SMTL ID : 2v8u.1

Atomic resolution structure of Mn catalase from Thermus Thermophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-hexamer

Ligands

30 x O: OXYGEN ATOM(Non-covalent)

O.1: 12 residues within 4Å: Chain A: E.36, E.70, H.73, E.155, G.185, H.188 Ligands: O.2, O.3, O.4, O.5, MN.6, MN.7 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.185 O.2: 10 residues within 4Å: Chain A: E.36, T.39, E.70, E.155 Ligands: O.1, O.3, O.4, O.5, MN.6, MN.7 No protein-ligand interaction detected (PLIP) O.3: 12 residues within 4Å: Chain A: E.36, E.70, H.73, E.155, G.185, H.188 Ligands: O.1, O.2, O.4, O.5, MN.6, MN.7 No protein-ligand interaction detected (PLIP) O.4: 10 residues within 4Å: Chain A: E.36, T.39, E.70, K.162 Ligands: O.1, O.2, O.3, O.5, MN.6, MN.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.39, A:K.162 O.5: 9 residues within 4Å: Chain A: E.36, H.73, K.162, L.181 Ligands: O.1, O.2, O.3, O.4, MN.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.162 O.20: 11 residues within 4Å: Chain B: E.70, H.73, E.155, G.185, H.188 Ligands: MN.18, MN.19, O.21, O.22, O.23, O.24 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.185 O.21: 10 residues within 4Å: Chain B: E.36, T.39, E.70, E.155 Ligands: MN.18, MN.19, O.20, O.22, O.23, O.24 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.39 O.22: 12 residues within 4Å: Chain B: E.36, E.70, H.73, E.155, G.185, H.188 Ligands: MN.18, MN.19, O.20, O.21, O.23, O.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.70, B:H.188 Water bridges: B:G.185 O.23: 10 residues within 4Å: Chain B: E.36, T.39, E.70, K.162 Ligands: MN.18, MN.19, O.20, O.21, O.22, O.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.39, B:T.39, B:K.162 O.24: 9 residues within 4Å: Chain B: E.36, H.73, K.162, L.181 Ligands: MN.18, O.20, O.21, O.22, O.23 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.73, B:K.162 O.27: 12 residues within 4Å: Chain C: E.36, E.70, H.73, E.155, G.185, H.188 Ligands: O.28, O.29, O.30, O.31, MN.32, MN.33 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.185 O.28: 10 residues within 4Å: Chain C: E.36, T.39, E.70, E.155 Ligands: O.27, O.29, O.30, O.31, MN.32, MN.33 No protein-ligand interaction detected (PLIP) O.29: 12 residues within 4Å: Chain C: E.36, E.70, H.73, E.155, G.185, H.188 Ligands: O.27, O.28, O.30, O.31, MN.32, MN.33 No protein-ligand interaction detected (PLIP) O.30: 10 residues within 4Å: Chain C: E.36, T.39, E.70, K.162 Ligands: O.27, O.28, O.29, O.31, MN.32, MN.33 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.39, C:K.162 O.31: 9 residues within 4Å: Chain C: E.36, H.73, K.162, L.181 Ligands: O.27, O.28, O.29, O.30, MN.32 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.162 O.46: 11 residues within 4Å: Chain D: E.70, H.73, E.155, G.185, H.188 Ligands: MN.44, MN.45, O.47, O.48, O.49, O.50 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.185 O.47: 10 residues within 4Å: Chain D: E.36, T.39, E.70, E.155 Ligands: MN.44, MN.45, O.46, O.48, O.49, O.50 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.39 O.48: 12 residues within 4Å: Chain D: E.36, E.70, H.73, E.155, G.185, H.188 Ligands: MN.44, MN.45, O.46, O.47, O.49, O.50 1 PLIP interactions: 1 interactions with chain D Water bridges: D:G.185 O.49: 10 residues within 4Å: Chain D: E.36, T.39, E.70, K.162 Ligands: MN.44, MN.45, O.46, O.47, O.48, O.50 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.39, D:T.39, D:K.162 O.50: 9 residues within 4Å: Chain D: E.36, H.73, K.162, L.181 Ligands: MN.44, O.46, O.47, O.48, O.49 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.36, D:K.162 O.53: 12 residues within 4Å: Chain E: E.36, E.70, H.73, E.155, G.185, H.188 Ligands: O.54, O.55, O.56, O.57, MN.58, MN.59 1 PLIP interactions: 1 interactions with chain E Water bridges: E:G.185 O.54: 10 residues within 4Å: Chain E: E.36, T.39, E.70, E.155 Ligands: O.53, O.55, O.56, O.57, MN.58, MN.59 No protein-ligand interaction detected (PLIP) O.55: 12 residues within 4Å: Chain E: E.36, E.70, H.73, E.155, G.185, H.188 Ligands: O.53, O.54, O.56, O.57, MN.58, MN.59 No protein-ligand interaction detected (PLIP) O.56: 10 residues within 4Å: Chain E: E.36, T.39, E.70, K.162 Ligands: O.53, O.54, O.55, O.57, MN.58, MN.59 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.39, E:K.162 O.57: 9 residues within 4Å: Chain E: E.36, H.73, K.162, L.181 Ligands: O.53, O.54, O.55, O.56, MN.58 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.162 O.72: 11 residues within 4Å: Chain F: E.70, H.73, E.155, G.185, H.188 Ligands: MN.70, MN.71, O.73, O.74, O.75, O.76 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.73, F:H.188 Water bridges: F:G.185 O.73: 10 residues within 4Å: Chain F: E.36, T.39, E.70, E.155 Ligands: MN.70, MN.71, O.72, O.74, O.75, O.76 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.39 O.74: 12 residues within 4Å: Chain F: E.36, E.70, H.73, E.155, G.185, H.188 Ligands: MN.70, MN.71, O.72, O.73, O.75, O.76 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.73, F:H.188 Water bridges: F:G.185 O.75: 10 residues within 4Å: Chain F: E.36, T.39, E.70, K.162 Ligands: MN.70, MN.71, O.72, O.73, O.74, O.76 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.39, F:T.39, F:K.162 O.76: 9 residues within 4Å: Chain F: E.36, H.73, K.162, L.181 Ligands: MN.70, O.72, O.73, O.74, O.75 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.73, F:K.162, F:K.162

