Nickel in PDB 5ol4: 1.28 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpt

All present enzymatic activity of 1.28 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpt:
3.5.1.5;

The structure of 1.28 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpt, PDB code: 5ol4 was solved by L.Mazzei, M.Cianci, F.Musiani, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	114.09 / 1.28
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.742, 131.742, 188.930, 90.00, 90.00, 120.00
R / Rfree (%)	11.9 / 13.7

The binding sites of Nickel atom in the 1.28 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpt (pdb code 5ol4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 1.28 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpt, PDB code: 5ol4:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the 1.28 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 1.28 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpt within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:11.2 occ:1.00 OQ1 C:KCX220 2.0 10.7 1.0 ND1 C:HIS249 2.0 10.7 1.0 NE2 C:HIS275 2.1 10.7 1.0 O4 C:9XN612 2.2 10.8 1.0 O1 C:9XN612 2.2 11.3 1.0 P2 C:9XN612 2.7 11.2 1.0 CE1 C:HIS249 2.9 10.7 1.0 O C:GLY280 3.0 13.6 1.0 CE1 C:HIS275 3.0 11.7 1.0 CD2 C:HIS275 3.0 10.9 1.0 CX C:KCX220 3.1 10.1 1.0 CG C:HIS249 3.1 10.7 1.0 OQ2 C:KCX220 3.4 10.5 1.0 CB C:HIS249 3.5 9.8 1.0 NE2 C:HIS222 3.6 10.0 1.0 NI C:NI602 3.7 10.2 1.0 N5 C:9XN612 3.9 10.7 1.0 CD2 C:HIS222 4.0 10.2 1.0 CE1 C:HIS137 4.0 10.2 1.0 S3 C:9XN612 4.0 13.0 1.0 NE2 C:HIS249 4.1 11.1 1.0 C C:GLY280 4.1 12.4 1.0 ND1 C:HIS275 4.1 11.3 1.0 CG C:HIS275 4.1 11.0 1.0 CD2 C:HIS249 4.2 10.8 1.0 NZ C:KCX220 4.2 9.9 1.0 NE2 C:HIS137 4.3 9.9 1.0 CE1 C:HIS222 4.5 10.1 1.0 OD2 C:ASP363 4.6 11.2 1.0 CE C:KCX220 4.6 9.9 1.0 CA C:HIS249 4.8 10.1 1.0 CA C:GLY280 4.9 12.1 1.0 N C:GLY281 4.9 11.7 1.0 CA C:GLY281 5.0 12.1 1.0

Nickel binding site 2 out of 2 in the 1.28 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpt


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 1.28 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpt within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni602 b:10.2 occ:1.00 OQ2 C:KCX220 2.0 10.5 1.0 NE2 C:HIS137 2.1 9.9 1.0 OD1 C:ASP363 2.1 9.6 1.0 NE2 C:HIS139 2.1 9.4 1.0 N5 C:9XN612 2.2 10.7 1.0 O1 C:9XN612 2.3 11.3 1.0 P2 C:9XN612 2.9 11.2 1.0 CE1 C:HIS139 2.9 9.9 1.0 CX C:KCX220 3.0 10.1 1.0 CG C:ASP363 3.0 9.9 1.0 CD2 C:HIS137 3.1 10.0 1.0 CE1 C:HIS137 3.1 10.2 1.0 CD2 C:HIS139 3.3 9.3 1.0 OD2 C:ASP363 3.3 11.2 1.0 OQ1 C:KCX220 3.4 10.7 1.0 O4 C:9XN612 3.6 10.8 1.0 NI C:NI601 3.7 11.2 1.0 O C:ALA366 4.0 11.7 1.0 CG2 C:THR172 4.1 9.9 1.0 ND1 C:HIS139 4.1 9.6 1.0 NZ C:KCX220 4.1 9.9 1.0 ND1 C:HIS137 4.2 9.7 1.0 CG C:HIS137 4.2 9.8 1.0 CG C:HIS139 4.3 9.2 1.0 O C:ALA170 4.3 9.8 1.0 CB C:ASP363 4.4 10.2 1.0 CB C:ALA366 4.5 10.4 1.0 S3 C:9XN612 4.5 13.0 1.0 CA C:ASP363 4.7 10.1 1.0 CD2 C:HIS275 4.9 10.9 1.0 NE2 C:HIS275 4.9 10.7 1.0 N C:THR172 4.9 9.2 1.0

L.Mazzei, M.Cianci, U.Contaldo, F.Musiani, S.Ciurli. Urease Inhibition in the Presence of N-(N-Butyl)Thiophosphoric Triamide, A Suicide Substrate: Structure and Kinetics. Biochemistry V. 56 5391 2017.
ISSN: ISSN 1520-4995
PubMed: 28857549
DOI: 10.1021/ACS.BIOCHEM.7B00750