Nickel in PDB 6h8j: 1.45 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto

All present enzymatic activity of 1.45 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto:
3.5.1.5;

The structure of 1.45 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto, PDB code: 6h8j was solved by L.Mazzei, M.Cianci, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.74 / 1.45
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.446, 131.446, 188.716, 90.00, 90.00, 120.00
R / Rfree (%)	12.4 / 14.3

The binding sites of Nickel atom in the 1.45 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto (pdb code 6h8j). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 1.45 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto, PDB code: 6h8j:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the 1.45 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 1.45 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:15.9 occ:1.00 OQ2 C:KCX220 1.9 15.1 1.0 NE2 C:HIS275 2.0 15.9 1.0 ND1 C:HIS249 2.0 14.7 1.0 O1 C:2PA613 2.1 15.2 1.0 O3 C:2PA613 2.2 15.5 1.0 P2 C:2PA613 2.7 15.6 1.0 CE1 C:HIS249 2.9 15.0 1.0 CE1 C:HIS275 3.0 17.4 1.0 CD2 C:HIS275 3.0 16.4 1.0 CX C:KCX220 3.0 15.3 1.0 O C:GLY280 3.1 18.1 1.0 CG C:HIS249 3.1 15.3 1.0 OQ1 C:KCX220 3.4 14.6 1.0 CB C:HIS249 3.5 14.4 1.0 NE2 C:HIS222 3.6 15.8 1.0 NI C:NI602 3.8 14.6 1.0 N5 C:2PA613 3.9 16.5 1.0 CD2 C:HIS222 4.0 14.6 1.0 N4 C:2PA613 4.0 14.8 1.0 CE1 C:HIS137 4.1 14.7 1.0 NE2 C:HIS249 4.1 15.2 1.0 ND1 C:HIS275 4.1 15.0 1.0 CG C:HIS275 4.1 15.5 1.0 C C:GLY280 4.2 17.2 1.0 NZ C:KCX220 4.2 14.3 1.0 CD2 C:HIS249 4.2 15.1 1.0 NE2 C:HIS137 4.3 14.6 1.0 CE1 C:HIS222 4.5 15.4 1.0 CE C:KCX220 4.6 14.0 1.0 OD2 C:ASP363 4.7 18.1 1.0 CA C:HIS249 4.8 14.1 1.0 CA C:GLY281 4.9 16.8 1.0 N C:GLY281 4.9 15.8 1.0

Nickel binding site 2 out of 2 in the 1.45 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 1.45 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni602 b:14.6 occ:1.00 OQ1 C:KCX220 2.1 14.6 1.0 NE2 C:HIS137 2.1 14.6 1.0 NE2 C:HIS139 2.1 12.4 1.0 OD1 C:ASP363 2.2 14.6 1.0 O3 C:2PA613 2.3 15.5 1.0 N4 C:2PA613 2.3 14.8 1.0 P2 C:2PA613 2.8 15.6 1.0 CE1 C:HIS139 2.9 13.3 1.0 CD2 C:HIS137 3.1 13.6 1.0 CE1 C:HIS137 3.1 14.7 1.0 CX C:KCX220 3.1 15.3 1.0 CG C:ASP363 3.1 15.9 1.0 CD2 C:HIS139 3.2 13.0 1.0 OD2 C:ASP363 3.4 18.1 1.0 OQ2 C:KCX220 3.4 15.1 1.0 O1 C:2PA613 3.7 15.2 1.0 NI C:NI601 3.8 15.9 1.0 O C:ALA366 4.0 18.4 1.0 CG2 C:THR172 4.0 13.4 1.0 ND1 C:HIS139 4.1 13.4 1.0 NZ C:KCX220 4.2 14.3 1.0 ND1 C:HIS137 4.2 14.6 1.0 N5 C:2PA613 4.2 16.5 1.0 CG C:HIS137 4.2 13.6 1.0 CG C:HIS139 4.3 13.2 1.0 O C:ALA170 4.3 14.2 1.0 CB C:ASP363 4.4 15.0 1.0 CB C:ALA366 4.5 14.7 1.0 CA C:ASP363 4.7 14.3 1.0 CD2 C:HIS275 4.9 16.4 1.0 NE2 C:HIS275 4.9 15.9 1.0 N C:THR172 4.9 13.0 1.0

L.Mazzei, M.Cianci, U.Contaldo, S.Ciurli. Insights Into Urease Inhibition By N-( N-Butyl) Phosphoric Triamide Through An Integrated Structural and Kinetic Approach. J.Agric.Food Chem. V. 67 2127 2019.
ISSN: ESSN 1520-5118
PubMed: 30735374
DOI: 10.1021/ACS.JAFC.8B04791