12 x MN: MANGANESE (II) ION(Non-covalent)

MN.6: 10 residues within 4Å: Chain A: E.36, T.39, E.70, H.73 Ligands: O.1, O.2, O.3, O.4, O.5, MN.7 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Ligand interactions Metal complexes: A:E.70, A:H.73, O.1, O.2, O.5 MN.7: 8 residues within 4Å: Chain A: E.70, E.155, H.188 Ligands: O.1, O.2, O.3, O.4, MN.6 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:E.70, A:E.155, A:H.188, O.1, O.2 MN.18: 10 residues within 4Å: Chain B: E.36, T.39, E.70, H.73 Ligands: MN.19, O.20, O.21, O.22, O.23, O.24 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.36, B:E.36, B:E.70, B:H.73, O.20 MN.19: 8 residues within 4Å: Chain B: E.70, E.155, H.188 Ligands: MN.18, O.20, O.21, O.22, O.23 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.70, B:E.155, B:E.155, B:H.188, O.20 MN.32: 10 residues within 4Å: Chain C: E.36, T.39, E.70, H.73 Ligands: O.27, O.28, O.29, O.30, O.31, MN.33 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Ligand interactions Metal complexes: C:E.70, C:H.73, O.27, O.28, O.31 MN.33: 8 residues within 4Å: Chain C: E.70, E.155, H.188 Ligands: O.27, O.28, O.29, O.30, MN.32 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Ligand interactions Metal complexes: C:E.70, C:E.155, C:H.188, O.27, O.28 MN.44: 10 residues within 4Å: Chain D: E.36, T.39, E.70, H.73 Ligands: MN.45, O.46, O.47, O.48, O.49, O.50 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Ligand interactions Metal complexes: D:E.36, D:E.70, D:H.73, O.47, O.50 MN.45: 8 residues within 4Å: Chain D: E.70, E.155, H.188 Ligands: MN.44, O.46, O.47, O.48, O.49 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:E.70, D:E.155, D:E.155, D:H.188, O.46 MN.58: 10 residues within 4Å: Chain E: E.36, T.39, E.70, H.73 Ligands: O.53, O.54, O.55, O.56, O.57, MN.59 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Ligand interactions Metal complexes: E:E.70, E:H.73, O.53, O.54, O.57 MN.59: 8 residues within 4Å: Chain E: E.70, E.155, H.188 Ligands: O.53, O.54, O.55, O.56, MN.58 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Ligand interactions Metal complexes: E:E.70, E:E.155, E:H.188, O.53, O.54 MN.70: 10 residues within 4Å: Chain F: E.36, T.39, E.70, H.73 Ligands: MN.71, O.72, O.73, O.74, O.75, O.76 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Ligand interactions Metal complexes: F:E.36, F:E.70, F:H.73, O.73, O.76 MN.71: 8 residues within 4Å: Chain F: E.70, E.155, H.188 Ligands: MN.70, O.72, O.73, O.74, O.75 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:E.70, F:E.155, F:E.155, F:H.188, O.72

