Nickel in PDB 8q2e: The 1.68-A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease Inhibited By Thiram and Bound to Dimethylditiocarbamate

All present enzymatic activity of The 1.68-A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease Inhibited By Thiram and Bound to Dimethylditiocarbamate:
3.5.1.5;

The structure of The 1.68-A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease Inhibited By Thiram and Bound to Dimethylditiocarbamate, PDB code: 8q2e was solved by L.Mazzei, M.Cianci, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	114.15 / 1.68
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.511, 131.511, 189.017, 90, 90, 120
R / Rfree (%)	13.8 / 16.3

The binding sites of Nickel atom in the The 1.68-A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease Inhibited By Thiram and Bound to Dimethylditiocarbamate (pdb code 8q2e). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The 1.68-A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease Inhibited By Thiram and Bound to Dimethylditiocarbamate, PDB code: 8q2e:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the The 1.68-A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease Inhibited By Thiram and Bound to Dimethylditiocarbamate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The 1.68-A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease Inhibited By Thiram and Bound to Dimethylditiocarbamate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni2314 b:25.2 occ:1.00 OQ1 C:KCX220 2.0 25.9 1.0 ND1 C:HIS249 2.0 21.2 1.0 NE2 C:HIS275 2.0 25.0 1.0 O C:OH2316 2.0 23.1 1.0 O C:HOH2401 2.0 21.7 1.0 CE1 C:HIS249 2.9 26.5 1.0 CE1 C:HIS275 3.0 27.0 1.0 CD2 C:HIS275 3.0 26.4 1.0 CG C:HIS249 3.0 24.8 1.0 CX C:KCX220 3.1 25.7 1.0 O C:GLY280 3.3 26.0 1.0 OQ2 C:KCX220 3.4 24.3 1.0 CB C:HIS249 3.5 23.7 1.0 O C:HOH2414 3.6 36.5 1.0 O C:HOH2402 3.6 25.6 1.0 NE2 C:HIS222 3.6 23.9 1.0 NI C:NI2315 3.6 23.9 1.0 CE1 C:HIS137 4.0 23.8 1.0 CD2 C:HIS222 4.0 23.2 1.0 NE2 C:HIS249 4.1 24.9 1.0 ND1 C:HIS275 4.1 24.6 1.0 CG C:HIS275 4.1 25.9 1.0 CD2 C:HIS249 4.2 23.1 1.0 NE2 C:HIS137 4.2 22.4 1.0 NZ C:KCX220 4.3 25.2 1.0 OD2 C:ASP363 4.3 25.9 1.0 C C:GLY280 4.3 27.8 1.0 CE1 C:HIS222 4.6 23.5 1.0 CE C:KCX220 4.7 24.1 1.0 O4 C:SO42317 4.7 53.3 1.0 CA C:HIS249 4.8 23.5 1.0 OD1 C:ASP363 4.9 25.9 1.0 CA C:GLY281 5.0 28.9 1.0

Nickel binding site 2 out of 2 in the The 1.68-A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease Inhibited By Thiram and Bound to Dimethylditiocarbamate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The 1.68-A X-Ray Crystal Structure of Sporosarcina Pasteurii Urease Inhibited By Thiram and Bound to Dimethylditiocarbamate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni2315 b:23.9 occ:1.00 OQ2 C:KCX220 2.0 24.3 1.0 O C:OH2316 2.0 23.1 1.0 O C:HOH2402 2.0 25.6 1.0 OD1 C:ASP363 2.1 25.9 1.0 NE2 C:HIS137 2.1 22.4 1.0 NE2 C:HIS139 2.1 19.9 1.0 CE1 C:HIS139 2.9 23.8 1.0 CX C:KCX220 3.0 25.7 1.0 CG C:ASP363 3.0 26.8 1.0 CD2 C:HIS137 3.1 24.4 1.0 CE1 C:HIS137 3.1 23.8 1.0 CD2 C:HIS139 3.2 22.5 1.0 OD2 C:ASP363 3.3 25.9 1.0 OQ1 C:KCX220 3.4 25.9 1.0 O C:HOH2401 3.4 21.7 1.0 NI C:NI2314 3.6 25.2 1.0 O C:HOH2414 3.8 36.5 1.0 CG2 C:THR172 4.1 21.5 1.0 NZ C:KCX220 4.1 25.2 1.0 ND1 C:HIS139 4.1 21.7 1.0 CB C:ALA366 4.2 25.0 0.5 CB C:ALA366 4.2 25.0 0.5 CG C:HIS137 4.2 23.5 1.0 ND1 C:HIS137 4.2 23.5 1.0 CG C:HIS139 4.3 20.6 1.0 CB C:ASP363 4.3 24.2 1.0 O C:ALA170 4.3 21.5 1.0 CA C:ASP363 4.6 21.5 1.0 NE2 C:HIS275 4.8 25.0 1.0 CD2 C:HIS275 4.8 26.4 1.0 N C:THR172 4.9 21.7 1.0

L.Mazzei, A.Paul, M.Cianci, M.Devodier, D.Mandelli, P.Carloni, S.Ciurli. Kinetic and Structural Details of Urease Inactivation By Thiuram Disulphides. J.Inorg.Biochem. V. 250 12398 2023.
ISSN: ISSN 0162-0134
PubMed: 37879152
DOI: 10.1016/J.JINORGBIO.2023.112398