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

The structure of A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with D-2-Hydroxyisovalerate, PDB code: 9eif 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)	29.71 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.024, 45.246, 118.218, 90, 91.06, 90
R / Rfree (%)	16.6 / 19.1

The binding sites of Nickel atom in the A Broad-Substrate Spectrum Lactate Racemase A From Isosphaera Pallida in Complex with D-2-Hydroxyisovalerate (pdb code 9eif). 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 D-2-Hydroxyisovalerate, PDB code: 9eif:
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 D-2-Hydroxyisovalerate


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-Hydroxyisovalerate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni506 b:10.3 occ:1.00 C4 A:4EY501 1.9 9.5 1.0 NE2 A:HIS199 2.1 10.9 0.5 NE2 A:HIS199 2.1 10.7 0.5 S7 A:4EY501 2.2 8.3 1.0 S2 A:4EY501 2.2 11.7 1.0 C3 A:4EY501 2.8 9.6 1.0 C5 A:4EY501 2.9 7.3 1.0 C7 A:4EY501 2.9 7.6 1.0 CE1 A:HIS199 3.1 12.7 0.5 CE1 A:HIS199 3.1 12.7 0.5 C1 A:4EY501 3.1 10.5 1.0 CD2 A:HIS199 3.1 9.9 0.5 CD2 A:HIS199 3.1 10.5 0.5 CG A:PRO187 3.6 7.7 1.0 CA A:VAD504 3.7 10.9 1.0 C2 A:4EY501 4.1 7.3 1.0 C6 A:4EY501 4.2 8.8 1.0 ND1 A:HIS199 4.2 12.8 0.5 CZ3 A:TRP198 4.2 9.5 1.0 ND1 A:HIS199 4.2 12.9 0.5 CG A:HIS199 4.2 10.0 0.5 CG A:HIS199 4.2 10.0 0.5 O2 A:4EY501 4.3 10.8 1.0 OE A:VAD504 4.3 11.2 1.0 NZ A:LYS183 4.3 6.5 1.0 CG2 A:VAD504 4.4 14.2 1.0 CB A:PRO187 4.4 8.0 1.0 C A:VAD504 4.5 10.1 1.0 CB A:VAD504 4.5 12.2 1.0 CD A:PRO187 4.6 8.1 1.0 N1 A:4EY501 4.6 7.0 1.0 O A:VAD504 4.7 10.5 1.0 CH2 A:TRP198 4.8 10.5 1.0 SD A:MET175 4.8 13.1 1.0 NE1 A:TRP356 4.9 12.1 1.0

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


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 D-2-Hydroxyisovalerate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni503 b:13.9 occ:1.00 C4 B:4EY501 1.9 11.8 1.0 NE2 B:HIS199 2.1 13.1 0.5 NE2 B:HIS199 2.1 13.0 0.5 S7 B:4EY501 2.2 11.6 1.0 S2 B:4EY501 2.2 15.4 1.0 C3 B:4EY501 2.8 12.8 1.0 C5 B:4EY501 2.9 11.6 1.0 C7 B:4EY501 2.9 14.7 1.0 CE1 B:HIS199 3.0 14.6 0.5 CD2 B:HIS199 3.1 12.8 0.5 CE1 B:HIS199 3.1 14.6 0.5 C1 B:4EY501 3.1 14.4 1.0 CD2 B:HIS199 3.1 13.0 0.5 CG B:PRO187 3.6 12.6 1.0 CA B:VAD502 3.8 14.5 1.0 ND1 B:HIS199 4.1 14.7 0.5 C2 B:4EY501 4.1 11.3 1.0 C6 B:4EY501 4.2 11.1 1.0 ND1 B:HIS199 4.2 14.8 0.5 CZ3 B:TRP198 4.2 14.8 1.0 CG B:HIS199 4.2 12.6 0.5 CG B:HIS199 4.2 12.7 0.5 O2 B:4EY501 4.3 15.7 1.0 OE B:VAD502 4.3 14.9 1.0 NZ B:LYS183 4.3 10.1 1.0 CG2 B:VAD502 4.3 18.4 1.0 CB B:PRO187 4.4 13.0 1.0 C B:VAD502 4.5 12.2 1.0 CD B:PRO187 4.6 13.9 1.0 CB B:VAD502 4.6 16.6 1.0 N1 B:4EY501 4.6 14.7 1.0 O B:VAD502 4.7 13.6 1.0 SD B:MET175 4.8 16.8 1.0 CH2 B:TRP198 4.8 15.2 1.0 NE1 B:TRP356 4.9 14.4 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