SMTL ID : 6kk8.1

XN joint refinement of manganese catalase from Thermus Thermophilus HB27

Coordinates

PDB Format Compare

Method

NEUTRON DIFFRACTION 2.35 Å

Oligo State

homo-hexamer

Ligands

12 x MN3: MANGANESE (III) ION(Non-covalent)

MN3.1: 9 residues within 4Å: Chain A: T.39, Y.43, E.70, E.155, G.185, H.188 Ligands: MN3.2, O.3, O.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:E.70, A:E.155, A:H.188, O.3, O.4 MN3.2: 10 residues within 4Å: Chain A: E.36, T.39, E.70, H.73, K.162, H.188 Ligands: MN3.1, O.3, O.4, O.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:E.36, A:E.70, A:H.73, O.3, O.5 MN3.8: 10 residues within 4Å: Chain B: T.39, Y.43, E.70, E.155, G.185, H.188 Ligands: MN3.9, O.10, O.11, O.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:E.70, B:E.155, B:H.188, O.10, O.11 MN3.9: 10 residues within 4Å: Chain B: E.36, T.39, E.70, H.73, L.181, H.188 Ligands: MN3.8, O.10, O.11, O.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:E.36, B:E.70, B:H.73, O.10, O.11 MN3.14: 9 residues within 4Å: Chain C: T.39, Y.43, E.70, E.155, G.185, H.188 Ligands: MN3.15, O.16, O.17 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.70, C:E.155, C:E.155, C:H.188 MN3.15: 10 residues within 4Å: Chain C: E.36, T.39, E.70, H.73, K.162, H.188 Ligands: MN3.14, O.16, O.17, O.18 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.36, C:E.70, C:H.73 MN3.21: 10 residues within 4Å: Chain D: T.39, Y.43, E.70, E.155, G.185, H.188 Ligands: MN3.22, O.23, O.24, O.25 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Ligand interactions Metal complexes: D:E.70, D:E.155, D:H.188, O.23, O.24 MN3.22: 10 residues within 4Å: Chain D: E.36, T.39, E.70, H.73, L.181, H.188 Ligands: MN3.21, O.23, O.24, O.25 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Ligand interactions Metal complexes: D:E.36, D:E.70, D:H.73, O.23, O.24 MN3.27: 9 residues within 4Å: Chain E: T.39, Y.43, E.70, E.155, G.185, H.188 Ligands: MN3.28, O.29, O.30 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Ligand interactions Metal complexes: E:E.70, E:E.155, E:H.188, O.29, O.30 MN3.28: 10 residues within 4Å: Chain E: E.36, T.39, E.70, H.73, K.162, H.188 Ligands: MN3.27, O.29, O.30, O.31 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Ligand interactions Metal complexes: E:E.36, E:E.70, E:H.73, O.29, O.30 MN3.34: 10 residues within 4Å: Chain F: T.39, Y.43, E.70, E.155, G.185, H.188 Ligands: MN3.35, O.36, O.37, O.38 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Ligand interactions Metal complexes: F:E.70, F:E.155, F:H.188, O.36, O.37 MN3.35: 10 residues within 4Å: Chain F: E.36, T.39, E.70, H.73, L.181, H.188 Ligands: MN3.34, O.36, O.37, O.38 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Ligand interactions Metal complexes: F:E.36, F:E.70, F:H.73, O.36, O.37

18 x O: OXYGEN ATOM(Non-covalent)

