SMTL ID : 1gwh.1

Atomic resolution structure of Micrococcus Lysodeikticus catalase complexed with NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 28 residues within 4Å: Chain A: R.58, R.59, P.60, H.61, R.97, G.116, F.117, A.118, V.131, G.132, N.133, P.143, F.146, G.201, S.202, H.203, L.284, F.319, M.335, R.339, A.342, Y.343, A.346, Q.347, R.350 Chain D: H.47, N.51 Ligands: ACT.4 30 PLIP interactions: 29 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:H.61, A:A.118, A:V.131, A:N.133, A:P.143, A:F.146, A:F.146, A:F.146, A:F.146, A:L.284, A:R.339, A:A.342, A:Y.343, A:Y.343, A:A.346 Hydrogen bonds: A:Q.347 Water bridges: A:R.58, A:R.97, A:A.118, A:A.317 Salt bridges: A:R.58, A:R.58, A:R.97, A:R.350 pi-Stacking: A:H.61, A:F.138, A:F.146 pi-Cation interactions: A:R.339 Metal complexes: A:Y.343, H2O.22 HEM.6: 28 residues within 4Å: Chain B: R.58, R.59, P.60, H.61, R.97, G.116, F.117, A.118, V.131, G.132, N.133, P.143, F.146, G.201, S.202, H.203, L.284, F.319, M.335, R.339, A.342, Y.343, A.346, Q.347, R.350 Chain C: H.47, N.51 Ligands: ACT.9 30 PLIP interactions: 29 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:H.61, B:A.118, B:V.131, B:N.133, B:P.143, B:F.146, B:F.146, B:F.146, B:F.146, B:L.284, B:R.339, B:A.342, B:Y.343, B:Y.343, B:A.346 Hydrogen bonds: B:Q.347 Water bridges: B:R.58, B:R.97, B:A.118, B:A.317 Salt bridges: B:R.58, B:R.58, B:R.97, B:R.350 pi-Stacking: B:H.61, B:F.138, B:F.146 pi-Cation interactions: B:R.339 Metal complexes: B:Y.343, H2O.44 HEM.11: 28 residues within 4Å: Chain B: H.47, N.51 Chain C: R.58, R.59, P.60, H.61, R.97, G.116, F.117, A.118, V.131, G.132, N.133, P.143, F.146, G.201, S.202, H.203, L.284, F.319, M.335, R.339, A.342, Y.343, A.346, Q.347, R.350 Ligands: ACT.14 30 PLIP interactions: 29 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:H.61, C:A.118, C:V.131, C:N.133, C:P.143, C:F.146, C:F.146, C:F.146, C:F.146, C:L.284, C:R.339, C:A.342, C:Y.343, C:Y.343, C:A.346 Hydrogen bonds: C:Q.347 Water bridges: C:R.58, C:R.97, C:A.118, C:A.317 Salt bridges: C:R.58, C:R.58, C:R.97, C:R.350 pi-Stacking: C:H.61, C:F.138, C:F.146 pi-Cation interactions: C:R.339 Metal complexes: C:Y.343, H2O.66 HEM.16: 28 residues within 4Å: Chain A: H.47, N.51 Chain D: R.58, R.59, P.60, H.61, R.97, G.116, F.117, A.118, V.131, G.132, N.133, P.143, F.146, G.201, S.202, H.203, L.284, F.319, M.335, R.339, A.342, Y.343, A.346, Q.347, R.350 Ligands: ACT.19 30 PLIP interactions: 29 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:H.61, D:A.118, D:V.131, D:N.133, D:P.143, D:F.146, D:F.146, D:F.146, D:F.146, D:L.284, D:R.339, D:A.342, D:Y.343, D:Y.343, D:A.346 Hydrogen bonds: D:Q.347 Water bridges: D:R.58, D:R.97, D:A.118, D:A.317 Salt bridges: D:R.58, D:R.58, D:R.97, D:R.350 pi-Stacking: D:H.61, D:F.138, D:F.146 pi-Cation interactions: D:R.339 Metal complexes: D:Y.343, H2O.88

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Covalent)

