SMTL ID : 3s0m.1

A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: H.90, H.92, E.96, H.135 Ligands: CO3.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.90, A:H.92, A:E.96, A:H.135, H2O.11 MN.2: 5 residues within 4Å: Chain A: H.268, H.270, E.275, H.314, E.328 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.268, A:H.270, A:H.314, H2O.8, H2O.14 MN.8: 5 residues within 4Å: Chain B: H.90, H.92, E.96, H.135 Ligands: CO3.10 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.90, B:H.92, B:E.96, B:H.135, H2O.25 MN.9: 5 residues within 4Å: Chain B: H.268, H.270, E.275, H.314, E.328 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.268, B:H.270, B:H.314, H2O.21, H2O.27 MN.15: 5 residues within 4Å: Chain C: H.90, H.92, E.96, H.135 Ligands: CO3.17 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.90, C:H.92, C:E.96, C:H.135, H2O.38 MN.16: 5 residues within 4Å: Chain C: H.268, H.270, E.275, H.314, E.328 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.268, C:H.270, C:H.314, H2O.35, H2O.40 MN.22: 5 residues within 4Å: Chain D: H.90, H.92, E.96, H.135 Ligands: CO3.24 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.90, D:H.92, D:E.96, D:H.135, H2O.51 MN.23: 5 residues within 4Å: Chain D: H.268, H.270, E.275, H.314, E.328 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.268, D:H.270, D:H.314, H2O.48, H2O.54 MN.29: 5 residues within 4Å: Chain E: H.90, H.92, E.96, H.135 Ligands: CO3.31 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.90, E:H.92, E:E.96, E:H.135, H2O.65 MN.30: 5 residues within 4Å: Chain E: H.268, H.270, E.275, H.314, E.328 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.268, E:H.270, E:H.314, H2O.62, H2O.67 MN.36: 5 residues within 4Å: Chain F: H.90, H.92, E.96, H.135 Ligands: CO3.38 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.90, F:H.92, F:E.96, F:H.135, H2O.78 MN.37: 5 residues within 4Å: Chain F: H.268, H.270, E.275, H.314, E.328 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.268, F:H.270, F:H.314, H2O.75, H2O.81

6 x CO3: CARBONATE ION(Non-functional Binders)

CO3.3: 9 residues within 4Å: Chain A: M.79, R.87, H.90, H.92, E.96, L.148, F.150, Y.195 Ligands: MN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.87 CO3.10: 9 residues within 4Å: Chain B: M.79, R.87, H.90, H.92, E.96, L.148, F.150, Y.195 Ligands: MN.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.87 CO3.17: 9 residues within 4Å: Chain C: M.79, R.87, H.90, H.92, E.96, L.148, F.150, Y.195 Ligands: MN.15 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.87 CO3.24: 9 residues within 4Å: Chain D: M.79, R.87, H.90, H.92, E.96, L.148, F.150, Y.195 Ligands: MN.22 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.87, D:Y.195 CO3.31: 9 residues within 4Å: Chain E: M.79, R.87, H.90, H.92, E.96, L.148, F.150, Y.195 Ligands: MN.29 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.87, E:Y.195 CO3.38: 9 residues within 4Å: Chain F: M.79, R.87, H.90, H.92, E.96, L.148, F.150, Y.195 Ligands: MN.36 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.87, F:Y.195

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

EDO.4: 1 residues within 4Å: Chain A: Q.200 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: P.171, E.173 Chain B: R.7, P.33, E.34 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: Q.25, N.26, K.44, K.283, A.284, N.299, Y.300, Q.301, I.319 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain B: Q.200 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: P.171, E.173 Chain C: R.7, P.33, E.34 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain B: Q.25, N.26, K.44, K.283, A.284, N.299, Y.300, Q.301, I.319 Ligand excluded by PLIP EDO.18: 1 residues within 4Å: Chain C: Q.200 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: R.7, P.33, E.34 Chain C: P.171, E.173 Ligand excluded by PLIP EDO.20: 9 residues within 4Å: Chain C: Q.25, N.26, K.44, K.283, A.284, N.299, Y.300, Q.301, I.319 Ligand excluded by PLIP EDO.25: 1 residues within 4Å: Chain D: Q.200 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain D: P.171, E.173 Chain E: R.7, P.33, E.34 Ligand excluded by PLIP EDO.27: 9 residues within 4Å: Chain D: Q.25, N.26, K.44, K.283, A.284, N.299, Y.300, Q.301, I.319 Ligand excluded by PLIP EDO.32: 1 residues within 4Å: Chain E: Q.200 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain E: P.171, E.173 Chain F: R.7, P.33, E.34 Ligand excluded by PLIP EDO.34: 9 residues within 4Å: Chain E: Q.25, N.26, K.44, K.283, A.284, N.299, Y.300, Q.301, I.319 Ligand excluded by PLIP EDO.39: 1 residues within 4Å: Chain F: Q.200 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain D: R.7, P.33, E.34 Chain F: P.171, E.173 Ligand excluded by PLIP EDO.41: 9 residues within 4Å: Chain F: Q.25, N.26, K.44, K.283, A.284, N.299, Y.300, Q.301, I.319 Ligand excluded by PLIP

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

PEG.7: 6 residues within 4Å: Chain A: R.80, K.82 Chain D: I.6, G.11, A.12, T.13 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.80, A:R.80, D:T.13 Water bridges: A:K.82, A:E.198 PEG.14: 6 residues within 4Å: Chain B: R.80, K.82 Chain F: I.6, G.11, A.12, T.13 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:T.13, B:R.80, B:R.80 Water bridges: B:K.82, B:E.198 PEG.21: 6 residues within 4Å: Chain C: R.80, K.82 Chain E: I.6, G.11, A.12, T.13 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:R.80, C:R.80, E:T.13 Water bridges: C:K.82, C:E.198 PEG.28: 6 residues within 4Å: Chain A: I.6, G.11, A.12, T.13 Chain D: R.80, K.82 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.80, D:R.80, A:T.13 Water bridges: D:K.82, A:G.11 PEG.35: 6 residues within 4Å: Chain C: I.6, G.11, A.12, T.13 Chain E: R.80, K.82 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:R.80, E:R.80, C:T.13 Water bridges: E:K.82, C:G.11 PEG.42: 6 residues within 4Å: Chain B: I.6, G.11, A.12, T.13 Chain F: R.80, K.82 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain B Hydrogen bonds: F:R.80, F:R.80, B:T.13 Water bridges: F:K.82, B:G.11

Links

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Citation

Saylor, B.T. et al., A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase. Biochemistry (2012)

Release Date

2012-04-25

Peptides

Oxalate decarboxylase oxdC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Oxalate decarboxylase oxdC