SMTL ID : 1jkv.1

Crystal Structure of Manganese Catalase from Lactobacillus plantarum complexed with azide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-hexamer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.57, D.61 Chain F: N.218, S.220, G.222, S.225 5 PLIP interactions: 2 interactions with chain F, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: F:S.220, F:G.222, A:D.61, A:D.61, H2O.52 CA.2: 6 residues within 4Å: Chain B: D.57, D.61 Chain C: N.218, S.220, G.222, S.225 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:S.220, C:G.222, B:D.61, B:D.61, H2O.23 CA.3: 6 residues within 4Å: Chain B: N.218, S.220, G.222, S.225 Chain C: D.57, D.61 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:S.220, B:G.222, C:D.61, C:D.61, H2O.15 CA.4: 6 residues within 4Å: Chain D: D.57, D.61 Chain E: N.218, S.220, G.222, S.225 5 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:S.220, E:G.222, D:D.61, D:D.61, H2O.44 CA.5: 6 residues within 4Å: Chain D: N.218, S.220, G.222, S.225 Chain E: D.57, D.61 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: D:S.220, D:G.222, E:D.61, E:D.61, H2O.35 CA.6: 6 residues within 4Å: Chain A: N.218, S.220, G.222, S.225 Chain F: D.57, D.61 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: A:S.220, A:G.222, F:D.61, F:D.61, H2O.5

18 x OH: HYDROXIDE ION(Non-covalent)

OH.7: 10 residues within 4Å: Chain A: E.35, E.66, H.69, E.148, H.181 Ligands: OH.8, OH.9, AZI.25, MN3.31, MN3.32 Ligand excluded by PLIP OH.8: 10 residues within 4Å: Chain A: E.35, E.66, R.147, E.148, E.178 Ligands: OH.7, OH.9, AZI.25, MN3.31, MN3.32 Ligand excluded by PLIP OH.9: 8 residues within 4Å: Chain A: E.35, H.69, L.174, E.178 Ligands: OH.7, OH.8, AZI.25, MN3.31 Ligand excluded by PLIP OH.10: 11 residues within 4Å: Chain B: E.35, E.66, H.69, E.148, E.178, H.181 Ligands: OH.11, OH.12, AZI.26, MN3.33, MN3.34 Ligand excluded by PLIP OH.11: 10 residues within 4Å: Chain B: E.35, E.66, R.147, E.148, E.178 Ligands: OH.10, OH.12, AZI.26, MN3.33, MN3.34 Ligand excluded by PLIP OH.12: 8 residues within 4Å: Chain B: E.35, H.69, L.174, E.178 Ligands: OH.10, OH.11, AZI.26, MN3.33 Ligand excluded by PLIP OH.13: 11 residues within 4Å: Chain C: E.35, E.66, H.69, E.148, E.178, H.181 Ligands: OH.14, OH.15, AZI.27, MN3.35, MN3.36 Ligand excluded by PLIP OH.14: 10 residues within 4Å: Chain C: E.35, E.66, R.147, E.148, E.178 Ligands: OH.13, OH.15, AZI.27, MN3.35, MN3.36 Ligand excluded by PLIP OH.15: 8 residues within 4Å: Chain C: E.35, H.69, L.174, E.178 Ligands: OH.13, OH.14, AZI.27, MN3.35 Ligand excluded by PLIP OH.16: 11 residues within 4Å: Chain D: E.35, E.66, H.69, E.148, E.178, H.181 Ligands: OH.17, OH.18, AZI.28, MN3.37, MN3.38 Ligand excluded by PLIP OH.17: 10 residues within 4Å: Chain D: E.35, E.66, R.147, E.148, E.178 Ligands: OH.16, OH.18, AZI.28, MN3.37, MN3.38 Ligand excluded by PLIP OH.18: 9 residues within 4Å: Chain D: E.35, E.66, H.69, L.174, E.178 Ligands: OH.16, OH.17, AZI.28, MN3.37 Ligand excluded by PLIP OH.19: 10 residues within 4Å: Chain E: E.66, H.69, E.148, E.178, H.181 Ligands: OH.20, OH.21, AZI.29, MN3.39, MN3.40 Ligand excluded by PLIP OH.20: 10 residues within 4Å: Chain E: E.35, E.66, R.147, E.148, E.178 Ligands: OH.19, OH.21, AZI.29, MN3.39, MN3.40 Ligand excluded by PLIP OH.21: 8 residues within 4Å: Chain E: E.35, H.69, L.174, E.178 Ligands: OH.19, OH.20, AZI.29, MN3.39 Ligand excluded by PLIP OH.22: 11 residues within 4Å: Chain F: E.35, E.66, H.69, E.148, E.178, H.181 Ligands: OH.23, OH.24, AZI.30, MN3.41, MN3.42 Ligand excluded by PLIP OH.23: 10 residues within 4Å: Chain F: E.35, E.66, R.147, E.148, E.178 Ligands: OH.22, OH.24, AZI.30, MN3.41, MN3.42 Ligand excluded by PLIP OH.24: 8 residues within 4Å: Chain F: E.35, H.69, L.174, E.178 Ligands: OH.22, OH.23, AZI.30, MN3.41 Ligand excluded by PLIP

