Nickel in PDB 4cex: 1.59 A Resolution Fluoride Inhibited Sporosarcina Pasteurii Urease

All present enzymatic activity of 1.59 A Resolution Fluoride Inhibited Sporosarcina Pasteurii Urease:
3.5.1.5;

The structure of 1.59 A Resolution Fluoride Inhibited Sporosarcina Pasteurii Urease, PDB code: 4cex was solved by S.Benini, M.Cianci, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	113.736 / 1.59
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.331, 131.331, 188.882, 90.00, 90.00, 120.00
R / Rfree (%)	12.97 / 15.02

The structure of 1.59 A Resolution Fluoride Inhibited Sporosarcina Pasteurii Urease also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Nickel atom in the 1.59 A Resolution Fluoride Inhibited Sporosarcina Pasteurii Urease (pdb code 4cex). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 1.59 A Resolution Fluoride Inhibited Sporosarcina Pasteurii Urease, PDB code: 4cex:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the 1.59 A Resolution Fluoride Inhibited Sporosarcina Pasteurii Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 1.59 A Resolution Fluoride Inhibited Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni600 b:9.7 occ:1.00 OQ1 C:KCX220 1.9 9.3 1.0 F C:F1571 2.0 8.3 1.0 NE2 C:HIS275 2.1 10.4 1.0 ND1 C:HIS249 2.1 8.2 1.0 F C:F1572 2.1 13.6 1.0 CE1 C:HIS249 3.0 9.3 1.0 CX C:KCX220 3.0 9.1 1.0 CD2 C:HIS275 3.0 10.1 1.0 CE1 C:HIS275 3.0 10.9 1.0 CG C:HIS249 3.1 9.1 1.0 OQ2 C:KCX220 3.3 8.9 1.0 O C:GLY280 3.3 12.0 1.0 NI C:NI601 3.5 8.8 1.0 CB C:HIS249 3.5 8.7 1.0 NE2 C:HIS222 3.6 9.3 1.0 O C:HOH2297 3.7 26.9 1.0 O C:HOH2189 3.7 10.7 1.0 CD2 C:HIS222 4.0 8.8 1.0 CE1 C:HIS137 4.0 8.1 1.0 NE2 C:HIS249 4.1 9.2 1.0 ND1 C:HIS275 4.1 10.1 1.0 CG C:HIS275 4.2 10.2 1.0 CD2 C:HIS249 4.2 9.0 1.0 NZ C:KCX220 4.2 8.7 1.0 NE2 C:HIS137 4.3 8.6 1.0 OD2 C:ASP363 4.4 10.7 1.0 C C:GLY280 4.4 10.9 1.0 CE1 C:HIS222 4.6 9.4 1.0 CE C:KCX220 4.7 8.4 1.0 CA C:HIS249 4.9 8.7 1.0 OD1 C:ASP363 5.0 9.4 1.0

Nickel binding site 2 out of 2 in the 1.59 A Resolution Fluoride Inhibited Sporosarcina Pasteurii Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 1.59 A Resolution Fluoride Inhibited Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:8.8 occ:1.00 F C:F1571 2.0 8.3 1.0 OQ2 C:KCX220 2.1 8.9 1.0 NE2 C:HIS139 2.1 7.4 1.0 O C:HOH2189 2.1 10.7 1.0 NE2 C:HIS137 2.1 8.6 1.0 OD1 C:ASP363 2.1 9.4 1.0 CE1 C:HIS139 2.9 8.0 1.0 CX C:KCX220 3.0 9.1 1.0 CG C:ASP363 3.0 10.3 1.0 CE1 C:HIS137 3.1 8.1 1.0 CD2 C:HIS137 3.1 8.6 1.0 CD2 C:HIS139 3.2 7.6 1.0 OD2 C:ASP363 3.3 10.7 1.0 OQ1 C:KCX220 3.4 9.3 1.0 NI C:NI600 3.5 9.7 1.0 F C:F1572 3.6 13.6 1.0 O C:ALA366 4.0 13.0 1.0 ND1 C:HIS139 4.1 8.0 1.0 CG2 C:THR172 4.1 9.3 1.0 NZ C:KCX220 4.1 8.7 1.0 ND1 C:HIS137 4.2 8.5 1.0 CG C:HIS137 4.2 8.5 1.0 CG C:HIS139 4.3 7.8 1.0 CB C:ASP363 4.4 9.7 1.0 CB C:ALA366 4.4 10.2 1.0 O C:HOH2297 4.4 26.9 1.0 O C:ALA170 4.5 10.2 1.0 CA C:ASP363 4.7 9.3 1.0 NE2 C:HIS275 4.8 10.4 1.0 CD2 C:HIS275 4.8 10.1 1.0 N C:THR172 4.9 8.6 1.0

S.Benini, M.Cianci, L.Mazzei, S.Ciurli. Fluoride Inhibition of Sporosarcina Pasteurii Urease: Structure and Thermodynamics. J.Biol.Inorg.Chem. 2014.
ISSN: ESSN 1432-1327
PubMed: 25113581
DOI: 10.1007/S00775-014-1182-X