Nickel in PDB 2ubp: Structure of Native Urease From Bacillus Pasteurii

All present enzymatic activity of Structure of Native Urease From Bacillus Pasteurii:
3.5.1.5;

The structure of Structure of Native Urease From Bacillus Pasteurii, PDB code: 2ubp was solved by S.Benini, W.R.Rypniewski, K.S.Wilson, S.Ciurli, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.357, 131.357, 189.756, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 20

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

Nickel binding site 1 out of 2 in the Structure of Native Urease From Bacillus Pasteurii


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Native Urease From Bacillus Pasteurii within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni901 b:19.1 occ:1.00 OQ2 C:KCX220 2.1 17.2 1.0 O C:HOH990 2.1 18.0 1.0 NE2 C:HIS275 2.2 16.1 1.0 O C:HOH972 2.2 16.8 1.0 ND1 C:HIS249 2.2 17.0 1.0 CD2 C:HIS275 3.1 17.9 1.0 CE1 C:HIS249 3.2 16.5 1.0 CE1 C:HIS275 3.2 13.9 1.0 CX C:KCX220 3.2 14.2 1.0 CG C:HIS249 3.2 18.1 1.0 O C:GLY280 3.3 23.2 1.0 CB C:HIS249 3.5 15.2 1.0 OQ1 C:KCX220 3.5 18.6 1.0 O C:HOH1046 3.5 22.8 1.0 NE2 C:HIS222 3.6 15.0 1.0 O C:HOH1043 3.7 22.4 1.0 NI C:NI902 3.7 17.9 1.0 CD2 C:HIS222 3.9 11.4 1.0 CE1 C:HIS137 4.1 17.8 1.0 ND1 C:HIS275 4.3 15.6 1.0 NE2 C:HIS137 4.3 17.2 1.0 CG C:HIS275 4.3 17.7 1.0 OD2 C:ASP363 4.3 15.5 1.0 NE2 C:HIS249 4.3 21.0 1.0 CD2 C:HIS249 4.3 17.2 1.0 O2 C:SO4900 4.4 39.2 1.0 C C:GLY280 4.4 22.0 1.0 NZ C:KCX220 4.5 15.4 1.0 CE1 C:HIS222 4.6 12.7 1.0 CE C:KCX220 4.8 15.9 1.0 CA C:HIS249 4.8 14.2 1.0 CA C:GLY281 4.9 19.8 1.0

Nickel binding site 2 out of 2 in the Structure of Native Urease From Bacillus Pasteurii


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Native Urease From Bacillus Pasteurii within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni902 b:17.9 occ:1.00 OQ1 C:KCX220 2.1 18.6 1.0 O C:HOH1043 2.1 22.4 1.0 O C:HOH990 2.2 18.0 1.0 NE2 C:HIS139 2.2 14.9 1.0 OD1 C:ASP363 2.2 15.6 1.0 NE2 C:HIS137 2.2 17.2 1.0 CE1 C:HIS139 3.0 13.9 1.0 CG C:ASP363 3.0 17.2 1.0 CX C:KCX220 3.1 14.2 1.0 CD2 C:HIS137 3.1 14.3 1.0 OD2 C:ASP363 3.3 15.5 1.0 CE1 C:HIS137 3.3 17.8 1.0 CD2 C:HIS139 3.3 14.3 1.0 OQ2 C:KCX220 3.4 17.2 1.0 O C:HOH972 3.4 16.8 1.0 NI C:NI901 3.7 19.1 1.0 O C:HOH1046 3.7 22.8 1.0 CG2 C:THR172 4.0 14.0 1.0 CB C:ALA366 4.1 17.9 1.0 ND1 C:HIS139 4.2 15.5 1.0 O C:ALA170 4.2 15.3 1.0 CG C:HIS137 4.3 11.8 1.0 NZ C:KCX220 4.3 15.4 1.0 ND1 C:HIS137 4.3 19.7 1.0 CB C:ASP363 4.3 12.9 1.0 CG C:HIS139 4.4 13.5 1.0 CA C:ASP363 4.6 14.7 1.0 N C:THR172 4.9 14.1 1.0 NE2 C:HIS275 5.0 16.1 1.0 CD2 C:HIS275 5.0 17.9 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