6 x AZI: AZIDE ION(Non-covalent)

AZI.25: 9 residues within 4Å: Chain A: E.35, H.69, V.155, L.174, E.178 Ligands: OH.7, OH.8, OH.9, MN3.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.178, A:E.178 AZI.26: 8 residues within 4Å: Chain B: E.35, H.69, L.174, E.178 Ligands: OH.10, OH.11, OH.12, MN3.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.35 AZI.27: 8 residues within 4Å: Chain C: E.35, H.69, L.174, E.178 Ligands: OH.13, OH.14, OH.15, MN3.35 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.35, C:H.69 AZI.28: 8 residues within 4Å: Chain D: E.35, H.69, L.174, E.178 Ligands: OH.16, OH.17, OH.18, MN3.37 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.35, D:H.69, D:E.178 Water bridges: D:E.35, D:E.35 AZI.29: 8 residues within 4Å: Chain E: E.35, H.69, L.174, E.178 Ligands: OH.19, OH.20, OH.21, MN3.39 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.35, E:H.69, E:E.178, E:E.178 AZI.30: 8 residues within 4Å: Chain F: E.35, H.69, L.174, E.178 Ligands: OH.22, OH.23, OH.24, MN3.41 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.35, F:E.35, F:H.69, F:E.178, F:E.178

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

MN3.31: 8 residues within 4Å: Chain A: E.35, E.66, H.69 Ligands: OH.7, OH.8, OH.9, AZI.25, MN3.32 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.35, A:E.66, A:H.69 MN3.32: 7 residues within 4Å: Chain A: E.66, R.147, E.148, H.181 Ligands: OH.7, OH.8, MN3.31 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.66, A:E.148, A:E.148, A:H.181 MN3.33: 8 residues within 4Å: Chain B: E.35, E.66, H.69 Ligands: OH.10, OH.11, OH.12, AZI.26, MN3.34 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.35, B:E.66, B:H.69 MN3.34: 7 residues within 4Å: Chain B: E.66, R.147, E.148, H.181 Ligands: OH.10, OH.11, MN3.33 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.66, B:E.148, B:E.148, B:H.181 MN3.35: 8 residues within 4Å: Chain C: E.35, E.66, H.69 Ligands: OH.13, OH.14, OH.15, AZI.27, MN3.36 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.35, C:E.66, C:H.69 MN3.36: 7 residues within 4Å: Chain C: E.66, R.147, E.148, H.181 Ligands: OH.13, OH.14, MN3.35 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.66, C:E.148, C:E.148, C:H.181 MN3.37: 8 residues within 4Å: Chain D: E.35, E.66, H.69 Ligands: OH.16, OH.17, OH.18, AZI.28, MN3.38 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.35, D:E.66, D:H.69 MN3.38: 7 residues within 4Å: Chain D: E.66, R.147, E.148, H.181 Ligands: OH.16, OH.17, MN3.37 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.66, D:E.148, D:E.148, D:H.181 MN3.39: 8 residues within 4Å: Chain E: E.35, E.66, H.69 Ligands: OH.19, OH.20, OH.21, AZI.29, MN3.40 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.35, E:E.66, E:H.69 MN3.40: 7 residues within 4Å: Chain E: E.66, R.147, E.148, H.181 Ligands: OH.19, OH.20, MN3.39 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.66, E:E.148, E:E.148, E:H.181 MN3.41: 8 residues within 4Å: Chain F: E.35, E.66, H.69 Ligands: OH.22, OH.23, OH.24, AZI.30, MN3.42 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.35, F:E.66, F:H.69 MN3.42: 7 residues within 4Å: Chain F: E.66, R.147, E.148, H.181 Ligands: OH.22, OH.23, MN3.41 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.66, F:E.148, F:E.148, F:H.181

