Nickel in PDB 6rkg: 1.32 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto at pH 7.5

All present enzymatic activity of 1.32 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto at pH 7.5:
3.5.1.5;

The structure of 1.32 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto at pH 7.5, PDB code: 6rkg was solved by L.Mazzei, M.Cianci, S.Benini, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.67 / 1.32
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.783, 131.783, 188.768, 90.00, 90.00, 120.00
R / Rfree (%)	12.2 / 14.3

The binding sites of Nickel atom in the 1.32 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto at pH 7.5 (pdb code 6rkg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 1.32 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto at pH 7.5, PDB code: 6rkg:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the 1.32 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto at pH 7.5


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 1.32 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:13.1 occ:1.00 OQ1 C:KCX220 2.0 12.5 1.0 NE2 C:HIS275 2.0 11.6 1.0 ND1 C:HIS249 2.0 12.7 1.0 O1 C:2PA617 2.1 12.0 1.0 O3 C:2PA617 2.3 13.2 1.0 P2 C:2PA617 2.7 12.1 1.0 CE1 C:HIS249 3.0 12.4 1.0 O C:GLY280 3.0 14.1 1.0 CE1 C:HIS275 3.0 13.2 1.0 CD2 C:HIS275 3.0 11.4 1.0 CX C:KCX220 3.0 11.7 1.0 CG C:HIS249 3.1 11.9 1.0 CB C:HIS249 3.5 11.2 1.0 OQ2 C:KCX220 3.5 11.7 1.0 NE2 C:HIS222 3.6 12.1 1.0 NI C:NI602 3.8 11.8 1.0 N5 C:2PA617 3.8 12.8 1.0 CD2 C:HIS222 4.0 11.5 1.0 N4 C:2PA617 4.0 11.7 1.0 C C:GLY280 4.1 12.8 1.0 NE2 C:HIS249 4.1 12.4 1.0 ND1 C:HIS275 4.1 12.9 1.0 CE1 C:HIS137 4.1 12.3 1.0 CG C:HIS275 4.1 12.2 1.0 CD2 C:HIS249 4.2 12.4 1.0 NZ C:KCX220 4.2 11.8 1.0 NE2 C:HIS137 4.4 12.3 1.0 CE1 C:HIS222 4.5 12.0 1.0 CE C:KCX220 4.6 11.4 1.0 OD2 C:ASP363 4.7 13.9 1.0 CA C:HIS249 4.7 11.1 1.0 CA C:GLY281 4.8 13.0 1.0 N C:GLY281 4.8 12.3 1.0 CA C:GLY280 5.0 13.2 1.0

Nickel binding site 2 out of 2 in the 1.32 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto at pH 7.5


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 1.32 A Resolution of Sporosarcina Pasteurii Urease Inhibited in the Presence of Nbpto at pH 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni602 b:11.8 occ:1.00 OQ2 C:KCX220 2.0 11.7 1.0 NE2 C:HIS137 2.1 12.3 1.0 NE2 C:HIS139 2.1 10.5 1.0 OD1 C:ASP363 2.1 11.3 1.0 O3 C:2PA617 2.3 13.2 1.0 N4 C:2PA617 2.3 11.7 1.0 P2 C:2PA617 2.8 12.1 1.0 CE1 C:HIS139 2.9 10.8 1.0 CD2 C:HIS137 3.0 11.7 1.0 CG C:ASP363 3.1 11.2 1.0 CX C:KCX220 3.1 11.7 1.0 CE1 C:HIS137 3.1 12.3 1.0 CD2 C:HIS139 3.3 10.8 1.0 OD2 C:ASP363 3.4 13.9 1.0 OQ1 C:KCX220 3.4 12.5 1.0 O1 C:2PA617 3.7 12.0 1.0 NI C:NI601 3.8 13.1 1.0 O C:ALA366 4.0 13.7 1.0 CG2 C:THR172 4.0 11.4 1.0 ND1 C:HIS139 4.1 10.7 1.0 NZ C:KCX220 4.2 11.8 1.0 ND1 C:HIS137 4.2 11.6 1.0 N5 C:2PA617 4.2 12.8 1.0 CG C:HIS137 4.2 11.3 1.0 CG C:HIS139 4.3 10.5 1.0 O C:ALA170 4.3 10.3 1.0 CB C:ASP363 4.4 11.7 1.0 CB C:ALA366 4.5 11.6 1.0 CA C:ASP363 4.7 11.6 1.0 CD2 C:HIS275 4.9 11.4 1.0 N C:THR172 4.9 10.5 1.0 NE2 C:HIS275 4.9 11.6 1.0

L.Mazzei, M.Cianci, S.Benini, S.Ciurli. The Impact of pH on Catalytically Critical Protein Conformational Changes: the Case of the Urease, A Nickel Enzyme. Chemistry V. 25 12145 2019.
ISSN: ISSN 0947-6539
PubMed: 31271481
DOI: 10.1002/CHEM.201902320