NDP.2: 13 residues within 4Å: Chain A: Y.183, P.187, R.188, N.198, Y.200, S.289, Q.290, K.291, R.295, L.433, V.437, F.438 Ligands: SO4.3 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Q.290 Hydrogen bonds: A:R.188, A:N.198, A:Y.200, A:Y.200, A:Q.290, A:K.291 Water bridges: A:R.188, A:Q.290, A:Q.290, A:Q.290, A:R.295, A:R.295, A:R.295, A:R.295, A:E.442 Salt bridges: A:R.188, A:R.295 pi-Cation interactions: A:R.188, A:R.188 NDP.7: 13 residues within 4Å: Chain B: Y.183, P.187, R.188, N.198, Y.200, S.289, Q.290, K.291, R.295, L.433, V.437, F.438 Ligands: SO4.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Q.290 Hydrogen bonds: B:R.188, B:N.198, B:Y.200, B:Y.200, B:Q.290, B:K.291 Water bridges: B:R.188, B:Q.290, B:Q.290, B:Q.290, B:R.295, B:R.295, B:R.295, B:R.295, B:E.442 Salt bridges: B:R.188, B:R.295 pi-Cation interactions: B:R.188, B:R.188 NDP.12: 13 residues within 4Å: Chain C: Y.183, P.187, R.188, N.198, Y.200, S.289, Q.290, K.291, R.295, L.433, V.437, F.438 Ligands: SO4.13 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:Q.290 Hydrogen bonds: C:R.188, C:N.198, C:Y.200, C:Q.290, C:K.291 Water bridges: C:R.188, C:Q.290, C:Q.290, C:Q.290, C:R.295, C:R.295, C:R.295, C:R.295, C:E.442 Salt bridges: C:R.188, C:R.295 pi-Cation interactions: C:R.188, C:R.188 NDP.17: 13 residues within 4Å: Chain D: Y.183, P.187, R.188, N.198, Y.200, S.289, Q.290, K.291, R.295, L.433, V.437, F.438 Ligands: SO4.18 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:Q.290 Hydrogen bonds: D:R.188, D:N.198, D:Y.200, D:Q.290, D:K.291 Water bridges: D:R.188, D:Q.290, D:Q.290, D:Q.290, D:R.295, D:R.295, D:R.295, D:R.295, D:E.442 Salt bridges: D:R.188, D:R.295 pi-Cation interactions: D:R.188, D:R.188

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: S.289, Q.290 Ligands: NDP.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.289, A:Q.290, A:Q.290 SO4.8: 3 residues within 4Å: Chain B: S.289, Q.290 Ligands: NDP.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.290, B:Q.290 SO4.13: 3 residues within 4Å: Chain C: S.289, Q.290 Ligands: NDP.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.289, C:Q.290, C:Q.290 SO4.18: 3 residues within 4Å: Chain D: S.289, Q.290 Ligands: NDP.17 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.290, D:Q.290

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 8 residues within 4Å: Chain A: P.60, H.61, V.101, N.133, F.138, F.146, I.150 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.101, A:F.138, A:F.146, A:I.150 Hydrogen bonds: A:N.133 Salt bridges: A:H.61 ACT.5: 7 residues within 4Å: Chain A: V.101, D.113, V.114, F.139, F.149, Q.153, L.184 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.101, A:V.114, A:F.139, A:F.149 Hydrogen bonds: A:D.113, A:V.114 ACT.9: 8 residues within 4Å: Chain B: P.60, H.61, V.101, N.133, F.138, F.146, I.150 Ligands: HEM.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.101, B:F.138, B:F.146, B:I.150 Hydrogen bonds: B:N.133 Salt bridges: B:H.61 ACT.10: 7 residues within 4Å: Chain B: V.101, D.113, V.114, F.139, F.149, Q.153, L.184 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.101, B:V.114, B:F.139, B:F.149 Hydrogen bonds: B:D.113, B:V.114 ACT.14: 8 residues within 4Å: Chain C: P.60, H.61, V.101, N.133, F.138, F.146, I.150 Ligands: HEM.11 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.101, C:F.138, C:F.146, C:I.150 Hydrogen bonds: C:N.133 Salt bridges: C:H.61 ACT.15: 7 residues within 4Å: Chain C: V.101, D.113, V.114, F.139, F.149, Q.153, L.184 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.101, C:V.114, C:F.139, C:F.149 Hydrogen bonds: C:V.114 ACT.19: 8 residues within 4Å: Chain D: P.60, H.61, V.101, N.133, F.138, F.146, I.150 Ligands: HEM.16 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.101, D:F.138, D:F.146, D:I.150 Hydrogen bonds: D:N.133 Salt bridges: D:H.61 ACT.20: 7 residues within 4Å: Chain D: V.101, D.113, V.114, F.139, F.149, Q.153, L.184 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.101, D:V.114, D:F.139, D:F.149 Hydrogen bonds: D:V.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murshudov, G.N. et al., The Structures of Micrococcus Lysodeikticus Catalase, its Ferryl Intermediate (Compound II) and Nadph Complex. Acta Crystallogr.,Sect.D (2002)

Release Date

2002-03-19

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Catalase

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