Fluorine 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:

Nickel

(Ni)

2 atoms

The binding sites of Fluorine 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 Fluorine atom.
In total 2 binding sites of Fluorine where determined in the 1.59 A Resolution Fluoride Inhibited Sporosarcina Pasteurii Urease, PDB code: 4cex:
Jump to Fluorine binding site number: 1; 2;

Fluorine 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 Fluorine with other atoms in the F 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:F1571 b:8.3 occ:1.00 NI C:NI601 2.0 8.8 1.0 NI C:NI600 2.0 9.7 1.0 OD2 C:ASP363 2.6 10.7 1.0 O C:HOH2189 2.7 10.7 1.0 F C:F1572 2.8 13.6 1.0 NE2 C:HIS137 2.8 8.6 1.0 OQ1 C:KCX220 2.9 9.3 1.0 CE1 C:HIS137 2.9 8.1 1.0 NE2 C:HIS275 2.9 10.4 1.0 CD2 C:HIS275 3.0 10.1 1.0 OD1 C:ASP363 3.0 9.4 1.0 OQ2 C:KCX220 3.0 8.9 1.0 O C:HOH2297 3.0 26.9 1.0 CG C:ASP363 3.1 10.3 1.0 CX C:KCX220 3.3 9.1 1.0 NE2 C:HIS139 4.1 7.4 1.0 O C:GLY280 4.1 12.0 1.0 ND1 C:HIS249 4.1 8.2 1.0 CD2 C:HIS137 4.1 8.6 1.0 ND1 C:HIS137 4.1 8.5 1.0 CE1 C:HIS275 4.2 10.9 1.0 O C:ALA366 4.2 13.0 1.0 CG C:HIS275 4.3 10.2 1.0 CB C:ASP363 4.5 9.7 1.0 NZ C:KCX220 4.6 8.7 1.0 CE1 C:HIS139 4.7 8.0 1.0 CE1 C:HIS249 4.7 9.3 1.0 CG C:HIS137 4.7 8.5 1.0 ND1 C:HIS275 4.9 10.1 1.0 NE2 C:HIS222 4.9 9.3 1.0 CG2 C:THR301 5.0 9.9 1.0

Fluorine 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 Fluorine with other atoms in the F 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:F1572 b:13.6 occ:1.00 NI C:NI600 2.1 9.7 1.0 O C:HOH2189 2.5 10.7 1.0 NE2 C:HIS222 2.7 9.3 1.0 F C:F1571 2.8 8.3 1.0 ND1 C:HIS249 2.8 8.2 1.0 CE1 C:HIS249 3.0 9.3 1.0 O C:HOH2297 3.2 26.9 1.0 OQ1 C:KCX220 3.2 9.3 1.0 O C:ALA170 3.4 10.2 1.0 OQ2 C:KCX220 3.5 8.9 1.0 NI C:NI601 3.6 8.8 1.0 CD2 C:HIS222 3.6 8.8 1.0 CE1 C:HIS222 3.7 9.4 1.0 O C:GLY280 3.7 12.0 1.0 CX C:KCX220 3.8 9.1 1.0 NE2 C:HIS275 4.0 10.4 1.0 O C:HOH2326 4.0 35.6 1.0 CG C:HIS249 4.1 9.1 1.0 NE2 C:HIS249 4.2 9.2 1.0 C C:ALA170 4.6 9.3 1.0 O C:HOH2248 4.6 31.0 1.0 O C:ALA366 4.7 13.0 1.0 CD2 C:HIS275 4.7 10.1 1.0 OD2 C:ASP363 4.7 10.7 1.0 CD2 C:HIS249 4.8 9.0 1.0 ND1 C:HIS222 4.8 8.8 1.0 CG C:HIS222 4.8 8.6 1.0 CE1 C:HIS275 4.8 10.9 1.0 O C:HOH2210 4.9 17.5 1.0 CB C:HIS249 4.9 8.7 1.0 CE1 C:HIS139 4.9 8.0 1.0 OD1 C:ASP363 4.9 9.4 1.0 NE2 C:HIS139 5.0 7.4 1.0 C C:GLY280 5.0 10.9 1.0 NZ C:KCX220 5.0 8.7 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