Nickel in PDB 3ubp: Diamidophosphate Inhibited Bacillus Pasteurii Urease

All present enzymatic activity of Diamidophosphate Inhibited Bacillus Pasteurii Urease:
3.5.1.5;

The structure of Diamidophosphate Inhibited Bacillus Pasteurii Urease, PDB code: 3ubp was solved by S.Benini, W.R.Rypniewski, K.S.Wilson, S.Miletti, S.Mangani, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.00 / 2.00
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.532, 131.532, 188.451, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 20

The binding sites of Nickel atom in the Diamidophosphate Inhibited Bacillus Pasteurii Urease (pdb code 3ubp). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Diamidophosphate Inhibited Bacillus Pasteurii Urease, PDB code: 3ubp:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Diamidophosphate Inhibited Bacillus Pasteurii Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Diamidophosphate Inhibited Bacillus Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni900 b:21.2 occ:1.00 ND1 C:HIS249 2.0 14.6 1.0 OQ2 C:KCX220 2.1 18.4 1.0 NE2 C:HIS275 2.1 12.7 1.0 O3 C:2PA902 2.2 14.5 1.0 O1 C:2PA902 2.3 18.6 1.0 P2 C:2PA902 2.7 19.8 1.0 CE1 C:HIS249 2.9 14.9 1.0 CG C:HIS249 3.0 16.0 1.0 CE1 C:HIS275 3.0 17.6 1.0 CD2 C:HIS275 3.1 18.7 1.0 CX C:KCX220 3.1 15.4 1.0 O C:GLY280 3.2 18.6 1.0 CB C:HIS249 3.4 9.5 1.0 NE2 C:HIS222 3.4 11.8 1.0 OQ1 C:KCX220 3.5 17.8 1.0 CD2 C:HIS222 3.8 10.2 1.0 NI C:NI901 3.8 16.8 1.0 N5 C:2PA902 3.8 16.6 1.0 NE2 C:HIS249 4.1 19.1 1.0 N4 C:2PA902 4.1 14.1 1.0 CD2 C:HIS249 4.1 13.1 1.0 CE1 C:HIS137 4.1 16.5 1.0 ND1 C:HIS275 4.2 16.4 1.0 CG C:HIS275 4.2 16.7 1.0 C C:GLY280 4.3 16.3 1.0 CE1 C:HIS222 4.4 11.5 1.0 NE2 C:HIS137 4.4 10.3 1.0 NZ C:KCX220 4.4 15.6 1.0 CE C:KCX220 4.6 12.3 1.0 CA C:HIS249 4.6 12.1 1.0 OD2 C:ASP363 4.7 16.1 1.0 CA C:GLY281 4.8 15.7 1.0 CG C:HIS222 4.9 11.7 1.0 N C:GLY281 4.9 14.4 1.0 CE1 C:HIS323 5.0 24.2 1.0

Nickel binding site 2 out of 2 in the Diamidophosphate Inhibited Bacillus Pasteurii Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Diamidophosphate Inhibited Bacillus Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni901 b:16.8 occ:1.00 OQ1 C:KCX220 1.9 17.8 1.0 OD1 C:ASP363 2.1 15.3 1.0 NE2 C:HIS137 2.1 10.3 1.0 NE2 C:HIS139 2.2 10.7 1.0 N4 C:2PA902 2.3 14.1 1.0 O1 C:2PA902 2.3 18.6 1.0 P2 C:2PA902 2.8 19.8 1.0 CE1 C:HIS139 2.9 10.9 1.0 CX C:KCX220 3.0 15.4 1.0 CG C:ASP363 3.0 13.2 1.0 CD2 C:HIS137 3.1 17.0 1.0 CE1 C:HIS137 3.1 16.5 1.0 OD2 C:ASP363 3.3 16.1 1.0 CD2 C:HIS139 3.3 10.7 1.0 OQ2 C:KCX220 3.4 18.4 1.0 O3 C:2PA902 3.6 14.5 1.0 NI C:NI900 3.8 21.2 1.0 O C:ALA366 3.9 14.1 1.0 CG2 C:THR172 4.0 10.6 1.0 ND1 C:HIS139 4.1 12.1 1.0 N5 C:2PA902 4.2 16.6 1.0 ND1 C:HIS137 4.2 13.8 1.0 NZ C:KCX220 4.3 15.6 1.0 CG C:HIS137 4.3 8.0 1.0 O C:ALA170 4.3 12.1 1.0 CG C:HIS139 4.4 10.2 1.0 CB C:ASP363 4.4 9.8 1.0 CB C:ALA366 4.4 9.9 1.0 CA C:ASP363 4.6 10.3 1.0 N C:THR172 4.8 9.9 1.0 CD2 C:HIS275 4.9 18.7 1.0 NE2 C:HIS275 4.9 12.7 1.0 C C:ALA366 5.0 11.9 1.0

S.Benini, W.R.Rypniewski, K.S.Wilson, S.Miletti, S.Ciurli, S.Mangani. A New Proposal For Urease Mechanism Based on the Crystal Structures of the Native and Inhibited Enzyme From Bacillus Pasteurii: Why Urea Hydrolysis Costs Two Nickels. Structure Fold.Des. V. 7 205 1999.
ISSN: ISSN 0969-2126
PubMed: 10368287
DOI: 10.1016/S0969-2126(99)80026-4