SMTL ID : 3rgs.1

Structural and kinetic analysis of the beef liver catalase with the ammonia as a ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 28 residues within 4Å: Chain A: R.69, V.70, V.71, H.72, R.109, G.128, F.129, V.143, G.144, N.145, F.150, A.155, F.158, G.213, S.214, H.215, L.296, F.331, M.347, R.351, A.354, Y.355, T.358, H.359, R.362 Chain D: M.58, D.62 Ligands: NH3.2 30 PLIP interactions: 30 interactions with chain A, Hydrophobic interactions: A:V.70, A:V.71, A:H.72, A:V.143, A:N.145, A:F.150, A:A.155, A:F.158, A:F.158, A:F.158, A:F.158, A:L.296, A:R.351, A:A.354, A:Y.355, A:Y.355 Water bridges: A:V.70, A:A.130, A:L.329, A:H.359 Salt bridges: A:R.69, A:R.69, A:R.109, A:H.359, A:R.362 pi-Stacking: A:H.72, A:F.150, A:F.158 pi-Cation interactions: A:R.351 Metal complexes: A:Y.355 HEM.3: 27 residues within 4Å: Chain B: R.69, V.70, V.71, H.72, R.109, G.128, F.129, V.143, G.144, N.145, F.150, A.155, F.158, G.213, S.214, L.296, F.331, M.347, R.351, A.354, Y.355, T.358, H.359, R.362 Chain C: M.58, D.62 Ligands: NH3.4 31 PLIP interactions: 31 interactions with chain B, Hydrophobic interactions: B:V.70, B:V.71, B:H.72, B:V.143, B:N.145, B:F.150, B:A.155, B:F.158, B:F.158, B:F.158, B:F.158, B:L.296, B:F.331, B:R.351, B:A.354, B:Y.355, B:Y.355 Water bridges: B:S.111, B:A.130, B:F.331, B:T.358, B:R.362 Salt bridges: B:R.69, B:R.69, B:R.109, B:H.359, B:R.362 pi-Stacking: B:H.72, B:F.158 pi-Cation interactions: B:R.351 Metal complexes: B:Y.355 HEM.5: 27 residues within 4Å: Chain B: M.58, D.62 Chain C: R.69, V.70, V.71, H.72, R.109, G.128, F.129, V.143, G.144, N.145, F.150, A.155, F.158, G.213, S.214, L.296, F.331, M.347, R.351, A.354, Y.355, T.358, H.359, R.362 Ligands: NH3.6 27 PLIP interactions: 27 interactions with chain C, Hydrophobic interactions: C:V.70, C:H.72, C:V.143, C:N.145, C:F.150, C:A.155, C:F.158, C:F.158, C:F.158, C:L.296, C:F.331, C:R.351, C:A.354, C:Y.355, C:Y.355 Water bridges: C:A.130, C:L.329, C:F.331 Salt bridges: C:R.69, C:R.69, C:R.109, C:H.359, C:R.362 pi-Stacking: C:H.72, C:F.150 pi-Cation interactions: C:R.351 Metal complexes: C:Y.355 HEM.7: 28 residues within 4Å: Chain A: M.58, D.62 Chain D: R.69, V.70, V.71, H.72, R.109, G.128, F.129, V.143, G.144, N.145, F.150, A.155, F.158, G.213, S.214, H.215, L.296, F.331, M.347, R.351, A.354, Y.355, T.358, H.359, R.362 Ligands: NH3.8 30 PLIP interactions: 30 interactions with chain D, Hydrophobic interactions: D:V.70, D:V.71, D:H.72, D:V.143, D:N.145, D:F.150, D:A.155, D:F.158, D:F.158, D:F.158, D:F.158, D:L.296, D:F.331, D:R.351, D:A.354, D:Y.355, D:Y.355 Water bridges: D:V.70, D:A.130, D:L.329, D:F.331 Salt bridges: D:R.69, D:R.69, D:R.109, D:H.359, D:R.362 pi-Stacking: D:H.72, D:F.158 pi-Cation interactions: D:R.351 Metal complexes: D:Y.355

4 x NH3: AMMONIA(Non-covalent)

NH3.2: 4 residues within 4Å: Chain A: V.71, H.72, F.158 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.72 NH3.4: 4 residues within 4Å: Chain B: V.71, H.72, F.158 Ligands: HEM.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.72 NH3.6: 3 residues within 4Å: Chain C: H.72, F.158 Ligands: HEM.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.72 NH3.8: 4 residues within 4Å: Chain D: V.71, H.72, F.158 Ligands: HEM.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Purwar, N. et al., Interaction of nitric oxide with catalase: structural and kinetic analysis. Biochemistry (2011)

Release Date

2011-05-11

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Catalase

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