Nickel in PDB 4ceu: 1.58 A Resolution Native Sporosarcina Pasteurii Urease

All present enzymatic activity of 1.58 A Resolution Native Sporosarcina Pasteurii Urease:
3.5.1.5;

The structure of 1.58 A Resolution Native Sporosarcina Pasteurii Urease, PDB code: 4ceu 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)	97.51 / 1.58
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.124, 131.124, 188.840, 90.00, 90.00, 120.00
R / Rfree (%)	13.515 / 15.495

The binding sites of Nickel atom in the 1.58 A Resolution Native Sporosarcina Pasteurii Urease (pdb code 4ceu). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 1.58 A Resolution Native Sporosarcina Pasteurii Urease, PDB code: 4ceu:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the 1.58 A Resolution Native 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 1.58 A Resolution Native Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni600 b:12.2 occ:1.00 OQ1 C:KCX220 1.9 12.0 1.0 NE2 C:HIS275 2.0 13.3 1.0 ND1 C:HIS249 2.0 10.5 1.0 O C:OH1571 2.1 11.4 1.0 O C:HOH2221 2.2 14.0 1.0 CE1 C:HIS275 2.9 13.1 1.0 CE1 C:HIS249 2.9 11.8 1.0 CX C:KCX220 3.1 11.4 1.0 CD2 C:HIS275 3.1 12.2 1.0 CG C:HIS249 3.1 11.5 1.0 O C:GLY280 3.3 13.1 1.0 OQ2 C:KCX220 3.4 10.9 1.0 CB C:HIS249 3.5 10.6 1.0 NE2 C:HIS222 3.6 11.4 1.0 O C:HOH2312 3.7 15.7 1.0 NI C:NI601 3.7 11.3 1.0 O C:HOH2196 3.7 12.0 1.0 CD2 C:HIS222 4.0 11.3 1.0 CE1 C:HIS137 4.0 10.7 1.0 ND1 C:HIS275 4.1 12.3 1.0 NE2 C:HIS249 4.1 11.4 1.0 CG C:HIS275 4.2 12.2 1.0 CD2 C:HIS249 4.2 11.2 1.0 NZ C:KCX220 4.2 10.6 1.0 C C:GLY280 4.3 12.6 1.0 NE2 C:HIS137 4.3 11.1 1.0 OD2 C:ASP363 4.3 12.5 1.0 O1 C:SO41582 4.4 28.2 1.0 CE1 C:HIS222 4.7 11.6 1.0 CE C:KCX220 4.7 10.5 1.0 CA C:HIS249 4.8 10.8 1.0 CA C:GLY281 4.9 13.1 1.0 N C:GLY281 5.0 12.5 1.0 OD1 C:ASP363 5.0 11.3 1.0

Nickel binding site 2 out of 2 in the 1.58 A Resolution Native 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 1.58 A Resolution Native Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:11.3 occ:1.00 O C:HOH2196 2.1 12.0 1.0 NE2 C:HIS139 2.1 9.2 1.0 OQ2 C:KCX220 2.1 10.9 1.0 OD1 C:ASP363 2.1 11.3 1.0 NE2 C:HIS137 2.1 11.1 1.0 O C:OH1571 2.1 11.4 1.0 CE1 C:HIS139 2.9 10.3 1.0 CG C:ASP363 3.0 12.4 1.0 CX C:KCX220 3.0 11.4 1.0 CE1 C:HIS137 3.1 10.7 1.0 CD2 C:HIS137 3.1 10.9 1.0 CD2 C:HIS139 3.2 9.3 1.0 OD2 C:ASP363 3.3 12.5 1.0 OQ1 C:KCX220 3.5 12.0 1.0 O C:HOH2221 3.6 14.0 1.0 NI C:NI600 3.7 12.2 1.0 O C:HOH2312 3.7 15.7 1.0 ND1 C:HIS139 4.1 9.5 1.0 CG2 C:THR172 4.1 11.5 1.0 CB C:ALA366 4.1 11.8 1.0 NZ C:KCX220 4.2 10.6 1.0 ND1 C:HIS137 4.2 10.9 1.0 CG C:HIS137 4.2 10.4 1.0 CG C:HIS139 4.3 9.7 1.0 O C:ALA170 4.3 11.5 1.0 CB C:ASP363 4.3 11.7 1.0 CA C:ASP363 4.6 11.5 1.0 NE2 C:HIS275 4.7 13.3 1.0 CD2 C:HIS275 4.9 12.2 1.0 N C:THR172 4.9 11.1 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