SMTL ID : 1gwf.1

Compound II structure of Micrococcus Lysodeikticus catalase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-tetramer

Ligands

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

HEM.1: 29 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, F.138, 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: O.7 29 PLIP interactions: 28 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:H.61, A:V.131, A:N.133, A:F.138, 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.146 pi-Cation interactions: A:R.339 Metal complexes: A:Y.343, O.7 HEM.8: 29 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, F.138, 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: O.14 29 PLIP interactions: 28 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:H.61, B:V.131, B:N.133, B:F.138, 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.146 pi-Cation interactions: B:R.339 Metal complexes: B:Y.343, O.14 HEM.15: 29 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, F.138, 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: O.21 28 PLIP interactions: 28 interactions with chain C, Hydrophobic interactions: C:H.61, C:V.131, C:N.133, C:F.138, 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.146 pi-Cation interactions: C:R.339 Metal complexes: C:Y.343 HEM.22: 29 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, F.138, 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: O.28 29 PLIP interactions: 28 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:H.61, D:V.131, D:N.133, D:F.138, 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.146 pi-Cation interactions: D:R.339 Metal complexes: D:Y.343, O.28

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

SO4.2: 4 residues within 4Å: Chain A: R.188, N.198, Y.200, R.295 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.198, A:Y.200, A:Y.200 Water bridges: A:R.188, A:R.188, A:Q.290, A:Q.290 Salt bridges: A:R.188, A:R.295 SO4.5: 5 residues within 4Å: Chain B: E.373 Chain D: R.59, E.104, K.154, R.155 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain D Water bridges: B:E.373, B:E.373, B:E.373, D:R.59, D:R.59, D:R.59 Hydrogen bonds: D:R.155 Salt bridges: D:R.59 SO4.6: 3 residues within 4Å: Chain A: R.25 Chain D: N.173, P.175 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Water bridges: A:R.25, A:R.25, D:E.176 Salt bridges: A:R.25 SO4.9: 4 residues within 4Å: Chain B: R.188, N.198, Y.200, R.295 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.198, B:Y.200, B:Y.200 Water bridges: B:R.188, B:R.188, B:Q.290, B:Q.290 Salt bridges: B:R.188, B:R.295 SO4.12: 5 residues within 4Å: Chain A: E.373 Chain C: R.59, E.104, K.154, R.155 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain C Water bridges: A:E.373, A:E.373, A:E.373, C:R.59, C:R.59, C:R.59 Hydrogen bonds: C:R.155 Salt bridges: C:R.59 SO4.13: 3 residues within 4Å: Chain B: R.25 Chain C: N.173, P.175 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Water bridges: B:R.25, B:R.25, C:E.176 Salt bridges: B:R.25 SO4.16: 4 residues within 4Å: Chain C: R.188, N.198, Y.200, R.295 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.198, C:Y.200 Water bridges: C:R.188, C:R.188, C:Q.290, C:Q.290 Salt bridges: C:R.188, C:R.295 SO4.19: 5 residues within 4Å: Chain B: R.59, E.104, K.154, R.155 Chain D: E.373 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:E.104, B:R.155 Water bridges: B:R.59, B:R.59, B:R.59, D:E.373, D:E.373, D:E.373, D:E.373 Salt bridges: B:R.59 SO4.20: 3 residues within 4Å: Chain B: N.173, P.175 Chain C: R.25 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Water bridges: B:N.173, B:E.176, B:E.176, C:R.25 Salt bridges: C:R.25 SO4.23: 4 residues within 4Å: Chain D: R.188, N.198, Y.200, R.295 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.198, D:Y.200 Water bridges: D:R.188, D:R.188, D:Q.290, D:Q.290 Salt bridges: D:R.188, D:R.295 SO4.26: 5 residues within 4Å: Chain A: R.59, E.104, K.154, R.155 Chain C: E.373 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:E.104, A:R.155 Water bridges: A:R.59, A:R.59, A:R.59, C:E.373, C:E.373, C:E.373, C:E.373 Salt bridges: A:R.59 SO4.27: 3 residues within 4Å: Chain A: N.173, P.175 Chain D: R.25 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Water bridges: D:R.25, A:N.173, A:E.176, A:E.176 Salt bridges: D:R.25

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

ACT.3: 6 residues within 4Å: Chain A: V.101, D.113, V.114, F.139, F.149, Q.153 7 PLIP interactions: 7 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, A:Q.153 ACT.4: 6 residues within 4Å: Chain A: R.112, Q.167, L.184, M.185, I.492, V.495 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.495 Hydrogen bonds: A:R.112 Water bridges: A:R.112, A:Q.153, A:Q.167, A:Q.167 ACT.10: 6 residues within 4Å: Chain B: V.101, D.113, V.114, F.139, F.149, Q.153 7 PLIP interactions: 7 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, B:Q.153 ACT.11: 6 residues within 4Å: Chain B: R.112, Q.167, L.184, M.185, I.492, V.495 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.495 Hydrogen bonds: B:R.112 Water bridges: B:R.112, B:Q.153, B:Q.167, B:Q.167 ACT.17: 6 residues within 4Å: Chain C: V.101, D.113, V.114, F.139, F.149, Q.153 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.101, C:V.114, C:F.139, C:F.149 Hydrogen bonds: C:V.114, C:Q.153 ACT.18: 6 residues within 4Å: Chain C: R.112, Q.167, L.184, M.185, I.492, V.495 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.495 Hydrogen bonds: C:R.112 Water bridges: C:R.112, C:Q.153, C:Q.167, C:Q.167 ACT.24: 6 residues within 4Å: Chain D: V.101, D.113, V.114, F.139, F.149, Q.153 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.101, D:V.114, D:F.139, D:F.149 Hydrogen bonds: D:V.114, D:Q.153 ACT.25: 6 residues within 4Å: Chain D: R.112, Q.167, L.184, M.185, I.492, V.495 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:V.495 Hydrogen bonds: D:R.112 Water bridges: D:R.112, D:Q.153, D:Q.167, D:Q.167

4 x O: OXYGEN ATOM(Non-covalent)

O.7: 5 residues within 4Å: Chain A: P.60, H.61, F.146, Y.343 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) O.14: 5 residues within 4Å: Chain B: P.60, H.61, F.146, Y.343 Ligands: HEM.8 No protein-ligand interaction detected (PLIP) O.21: 5 residues within 4Å: Chain C: P.60, H.61, F.146, Y.343 Ligands: HEM.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.343 O.28: 5 residues within 4Å: Chain D: P.60, H.61, F.146, Y.343 Ligands: HEM.22 No protein-ligand interaction detected (PLIP)

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

2002-04-26

Peptides

Catalase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Catalase

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