Nickel in PDB 9eia: A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with Copurified D-Lactate

The structure of A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with Copurified D-Lactate, PDB code: 9eia was solved by S.Gatreddi, R.P.Hausinger, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.07 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.42, 45.514, 119.14, 90, 91.2, 90
R / Rfree (%)	17.4 / 21.2

The binding sites of Nickel atom in the A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with Copurified D-Lactate (pdb code 9eia). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with Copurified D-Lactate, PDB code: 9eia:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with Copurified D-Lactate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with Copurified D-Lactate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni506 b:10.3 occ:1.00 C4 A:4EY503 2.0 12.3 1.0 NE2 A:HIS199 2.0 10.5 0.5 NE2 A:HIS199 2.1 10.4 0.5 S2 A:4EY503 2.2 12.5 1.0 S7 A:4EY503 2.2 8.9 1.0 C3 A:4EY503 2.9 8.7 1.0 C5 A:4EY503 2.9 9.1 1.0 C7 A:4EY503 3.0 8.2 1.0 CE1 A:HIS199 3.0 14.6 0.5 CE1 A:HIS199 3.0 14.6 0.5 CD2 A:HIS199 3.0 9.8 0.5 CD2 A:HIS199 3.1 10.3 0.5 C1 A:4EY503 3.1 10.3 1.0 CG A:PRO187 3.6 9.2 1.0 CA A:LAC505 3.9 17.6 1.0 ND1 A:HIS199 4.1 13.5 0.5 ND1 A:HIS199 4.2 13.4 0.5 C2 A:4EY503 4.2 8.9 1.0 CG A:HIS199 4.2 11.2 0.5 CG A:HIS199 4.2 11.2 0.5 C6 A:4EY503 4.2 7.5 1.0 CZ3 A:TRP198 4.2 12.1 1.0 O2 A:4EY503 4.3 12.2 1.0 CB A:PRO187 4.3 9.5 1.0 NZ A:LYS183 4.4 8.2 1.0 OHN A:LAC505 4.4 11.3 1.0 CD A:PRO187 4.6 7.7 1.0 C A:LAC505 4.6 12.9 1.0 N1 A:4EY503 4.7 8.0 1.0 SD A:MET175 4.7 20.0 1.0 O A:LAC505 4.7 12.3 1.0 NE1 A:TRP356 4.8 11.3 1.0 CH2 A:TRP198 4.8 12.6 1.0 CB A:LAC505 4.9 13.8 1.0

Nickel binding site 2 out of 2 in the A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with Copurified D-Lactate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with Copurified D-Lactate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni706 b:14.9 occ:1.00 C4 B:4EY702 1.9 15.6 1.0 NE2 B:HIS199 2.1 15.4 1.0 S7 B:4EY702 2.2 12.2 1.0 S2 B:4EY702 2.3 17.8 1.0 C3 B:4EY702 2.8 13.6 1.0 C5 B:4EY702 2.9 12.4 1.0 C7 B:4EY702 3.0 15.9 1.0 CD2 B:HIS199 3.1 13.8 1.0 CE1 B:HIS199 3.1 18.1 1.0 C1 B:4EY702 3.1 16.0 1.0 CG B:PRO187 3.6 13.9 1.0 CA B:LAC705 3.9 23.5 1.0 C2 B:4EY702 4.1 12.2 1.0 ND1 B:HIS199 4.2 19.8 1.0 CZ3 B:TRP198 4.2 16.0 1.0 C6 B:4EY702 4.2 12.6 1.0 CG B:HIS199 4.2 13.3 1.0 CB B:PRO187 4.3 14.7 1.0 O2 B:4EY702 4.3 18.5 1.0 NZ B:LYS183 4.4 10.3 1.0 OHN B:LAC705 4.4 17.9 1.0 CD B:PRO187 4.5 12.9 1.0 C B:LAC705 4.5 16.6 1.0 N1 B:4EY702 4.6 13.3 1.0 SD B:MET175 4.7 23.3 1.0 O B:LAC705 4.7 14.4 1.0 NE1 B:TRP356 4.8 16.0 1.0 CH2 B:TRP198 4.8 17.4 1.0 CB B:LAC705 4.9 18.0 1.0

S.Gatreddi, J.Urdiain-Arraiza, B.Desguin, R.P.Hausinger, J.Hu. Structural Basis For Catalysis and Substrate Specificity of A Lara Racemase with A Broad Substrate Spectrum. Biorxiv 2024.
ISSN: ISSN 2692-8205
PubMed: 39651260
DOI: 10.1101/2024.11.28.625916