SMTL ID : 6utq.1

LarE, a sulfur transferase involved in synthesis of the cofactor for lactate racemase in complex with cadmium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-hexamer

Ligands

7 x CD: CADMIUM ION(Non-covalent)

CD.1: 3 residues within 4Å: Chain A: D.231 Chain B: D.231 Chain C: D.231 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:D.231, B:D.231, C:D.231, C:D.231, H2O.3 CD.2: 2 residues within 4Å: Chain A: H.190 Ligands: SO4.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.190, H2O.1, H2O.1, H2O.1, H2O.1 CD.6: 2 residues within 4Å: Chain B: H.88, D.95 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.88, H2O.2, H2O.3, H2O.3, H2O.3 CD.7: 2 residues within 4Å: Chain B: D.218 Chain D: H.216 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.218, H2O.3, H2O.5 CD.10: 1 residues within 4Å: Chain C: H.190 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.190, H2O.4, H2O.4, H2O.4, H2O.4 CD.13: 3 residues within 4Å: Chain D: D.231 Chain E: D.231 Chain F: D.231 5 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:D.231, F:D.231, E:D.231, E:D.231, H2O.6 CD.14: 1 residues within 4Å: Chain D: H.88 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:H.88, H2O.6, H2O.6, H2O.6, H2O.6

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: C.176, S.180, R.212, R.214, R.259 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.180 Salt bridges: A:R.212, A:R.214, A:R.259 PO4.8: 5 residues within 4Å: Chain B: C.176, S.180, R.212, R.214, R.259 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.180, B:S.180 Salt bridges: B:R.212, B:R.214, B:R.259 PO4.11: 4 residues within 4Å: Chain C: S.180, R.212, R.214, R.259 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.180, C:R.181 Salt bridges: C:R.212, C:R.214, C:R.259 PO4.15: 5 residues within 4Å: Chain D: S.180, R.181, R.212, R.214, R.259 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.180, D:S.180 Salt bridges: D:R.212, D:R.214, D:R.259 PO4.17: 6 residues within 4Å: Chain E: C.176, S.180, R.181, R.212, R.214, R.259 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:S.180, E:R.181 Salt bridges: E:R.212, E:R.214, E:R.259 PO4.19: 5 residues within 4Å: Chain F: C.176, S.180, R.212, R.214, R.259 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.180, F:S.180 Salt bridges: F:R.212, F:R.214, F:R.259

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

SO4.4: 4 residues within 4Å: Chain A: K.90, T.189, H.190 Ligands: CD.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.190 Water bridges: A:K.90, A:K.90, A:D.191 Salt bridges: A:K.90, A:H.190 SO4.5: 6 residues within 4Å: Chain A: S.26, G.28, I.29, D.30, S.31, G.123 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.26, A:G.28, A:D.30, A:S.31 SO4.9: 5 residues within 4Å: Chain B: S.26, G.28, D.30, S.31, G.123 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.26, B:G.28, B:G.28, B:D.30, B:D.30, B:S.31, B:G.123 SO4.12: 4 residues within 4Å: Chain C: S.26, G.28, D.30, S.31 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.26, C:S.26, C:G.28, C:D.30, C:D.30, C:S.31 SO4.16: 6 residues within 4Å: Chain D: S.26, G.28, I.29, D.30, S.31, G.123 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.26, D:S.26, D:G.28, D:D.30, D:D.30, D:S.31, D:G.123 SO4.18: 6 residues within 4Å: Chain E: S.26, G.28, I.29, D.30, S.31, G.123 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:S.26, E:G.28, E:D.30, E:D.30, E:S.31, E:S.31 SO4.20: 5 residues within 4Å: Chain F: S.26, G.28, D.30, S.31, G.123 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:S.26, F:G.28, F:D.30, F:S.31, F:S.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fellner, M. et al., Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE. Sci Rep (2020)

Release Date

2019-11-06

Peptides

ATP-dependent sacrificial sulfur transferase LarE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ATP-dependent sacrificial sulfur transferase LarE

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