SMTL ID : 1o9i.1

Crystal structure of the Y42F mutant of manganese catalase from Lactobacillus plantarum at 1.33A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

homo-hexamer

Ligands

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

MN3.1: 5 residues within 4Å: Chain A: E.35, E.66, H.69 Ligands: MN3.2, O.4 6 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.35, A:E.66, A:H.69, O.4, H2O.9, H2O.9 MN3.2: 6 residues within 4Å: Chain A: E.66, R.147, E.148, H.181 Ligands: MN3.1, O.4 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:E.66, A:E.148, A:H.181, O.4, H2O.9 MN3.8: 5 residues within 4Å: Chain B: E.35, E.66, H.69 Ligands: MN3.9, O.11 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:E.66, B:H.69, O.11, H2O.19, H2O.19 MN3.9: 6 residues within 4Å: Chain B: E.66, R.147, E.148, H.181 Ligands: MN3.8, O.11 5 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:E.66, B:E.148, B:H.181, O.11, H2O.19 MN3.12: 5 residues within 4Å: Chain C: E.35, E.66, H.69 Ligands: MN3.13, O.15 5 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: C:E.66, C:H.69, O.15, H2O.28, H2O.28 MN3.13: 6 residues within 4Å: Chain C: E.66, R.147, E.148, H.181 Ligands: MN3.12, O.15 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:E.66, C:E.148, C:H.181, O.15, H2O.28 MN3.16: 5 residues within 4Å: Chain D: E.35, E.66, H.69 Ligands: MN3.17, O.19 5 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: D:E.66, D:H.69, O.19, H2O.37, H2O.37 MN3.17: 6 residues within 4Å: Chain D: E.66, R.147, E.148, H.181 Ligands: MN3.16, O.19 5 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: D:E.66, D:E.148, D:H.181, O.19, H2O.37 MN3.20: 5 residues within 4Å: Chain E: E.35, E.66, H.69 Ligands: MN3.21, O.23 5 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: E:E.35, E:E.66, E:H.69, O.23, H2O.47 MN3.21: 6 residues within 4Å: Chain E: E.66, R.147, E.148, H.181 Ligands: MN3.20, O.23 5 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: E:E.66, E:E.148, E:H.181, O.23, H2O.47 MN3.26: 5 residues within 4Å: Chain F: E.35, E.66, H.69 Ligands: MN3.27, O.29 5 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: F:E.66, F:H.69, O.29, H2O.56, H2O.56 MN3.27: 6 residues within 4Å: Chain F: E.66, R.147, E.148, H.181 Ligands: MN3.26, O.29 5 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: F:E.66, F:E.148, F:H.181, O.29, H2O.56

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.57, D.61 Chain F: N.218, S.220, G.222, S.225 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain F Metal complexes: A:D.57, A:D.57, A:D.61, F:S.220, F:G.222 CA.10: 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, 3 interactions with chain B Metal complexes: C:S.220, C:G.222, B:D.57, B:D.57, B:D.61 CA.14: 6 residues within 4Å: Chain B: N.218, S.220, G.222, S.225 Chain C: D.57, D.61 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:D.57, C:D.57, C:D.61, B:S.220, B:G.222 CA.18: 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, 3 interactions with chain D Metal complexes: E:S.220, E:G.222, D:D.57, D:D.57, D:D.61 CA.22: 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 E, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:D.57, E:D.61, D:S.220, D:G.222, H2O.35 CA.28: 6 residues within 4Å: Chain A: N.218, S.220, G.222, S.225 Chain F: D.57, D.61 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain A Metal complexes: F:D.57, F:D.57, F:D.61, A:S.220, A:G.222

6 x O: OXYGEN ATOM(Non-covalent)

O.4: 8 residues within 4Å: Chain A: E.35, E.66, H.69, E.148, E.178, H.181 Ligands: MN3.1, MN3.2 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.178, A:E.178 O.11: 8 residues within 4Å: Chain B: E.35, E.66, H.69, E.148, E.178, H.181 Ligands: MN3.8, MN3.9 No protein-ligand interaction detected (PLIP) O.15: 8 residues within 4Å: Chain C: E.35, E.66, H.69, E.148, E.178, H.181 Ligands: MN3.12, MN3.13 No protein-ligand interaction detected (PLIP) O.19: 8 residues within 4Å: Chain D: E.35, E.66, H.69, E.148, E.178, H.181 Ligands: MN3.16, MN3.17 No protein-ligand interaction detected (PLIP) O.23: 8 residues within 4Å: Chain E: E.35, E.66, H.69, E.148, E.178, H.181 Ligands: MN3.20, MN3.21 1 PLIP interactions: 1 interactions with chain E Water bridges: E:E.178 O.29: 8 residues within 4Å: Chain F: E.35, E.66, H.69, E.148, E.178, H.181 Ligands: MN3.26, MN3.27 1 PLIP interactions: 1 interactions with chain F Water bridges: F:E.178

5 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 3 residues within 4Å: Chain A: P.259, R.260 Chain F: E.89 No protein-ligand interaction detected (PLIP) MES.24: 1 residues within 4Å: Chain E: K.92 2 PLIP interactions: 2 interactions with chain E Water bridges: E:E.89 Salt bridges: E:K.92 MES.25: 2 residues within 4Å: Chain E: R.16, S.17 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.17 MES.30: 3 residues within 4Å: Chain A: G.250, I.251 Chain F: K.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:I.251 Salt bridges: F:K.7 MES.31: 4 residues within 4Å: Chain B: E.89 Chain C: R.260 Chain F: S.160, R.168 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Salt bridges: F:R.168 Water bridges: C:R.260

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain F: K.255, P.256, G.257 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.255 NA.7: 3 residues within 4Å: Chain D: K.255, P.256, G.257 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whittaker, M.M. et al., Outer Sphere Mutagenesis of Lactobacillus Plantarum Manganese Catalase Disrupts the Cluster Core. Mechanistic Implications. Eur.J.Biochem. (2003)

Release Date

2003-12-18

Peptides

Manganese catalase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Manganese catalase