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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 28 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, A.343, F.345, M.361, G.364, R.365, S.368, Y.369, T.372, Q.373, R.376 Chain B: L.67, D.71 24 PLIP interactions: 1 interactions with chain B, 23 interactions with chain A, Hydrophobic interactions: B:L.67, A:V.79, A:V.80, 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 Hydrogen bonds: A:Q.373 Water bridges: A:V.79 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 A: L.67, D.71 Chain B: R.78, V.79, V.80, H.81, R.123, S.125, 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 29 PLIP interactions: 28 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:V.79, B:V.80, B:H.81, B:V.157, B:F.164, B:A.169, B:F.172, B:F.172, B:F.172, B:F.172, B:V.228, B:V.228, B:R.365, A:L.67 Hydrogen bonds: B:S.125, B:S.125, B:T.372, B:Q.373 Water bridges: B:R.78, B:V.79, B:F.345 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.9: 28 residues within 4Å: 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, 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 24 PLIP interactions: 23 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:V.79, C:V.80, 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, D:L.67 Hydrogen bonds: C:Q.373 Water bridges: C:V.79 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.13: 28 residues within 4Å: Chain C: L.67, D.71 Chain D: R.78, V.79, V.80, H.81, R.123, S.125, 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 D, 1 interactions with chain C, Hydrophobic interactions: D:V.79, D:V.80, D:H.81, D:V.157, D:F.164, D:A.169, D:F.172, D:F.172, D:F.172, D:F.172, D:V.228, D:V.228, D:R.365, C:L.67 Hydrogen bonds: D:S.125, D:S.125, D:Q.373 Water bridges: D:R.78, D:V.79, D:F.345 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

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

CL.2: 6 residues within 4Å: Chain A: R.374, P.379, N.380, L.382 Chain C: R.36, H.69 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: L.33, K.66 Chain C: N.396 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.487 Chain D: L.422, L.423 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain B: K.66 Chain D: N.396 Ligand excluded by PLIP CL.7: 7 residues within 4Å: Chain B: R.374, P.379, N.380, Y.381, L.382 Chain D: R.36, H.69 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain B: F.222, Q.251, R.254 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain A: R.36, H.69 Chain C: R.374, P.379, N.380, L.382 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: N.396 Chain C: L.33, K.66 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: L.422, L.423 Chain C: R.487 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: N.396 Chain D: K.66 Ligand excluded by PLIP CL.15: 7 residues within 4Å: Chain B: R.36, H.69 Chain D: R.374, P.379, N.380, Y.381, L.382 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain D: F.222, Q.251, R.254 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
A

B
B

C
A

D
B

CATALASE

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