SMTL ID : 4r42.1

Crystal structure of KatB, a manganese catalase from Anabaena PCC7120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: E.35, E.65, H.68, Y.140, E.163 Ligands: MN.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.35, A:E.65, A:H.68, A:E.163, H2O.5 MN.2: 6 residues within 4Å: Chain A: Y.42, E.65, E.133, E.163, H.166 Ligands: MN.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.65, A:E.133, A:E.163, A:H.166, H2O.5 MN.7: 7 residues within 4Å: Chain B: E.35, E.65, H.68, Y.140, E.163, H.166 Ligands: MN.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.35, B:E.65, B:H.68, B:E.163, H2O.6 MN.8: 6 residues within 4Å: Chain B: Y.42, E.65, E.133, E.163, H.166 Ligands: MN.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.65, B:E.133, B:E.163, B:H.166, H2O.10 MN.12: 6 residues within 4Å: Chain C: E.35, E.65, H.68, Y.140, E.163 Ligands: MN.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.35, C:E.65, C:H.68, C:E.163, H2O.11 MN.13: 6 residues within 4Å: Chain C: Y.42, E.65, E.133, E.163, H.166 Ligands: MN.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.65, C:E.133, C:E.163, C:H.166, H2O.14 MN.17: 6 residues within 4Å: Chain D: E.35, E.65, H.68, Y.140, E.163 Ligands: MN.18 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.35, D:E.65, D:H.68, D:E.163, H2O.19 MN.18: 6 residues within 4Å: Chain D: Y.42, E.65, E.133, E.163, H.166 Ligands: MN.17 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.65, D:E.133, D:E.163, D:H.166, H2O.19 MN.23: 7 residues within 4Å: Chain E: E.35, E.65, H.68, Y.140, E.163, H.166 Ligands: MN.24 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.35, E:E.65, E:H.68, E:E.163, H2O.21 MN.24: 6 residues within 4Å: Chain E: Y.42, E.65, E.133, E.163, H.166 Ligands: MN.23 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.65, E:E.133, E:E.163, E:H.166, H2O.25 MN.28: 6 residues within 4Å: Chain F: E.35, E.65, H.68, Y.140, E.163 Ligands: MN.29 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.35, F:E.65, F:H.68, F:E.163, H2O.26 MN.29: 6 residues within 4Å: Chain F: Y.42, E.65, E.133, E.163, H.166 Ligands: MN.28 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.65, F:E.133, F:E.163, F:H.166, H2O.29

10 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.56, D.60 Chain D: N.199, S.201 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: A:D.56, A:D.60, D:S.201, H2O.1, H2O.5 CA.4: 3 residues within 4Å: Chain A: Q.107 Chain C: Q.107 Chain E: Q.107 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: A:Q.107, C:Q.107, E:Q.107, H2O.1, H2O.14 CA.9: 3 residues within 4Å: Chain B: N.109 Chain D: N.109 Chain F: N.109 No protein-ligand interaction detected (PLIP) CA.10: 7 residues within 4Å: Chain A: K.6 Chain B: D.56, D.60 Chain C: Y.197, N.199, S.201, S.202 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:S.201, B:D.56, B:D.60, H2O.12, H2O.12 CA.14: 5 residues within 4Å: Chain B: Y.197, N.199, S.201 Chain C: D.56, D.60 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.56, C:D.60, C:D.60, H2O.11, H2O.11 CA.19: 4 residues within 4Å: Chain A: N.199, S.201 Chain D: D.56, D.60 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: A:S.201, D:D.56, D:D.60, H2O.16, H2O.19 CA.20: 3 residues within 4Å: Chain B: Q.107 Chain D: Q.107 Chain F: Q.107 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: D:Q.107, F:Q.107, B:Q.107, H2O.15, H2O.29 CA.25: 3 residues within 4Å: Chain A: N.109 Chain C: N.109 Chain E: N.109 No protein-ligand interaction detected (PLIP) CA.26: 7 residues within 4Å: Chain D: K.6 Chain E: D.56, D.60 Chain F: Y.197, N.199, S.201, S.202 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: E:D.56, E:D.60, F:S.201, H2O.26, H2O.27 CA.30: 5 residues within 4Å: Chain E: Y.197, N.199, S.201 Chain F: D.56, D.60 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.56, F:D.60, F:D.60, H2O.26, H2O.26

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 7 residues within 4Å: Chain A: I.144, K.145, S.147, P.148, D.149, E.150, K.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.153 PGE.15: 6 residues within 4Å: Chain C: I.144, K.145, S.147, D.149, E.150, K.153 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.147, C:E.150, C:K.153 PGE.21: 7 residues within 4Å: Chain D: I.144, K.145, S.147, P.148, D.149, E.150, K.153 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.150, D:K.153 PGE.31: 6 residues within 4Å: Chain F: I.144, K.145, S.147, D.149, E.150, K.153 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.147, F:E.150, F:K.153

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 12 residues within 4Å: Chain A: N.18, R.20, F.21, Q.23, L.24, S.91, T.92, L.146, P.148 Chain E: K.90, S.91 Ligands: P6G.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.18, A:R.20, A:S.91, A:L.146 PG4.22: 12 residues within 4Å: Chain B: K.90, S.91 Chain D: N.18, R.20, F.21, Q.23, L.24, S.91, T.92, L.146, P.148 Ligands: P6G.32 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.18, D:R.20, D:S.91, D:L.146

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 6 residues within 4Å: Chain B: I.144, K.145, S.147, D.149, E.150, K.153 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.147, B:K.153 PEG.27: 6 residues within 4Å: Chain E: I.144, K.145, S.147, D.149, E.150, K.153 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.147, E:K.153

2 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.16: 14 residues within 4Å: Chain A: K.90, S.91 Chain C: R.20, Q.23, L.24, K.90, S.91, T.92 Chain E: R.20, Q.23, L.24, S.91, T.92 Ligands: PG4.6 7 PLIP interactions: 2 interactions with chain E, 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: E:R.20, E:R.20, C:R.20, C:R.20, C:R.20, A:K.90 Water bridges: C:Q.23 P6G.32: 14 residues within 4Å: Chain B: R.20, Q.23, L.24, S.91, T.92 Chain D: K.90, S.91 Chain F: R.20, Q.23, L.24, K.90, S.91, T.92 Ligands: PG4.22 7 PLIP interactions: 4 interactions with chain F, 1 interactions with chain D, 2 interactions with chain B Hydrogen bonds: F:R.20, F:R.20, F:R.20, D:K.90, B:R.20, B:R.20 Water bridges: F:Q.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bihani, S.C. et al., KatB, a cyanobacterial Mn-catalase with unique active site configuration: Implications for enzyme function. Free Radic. Biol. Med. (2016)

Release Date

2015-08-19

Peptides

Alr3090 protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Alr3090 protein