15 x LI: LITHIUM ION(Non-covalent)

LI.8: 4 residues within 4Å: Chain A: E.17, Q.18, D.19 Ligands: SO4.10 No protein-ligand interaction detected (PLIP) LI.9: 2 residues within 4Å: Chain A: E.239, D.240 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.240, H2O.5, H2O.7, H2O.16, H2O.16 LI.12: 2 residues within 4Å: Chain A: M.225, D.255 No protein-ligand interaction detected (PLIP) LI.15: 4 residues within 4Å: Chain B: E.11, L.12, P.13 Ligands: SO4.25 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:L.12, H2O.23, H2O.23 LI.16: 4 residues within 4Å: Chain B: Q.9, I.10, Y.180, P.266 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Q.9, H2O.23, H2O.34 LI.34: 4 residues within 4Å: Chain C: E.17, Q.18, D.19 Ligands: SO4.36 No protein-ligand interaction detected (PLIP) LI.35: 2 residues within 4Å: Chain C: E.239, D.240 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.240, H2O.47, H2O.48, H2O.58, H2O.58 LI.38: 2 residues within 4Å: Chain C: M.225, D.255 No protein-ligand interaction detected (PLIP) LI.41: 4 residues within 4Å: Chain D: E.11, L.12, P.13 Ligands: SO4.51 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:L.12, H2O.64, H2O.65 LI.42: 4 residues within 4Å: Chain D: Q.9, I.10, Y.180, P.266 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:Q.9, H2O.64, H2O.75 LI.60: 4 residues within 4Å: Chain E: E.17, Q.18, D.19 Ligands: SO4.62 No protein-ligand interaction detected (PLIP) LI.61: 2 residues within 4Å: Chain E: E.239, D.240 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.240, H2O.88, H2O.90, H2O.99, H2O.99 LI.64: 2 residues within 4Å: Chain E: M.225, D.255 No protein-ligand interaction detected (PLIP) LI.67: 4 residues within 4Å: Chain F: E.11, L.12, P.13 Ligands: SO4.77 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:L.12, H2O.106, H2O.106 LI.68: 4 residues within 4Å: Chain F: Q.9, I.10, Y.180, P.266 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:Q.9, H2O.106, H2O.117

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

SO4.10: 6 residues within 4Å: Chain A: P.15, K.16, E.17, N.171, P.172 Ligands: LI.8 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: F.229, P.266, T.267, G.268 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain A: T.257, E.258 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain A: R.231 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: K.194, K.249, G.250, A.251 Ligand excluded by PLIP SO4.25: 2 residues within 4Å: Chain B: M.14 Ligands: LI.15 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain B: K.57, E.239, D.240, Y.241, R.242 Ligand excluded by PLIP SO4.36: 6 residues within 4Å: Chain C: P.15, K.16, E.17, N.171, P.172 Ligands: LI.34 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain C: F.229, P.266, T.267, G.268 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain C: T.257, E.258 Ligand excluded by PLIP SO4.40: 1 residues within 4Å: Chain C: R.231 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain D: K.194, K.249, G.250, A.251 Ligand excluded by PLIP SO4.51: 2 residues within 4Å: Chain D: M.14 Ligands: LI.41 Ligand excluded by PLIP SO4.52: 5 residues within 4Å: Chain D: K.57, E.239, D.240, Y.241, R.242 Ligand excluded by PLIP SO4.62: 6 residues within 4Å: Chain E: P.15, K.16, E.17, N.171, P.172 Ligands: LI.60 Ligand excluded by PLIP SO4.63: 4 residues within 4Å: Chain E: F.229, P.266, T.267, G.268 Ligand excluded by PLIP SO4.65: 2 residues within 4Å: Chain E: T.257, E.258 Ligand excluded by PLIP SO4.66: 1 residues within 4Å: Chain E: R.231 Ligand excluded by PLIP SO4.69: 4 residues within 4Å: Chain F: K.194, K.249, G.250, A.251 Ligand excluded by PLIP SO4.77: 2 residues within 4Å: Chain F: M.14 Ligands: LI.67 Ligand excluded by PLIP SO4.78: 5 residues within 4Å: Chain F: K.57, E.239, D.240, Y.241, R.242 Ligand excluded by PLIP

Links

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Citation

Antonyuk, S.V. et al., Three-Dimentional Structure of the Enzyme Dimanganese Catalase from Thermus Thermophilus at 1 Angstrom Resolution. Crystallogr.Rep.(Transl. Kristallografiya) (2000)

Release Date

2007-09-25

Peptides

MANGANESE-CONTAINING PSEUDOCATALASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

MANGANESE-CONTAINING PSEUDOCATALASE

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