SMTL ID : 6bwr.1

LarC2, the C-terminal domain of a cyclometallase involved in the synthesis of the NPN cofactor of lactate racemase, in complex with nickel

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-hexamer

Ligands

12 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 1 residues within 4Å: Chain A: D.99 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.99, H2O.1 NI.2: 3 residues within 4Å: Chain A: E.18 Chain F: D.13, D.14 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: A:E.18, F:D.14, H2O.15 NI.3: 1 residues within 4Å: Chain B: H.128 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.128, H2O.4, H2O.4 NI.4: 1 residues within 4Å: Chain B: D.59 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.59, H2O.5, H2O.5, H2O.5 NI.5: 1 residues within 4Å: Chain C: D.99 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.99, H2O.7 NI.6: 3 residues within 4Å: Chain B: D.13, D.14 Chain C: E.18 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:D.14, C:E.18, H2O.3 NI.7: 1 residues within 4Å: Chain D: H.128 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.128, H2O.10, H2O.10 NI.8: 1 residues within 4Å: Chain D: D.59 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.59, H2O.11, H2O.11, H2O.11 NI.9: 1 residues within 4Å: Chain E: D.99 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.99, H2O.12 NI.10: 3 residues within 4Å: Chain D: D.13, D.14 Chain E: E.18 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: E:E.18, D:D.14, H2O.9 NI.11: 1 residues within 4Å: Chain F: H.128 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.128, H2O.15, H2O.16 NI.12: 1 residues within 4Å: Chain F: D.59 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.59, H2O.16, H2O.17, H2O.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Desguin, B. et al., Biosynthesis of the nickel-pincer nucleotide cofactor of lactate racemase requires a CTP-dependent cyclometallase. J. Biol. Chem. (2018)

Release Date

2018-06-20

Peptides

Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

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