Nickel in PDB 5a6t: 1.65 A Resolution Sulphite Inhibited Sporosarcina Pasteurii Urease

All present enzymatic activity of 1.65 A Resolution Sulphite Inhibited Sporosarcina Pasteurii Urease:
3.5.1.5;

The structure of 1.65 A Resolution Sulphite Inhibited Sporosarcina Pasteurii Urease, PDB code: 5a6t was solved by L.Mazzei, M.Cianci, S.Benini, L.Bertini, F.Musiani, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	113.68 / 1.65
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.262, 131.262, 189.072, 90.00, 90.00, 120.00
R / Rfree (%)	12.9 / 15.2

The binding sites of Nickel atom in the 1.65 A Resolution Sulphite Inhibited Sporosarcina Pasteurii Urease (pdb code 5a6t). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 1.65 A Resolution Sulphite Inhibited Sporosarcina Pasteurii Urease, PDB code: 5a6t:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the 1.65 A Resolution Sulphite 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 1.65 A Resolution Sulphite Inhibited Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1571 b:18.5 occ:1.00 OQ2 C:KCX220 2.0 15.6 1.0 O3 C:SO31573 2.0 22.1 1.0 NE2 C:HIS275 2.0 16.8 1.0 ND1 C:HIS249 2.0 14.7 1.0 O1 C:SO31573 2.1 23.5 1.0 S C:SO31573 2.8 25.1 1.0 CE1 C:HIS249 2.9 16.8 1.0 CX C:KCX220 3.0 16.0 1.0 CE1 C:HIS275 3.0 16.6 1.0 CD2 C:HIS275 3.0 16.2 1.0 CG C:HIS249 3.1 15.3 1.0 OQ1 C:KCX220 3.4 15.9 1.0 O C:GLY280 3.4 17.4 1.0 NI C:NI1572 3.5 16.1 1.0 CB C:HIS249 3.5 14.8 1.0 NE2 C:HIS222 3.6 16.0 1.0 O2 C:SO31573 3.8 28.2 1.0 CD2 C:HIS222 3.9 14.7 1.0 CE1 C:HIS137 4.0 14.9 1.0 NE2 C:HIS249 4.1 15.7 1.0 ND1 C:HIS275 4.1 16.8 1.0 NE2 C:HIS137 4.2 14.8 1.0 CG C:HIS275 4.2 15.6 1.0 NZ C:KCX220 4.2 14.6 1.0 CD2 C:HIS249 4.2 14.8 1.0 OD2 C:ASP363 4.3 18.4 1.0 C C:GLY280 4.5 16.5 1.0 O C:HOH2240 4.6 35.8 1.0 CE1 C:HIS222 4.6 15.5 1.0 CE C:KCX220 4.7 15.1 1.0 OD1 C:ASP363 4.8 17.1 1.0 CA C:HIS249 4.8 13.3 1.0

Nickel binding site 2 out of 2 in the 1.65 A Resolution Sulphite 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 1.65 A Resolution Sulphite Inhibited Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1572 b:16.1 occ:1.00 OQ1 C:KCX220 2.0 15.9 1.0 NE2 C:HIS139 2.1 12.9 1.0 NE2 C:HIS137 2.1 14.8 1.0 OD1 C:ASP363 2.1 17.1 1.0 O3 C:SO31573 2.1 22.1 1.0 O2 C:SO31573 2.2 28.2 1.0 S C:SO31573 2.7 25.1 1.0 CE1 C:HIS139 2.9 15.7 1.0 CX C:KCX220 3.0 16.0 1.0 CD2 C:HIS137 3.0 14.6 1.0 CG C:ASP363 3.0 19.7 1.0 CE1 C:HIS137 3.1 14.9 1.0 CD2 C:HIS139 3.2 13.5 1.0 OD2 C:ASP363 3.4 18.4 1.0 OQ2 C:KCX220 3.4 15.6 1.0 NI C:NI1571 3.5 18.5 1.0 O1 C:SO31573 3.7 23.5 1.0 CG2 C:THR172 4.0 14.8 1.0 ND1 C:HIS139 4.1 13.1 1.0 NZ C:KCX220 4.1 14.6 1.0 ND1 C:HIS137 4.2 15.4 1.0 CG C:HIS137 4.2 14.0 1.0 CB C:ALA366 4.2 15.0 1.0 CG C:HIS139 4.3 12.4 1.0 CB C:ASP363 4.3 16.0 1.0 O C:ALA170 4.5 15.5 1.0 CA C:ASP363 4.6 14.3 1.0 NE2 C:HIS275 4.7 16.8 1.0 CD2 C:HIS275 4.7 16.2 1.0 N C:THR172 4.9 13.6 1.0

L.Mazzei, M.Cianci, S.Benini, L.Bertini, F.Musiani, S.Ciurli. Kinetic and Structural Studies Reveal A Unique Binding Mode of Sulfite to the Nickel Center in Urease. J.Inorg.Biochem. V. 154 42 2015.
ISSN: ISSN 0162-0134
PubMed: 26580226
DOI: 10.1016/J.JINORGBIO.2015.11.003