SMTL ID : 4cab.2 (1 other biounit)

The refined structure of catalase DR1998 from Deinococcus radiodurans at 2.6 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 27 residues within 4Å: Chain A: R.78, V.79, V.80, H.81, R.123, G.142, F.143, V.157, G.158, N.159, F.164, A.169, F.172, V.228, N.229, D.310, F.345, M.361, G.364, R.365, S.368, Y.369, T.372, Q.373, R.376 Chain C: L.67, D.71 29 PLIP interactions: 28 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: A:V.79, A:H.81, A:V.157, A:F.164, A:F.164, A:F.172, A:F.172, A:F.172, A:F.172, A:V.228, A:V.228, A:R.365, A:Y.369, A:T.372, C:L.67 Hydrogen bonds: A:S.125, A:S.125, A:T.372, A:Q.373 Water bridges: A:A.343, A:R.376 Salt bridges: A:R.78, A:R.78, A:R.123, A:R.376 pi-Stacking: A:H.81, A:F.172 pi-Cation interactions: A:R.365 Metal complexes: A:Y.369 HEM.5: 28 residues within 4Å: Chain B: R.78, V.79, V.80, H.81, R.123, G.142, F.143, V.157, G.158, N.159, F.164, A.169, F.172, V.228, N.229, D.310, A.343, F.345, M.361, G.364, R.365, S.368, Y.369, T.372, Q.373, R.376 Chain D: L.67, D.71 25 PLIP interactions: 24 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: B:V.79, B:V.80, B:H.81, B:V.157, B:F.164, B:F.164, B:F.172, B:F.172, B:F.172, B:F.172, B:V.228, B:V.228, B:R.365, B:T.372, D:L.67 Hydrogen bonds: B:Q.373 Water bridges: B:S.125 Salt bridges: B:R.78, B:R.78, B:R.123, B:R.376 pi-Stacking: B:H.81, B:F.172 pi-Cation interactions: B:R.365 Metal complexes: B:Y.369 HEM.7: 27 residues within 4Å: Chain A: L.67, D.71 Chain C: R.78, V.79, V.80, H.81, R.123, G.142, F.143, V.157, G.158, N.159, F.164, A.169, F.172, V.228, N.229, D.310, F.345, M.361, G.364, R.365, S.368, Y.369, T.372, Q.373, R.376 28 PLIP interactions: 27 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:V.79, C:H.81, C:V.157, C:F.164, C:F.164, C:F.172, C:F.172, C:F.172, C:F.172, C:V.228, C:V.228, C:R.365, C:Y.369, C:T.372, A:L.67 Hydrogen bonds: C:S.125, C:S.125, C:Q.373 Water bridges: C:A.343, C:R.376 Salt bridges: C:R.78, C:R.78, C:R.123, C:R.376 pi-Stacking: C:H.81, C:F.172 pi-Cation interactions: C:R.365 Metal complexes: C:Y.369 HEM.11: 28 residues within 4Å: Chain B: L.67, D.71 Chain D: R.78, V.79, V.80, H.81, R.123, G.142, F.143, V.157, G.158, N.159, F.164, A.169, F.172, V.228, N.229, D.310, A.343, F.345, M.361, G.364, R.365, S.368, Y.369, T.372, Q.373, R.376 25 PLIP interactions: 24 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:V.79, D:V.80, D:H.81, D:V.157, D:F.164, D:F.164, D:F.172, D:F.172, D:F.172, D:F.172, D:V.228, D:V.228, D:R.365, D:T.372, B:L.67 Hydrogen bonds: D:Q.373 Water bridges: D:S.125 Salt bridges: D:R.78, D:R.78, D:R.123, D:R.376 pi-Stacking: D:H.81, D:F.172 pi-Cation interactions: D:R.365 Metal complexes: D:Y.369

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

CL.2: 3 residues within 4Å: Chain A: K.66 Chain D: N.396, Q.397 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: P.438, R.439 Ligand excluded by PLIP CL.4: 7 residues within 4Å: Chain A: R.374, P.379, N.380, Y.381, L.382 Chain D: R.36, H.69 Ligand excluded by PLIP CL.6: 7 residues within 4Å: Chain B: R.374, P.379, N.380, Y.381, L.382 Chain C: R.36, H.69 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: N.396, Q.397 Chain C: K.66 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain C: P.438, R.439 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain B: R.36, H.69 Chain C: R.374, P.379, N.380, Y.381, L.382 Ligand excluded by PLIP CL.12: 7 residues within 4Å: Chain A: R.36, H.69 Chain D: R.374, P.379, N.380, Y.381, L.382 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borges, P.T. et al., Structure of the Mono-Functional Heme Catalase Dr1998 from Deinococcus Radiodurans. FEBS J. (2014)

Release Date

2014-07-09

Peptides

CATALASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

CATALASE

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