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

EDO.43: 7 residues within 4Å: Chain A: S.74, T.75, G.78, N.115, A.116 Chain B: W.47 Chain F: I.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.75, A:A.116 EDO.44: 7 residues within 4Å: Chain A: L.29, S.74, A.116, S.117, L.118 Chain B: S.44, W.47 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:S.44, A:S.74, A:S.74 Hydrogen bonds: A:S.74, A:S.117 EDO.45: 6 residues within 4Å: Chain A: R.142, V.145, Q.189 Chain F: R.142, V.145, Q.189 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:Q.189, F:Q.189 EDO.46: 7 residues within 4Å: Chain A: W.47 Chain B: S.74, T.75, G.78, N.115, A.116 Chain C: I.254 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.75, B:A.116 EDO.47: 7 residues within 4Å: Chain A: S.44, W.47 Chain B: L.29, S.74, A.116, S.117, L.118 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:S.44 Hydrogen bonds: B:S.74, B:S.117 EDO.48: 7 residues within 4Å: Chain B: I.254 Chain C: S.74, T.75, G.78, N.115, A.116 Chain E: W.47 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.75, C:A.116 EDO.49: 7 residues within 4Å: Chain C: L.29, S.74, A.116, S.117, L.118 Chain E: S.44, W.47 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:S.117 Water bridges: E:S.133 EDO.50: 6 residues within 4Å: Chain B: R.142, V.145, Q.189 Chain C: R.142, V.145, Q.189 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Q.189, C:Q.189 EDO.51: 7 residues within 4Å: Chain D: S.74, T.75, G.78, N.115, A.116 Chain E: I.254 Chain F: W.47 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.75, D:A.116 EDO.52: 7 residues within 4Å: Chain D: L.29, S.74, A.116, S.117, L.118 Chain F: S.44, W.47 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain D Water bridges: F:S.44 Hydrogen bonds: D:S.74, D:S.117 EDO.53: 6 residues within 4Å: Chain D: R.142, V.145, Q.189 Chain E: R.142, V.145, Q.189 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:Q.189, E:Q.189 EDO.54: 7 residues within 4Å: Chain C: W.47 Chain D: I.254 Chain E: S.74, T.75, G.78, N.115, A.116 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.75, E:A.116 EDO.55: 6 residues within 4Å: Chain C: S.44, W.47 Chain E: S.74, A.116, S.117, L.118 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain C Water bridges: E:A.116, C:S.44 Hydrogen bonds: C:S.44 EDO.56: 7 residues within 4Å: Chain A: I.254 Chain D: W.47 Chain F: S.74, T.75, G.78, N.115, A.116 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.75, F:A.116 EDO.57: 7 residues within 4Å: Chain D: S.44, W.47 Chain F: L.29, S.74, A.116, S.117, L.118 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:S.74, F:S.117 Water bridges: D:S.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barynin, V.V. et al., Crystal structure of manganese catalase from Lactobacillus plantarum. Structure (2001)

Release Date

2002-07-13

Peptides

pseudocatalase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

pseudocatalase

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