.94, 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 pi-Cation interactions: C:R.336 Metal complexes: C:Y.340 HEM.18: 26 residues within 4Å: Chain A: D.47 Chain D: 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 Ligands: HEM.19 28 PLIP interactions: 28 interactions with chain D, Hydrophobic interactions: D:V.55, D:V.56, D:H.57, D:V.128, D:N.130, 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:A.314, D:T.343 Salt bridges: D:R.54, D:R.94, D:R.347 pi-Cation interactions: D:R.336 Metal complexes: D:Y.340 HEM.19: 28 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.18 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: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:V.199, D:L.332, D:L.332, D:R.336, D:Y.340, D:Y.340, A:L.43 Hydrogen bonds: D:Q.344 Water bridges: D:V.55, D:R.94, D:A.115 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

6 x JZ3: Guaiacol(Non-covalent)

JZ3.3: 10 residues within 4Å: Chain A: I.99, R.109, D.110, P.111, F.136, L.150, Q.159, Y.164, L.181, F.182 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.164, A:L.181, A:F.182 Hydrogen bonds: A:D.110, A:Q.159 JZ3.9: 9 residues within 4Å: Chain B: I.99, R.109, D.110, P.111, F.136, L.150, Q.159, Y.164, L.181 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.150, B:L.181 Hydrogen bonds: B:D.110, B:Q.159 JZ3.10: 7 residues within 4Å: Chain B: L.457, I.460, C.461, Y.464, I.482, Y.485, L.486 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.457, B:I.460, B:Y.464, B:Y.464, B:I.482, B:I.482, B:L.486 JZ3.15: 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 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.164, C:L.181, C:F.182 Hydrogen bonds: C:D.110, C:Q.159 JZ3.20: 10 residues within 4Å: Chain D: I.99, R.109, D.110, P.111, F.136, L.150, Q.159, Y.164, L.181, F.182 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.150, D:L.181, D:F.182 Hydrogen bonds: D:D.110, D:D.110, D:Q.159 pi-Stacking: D:Y.164 JZ3.21: 7 residues within 4Å: Chain D: L.457, I.460, C.461, Y.464, I.482, Y.485, L.486 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.457, D:I.460, D:Y.464, D:Y.464, D:I.482, D:I.482, D:L.486

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

CL.4: 2 residues within 4Å: Chain A: R.48 Chain B: R.48 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: N.366, N.367 Chain C: K.42 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: N.366, N.367 Chain D: K.42 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain C: R.48 Chain D: R.48 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain A: K.42 Chain C: N.366, N.367 Ligand excluded by PLIP CL.22: 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.6: 2 residues within 4Å: Chain A: S.72, E.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.72 NA.12: 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

Related Entries With Identical Sequence