Nickel in PDB 9eid: A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with D-2-Hydroxybutyrate

The structure of A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with D-2-Hydroxybutyrate, PDB code: 9eid 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)	29.11 / 1.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.725, 79.613, 104.775, 90, 90, 90
R / Rfree (%)	15.1 / 16.6

The binding sites of Nickel atom in the A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with D-2-Hydroxybutyrate (pdb code 9eid). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with D-2-Hydroxybutyrate, PDB code: 9eid:

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


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 D-2-Hydroxybutyrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni503 b:7.5 occ:0.79 C4 A:4EY502 1.9 7.9 1.0 NE2 A:HIS199 2.1 8.7 0.5 NE2 A:HIS199 2.1 9.2 0.5 S2 A:4EY502 2.2 10.6 1.0 S7 A:4EY502 2.2 8.3 1.0 C3 A:4EY502 2.9 7.9 1.0 C5 A:4EY502 2.9 7.8 1.0 C7 A:4EY502 3.0 6.8 1.0 CE1 A:HIS199 3.0 12.4 0.5 C1 A:4EY502 3.1 7.4 1.0 CD2 A:HIS199 3.1 7.8 0.5 CD2 A:HIS199 3.1 9.8 0.5 CE1 A:HIS199 3.1 12.4 0.5 CG A:PRO187 3.6 8.5 1.0 CAB A:UCU501 3.8 14.5 1.0 ND1 A:HIS199 4.1 10.5 0.5 C2 A:4EY502 4.2 8.0 1.0 C6 A:4EY502 4.2 8.6 1.0 ND1 A:HIS199 4.2 10.6 0.5 CZ3 A:TRP198 4.2 10.8 1.0 CG A:HIS199 4.2 9.6 0.5 CG A:HIS199 4.2 9.7 0.5 O2 A:4EY502 4.3 9.3 1.0 OAG A:UCU501 4.4 11.1 1.0 NZ A:LYS183 4.4 7.7 1.0 CB A:PRO187 4.4 7.2 1.0 CAD A:UCU501 4.5 21.5 1.0 CAA A:UCU501 4.5 6.7 1.0 CD A:PRO187 4.6 7.3 1.0 OAF A:UCU501 4.6 10.5 1.0 N1 A:4EY502 4.6 7.0 1.0 CAC A:UCU501 4.7 13.6 1.0 CH2 A:TRP198 4.8 10.7 1.0 SD A:MET175 4.8 11.8 1.0 NE1 A:TRP356 4.8 9.8 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