O.3: 8 residues within 4Å: Chain A: E.36, T.39, E.70, E.155 Ligands: MN3.1, MN3.2, O.4, O.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.39 O.4: 10 residues within 4Å: Chain A: H.73, E.155, L.181, R.184, G.185, H.188 Ligands: MN3.1, MN3.2, O.3, O.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.155, A:G.185 O.5: 7 residues within 4Å: Chain A: E.36, H.73, K.162, L.181 Ligands: MN3.2, O.3, O.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.162 O.10: 9 residues within 4Å: Chain B: E.36, T.39, E.70, E.155, K.162 Ligands: MN3.8, MN3.9, O.11, O.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.39 O.11: 10 residues within 4Å: Chain B: E.70, H.73, E.155, R.184, G.185, H.188 Ligands: MN3.8, MN3.9, O.10, O.12 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.73, B:H.188 O.12: 10 residues within 4Å: Chain B: E.36, H.73, K.162, L.181, R.184, G.185 Ligands: MN3.8, MN3.9, O.10, O.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.162, B:G.185 O.16: 8 residues within 4Å: Chain C: E.36, T.39, E.70, E.155 Ligands: MN3.14, MN3.15, O.17, O.18 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.36, C:T.39 O.17: 10 residues within 4Å: Chain C: H.73, E.155, L.181, R.184, G.185, H.188 Ligands: MN3.14, MN3.15, O.16, O.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.73, C:G.185, C:G.185, C:H.188 O.18: 7 residues within 4Å: Chain C: E.36, H.73, K.162, L.181 Ligands: MN3.15, O.16, O.17 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.73, C:K.162, C:L.181 O.23: 9 residues within 4Å: Chain D: E.36, T.39, E.70, E.155, K.162 Ligands: MN3.21, MN3.22, O.24, O.25 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.39 O.24: 10 residues within 4Å: Chain D: E.70, H.73, E.155, R.184, G.185, H.188 Ligands: MN3.21, MN3.22, O.23, O.25 No protein-ligand interaction detected (PLIP) O.25: 10 residues within 4Å: Chain D: E.36, H.73, K.162, L.181, R.184, G.185 Ligands: MN3.21, MN3.22, O.23, O.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.162, D:G.185, D:G.185 O.29: 8 residues within 4Å: Chain E: E.36, T.39, E.70, E.155 Ligands: MN3.27, MN3.28, O.30, O.31 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.39 O.30: 10 residues within 4Å: Chain E: H.73, E.155, L.181, R.184, G.185, H.188 Ligands: MN3.27, MN3.28, O.29, O.31 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.185, E:G.185 O.31: 7 residues within 4Å: Chain E: E.36, H.73, K.162, L.181 Ligands: MN3.28, O.29, O.30 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.73, E:K.162, E:L.181 O.36: 9 residues within 4Å: Chain F: E.36, T.39, E.70, E.155, K.162 Ligands: MN3.34, MN3.35, O.37, O.38 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:T.39 O.37: 10 residues within 4Å: Chain F: E.70, H.73, E.155, R.184, G.185, H.188 Ligands: MN3.34, MN3.35, O.36, O.38 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:H.73, F:H.188 O.38: 10 residues within 4Å: Chain F: E.36, H.73, K.162, L.181, R.184, G.185 Ligands: MN3.34, MN3.35, O.36, O.37 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.36, F:K.162, F:G.185

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 10 residues within 4Å: Chain A: Q.46, F.50, R.51, I.63, G.142, N.143, L.144, D.147 Chain B: A.282, P.283 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.51, A:G.142, A:G.142, A:N.143, A:L.144, A:D.147 Water bridges: A:F.50 EDO.13: 10 residues within 4Å: Chain A: A.282, P.283 Chain B: Q.46, F.50, R.51, L.56, G.142, N.143, L.144, D.147 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.51, B:G.142, B:G.142, B:N.143, B:L.144, B:D.147, B:D.147 EDO.19: 10 residues within 4Å: Chain C: Q.46, F.50, R.51, I.63, G.142, N.143, L.144, D.147 Chain D: A.282, P.283 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.51, C:G.142, C:G.142, C:L.144, C:D.147, C:D.147 EDO.26: 10 residues within 4Å: Chain C: A.282, P.283 Chain D: Q.46, F.50, R.51, L.56, G.142, N.143, L.144, D.147 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.51, D:G.142, D:G.142, D:N.143, D:D.147, D:D.147 EDO.32: 10 residues within 4Å: Chain E: Q.46, F.50, R.51, I.63, G.142, N.143, L.144, D.147 Chain F: A.282, P.283 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:R.51, E:G.142, E:G.142, E:N.143, E:L.144, E:D.147 Water bridges: E:F.50 EDO.39: 10 residues within 4Å: Chain E: A.282, P.283 Chain F: Q.46, F.50, R.51, L.56, G.142, N.143, L.144, D.147 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:R.51, F:G.142, F:G.142, F:L.144, F:D.147

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

SO4.7: 5 residues within 4Å: Chain A: F.229, Y.234, P.266, T.267, G.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.267, A:G.268 Water bridges: A:Y.234 SO4.20: 5 residues within 4Å: Chain C: F.229, Y.234, P.266, T.267, G.268 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.267, C:T.267, C:G.268 Water bridges: C:Y.234 SO4.33: 5 residues within 4Å: Chain E: F.229, Y.234, P.266, T.267, G.268 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.267, E:G.268 Water bridges: E:Y.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamada, T. et al., Single-crystal time-of-flight neutron Laue methods: application to manganese catalase from Thermus thermophilus HB27. J.Appl.Crystallogr. (2019)

Release Date

2019-09-04

Peptides

Pseudocatalase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Pseudocatalase

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