Nickel in PDB 4ac7: The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Citrate

All present enzymatic activity of The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Citrate:
3.5.1.5;

The structure of The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Citrate, PDB code: 4ac7 was solved by S.Benini, P.Kosikowska, M.Cianci, A.Gonzalez Vara, L.Berlicki, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	113.93 / 1.50
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.555, 131.555, 189.521, 90.00, 90.00, 120.00
R / Rfree (%)	11.7 / 14.6

The binding sites of Nickel atom in the The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Citrate (pdb code 4ac7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Citrate, PDB code: 4ac7:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Citrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni600 b:11.1 occ:1.00 OQ1 C:KCX220 2.0 10.6 1.0 O C:OH1571 2.0 8.6 1.0 ND1 C:HIS249 2.0 9.5 1.0 NE2 C:HIS275 2.1 10.8 1.0 OB2 C:FLC1572 2.1 13.5 1.0 CE1 C:HIS249 3.0 11.1 1.0 CD2 C:HIS275 3.0 10.3 1.0 CX C:KCX220 3.1 10.7 1.0 CE1 C:HIS275 3.1 12.0 1.0 CBC C:FLC1572 3.1 14.4 1.0 CG C:HIS249 3.1 11.2 1.0 OQ2 C:KCX220 3.3 9.8 1.0 NI C:NI601 3.5 10.3 1.0 O C:GLY280 3.5 13.4 1.0 OB1 C:FLC1572 3.5 11.7 1.0 CB C:HIS249 3.6 10.6 1.0 OA1 C:FLC1572 3.6 17.5 1.0 NE2 C:HIS222 3.7 11.2 1.0 CE1 C:HIS137 4.0 10.2 1.0 CD2 C:HIS222 4.1 11.2 1.0 CAC C:FLC1572 4.1 17.8 1.0 NE2 C:HIS249 4.1 11.8 1.0 ND1 C:HIS275 4.2 10.8 1.0 CG C:HIS275 4.2 9.9 1.0 NE2 C:HIS137 4.2 9.8 1.0 NZ C:KCX220 4.2 9.5 1.0 CD2 C:HIS249 4.2 10.9 1.0 OD2 C:ASP363 4.3 11.5 1.0 CB C:FLC1572 4.4 16.6 1.0 OA2 C:FLC1572 4.5 19.8 1.0 C C:GLY280 4.6 11.7 1.0 CE1 C:HIS222 4.7 12.4 1.0 CE C:KCX220 4.7 9.8 1.0 CG C:FLC1572 4.8 19.2 1.0 CA C:FLC1572 4.8 19.7 1.0 CA C:HIS249 4.9 10.1 1.0 OD1 C:ASP363 4.9 9.8 1.0

Nickel binding site 2 out of 2 in the The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Citrate


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Citrate within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:10.3 occ:1.00 O C:OH1571 2.0 8.6 1.0 NE2 C:HIS139 2.1 8.0 1.0 OQ2 C:KCX220 2.1 9.8 1.0 NE2 C:HIS137 2.1 9.8 1.0 OB1 C:FLC1572 2.1 11.7 1.0 OD1 C:ASP363 2.2 9.8 1.0 CE1 C:HIS139 2.9 10.1 1.0 CX C:KCX220 3.0 10.7 1.0 CE1 C:HIS137 3.0 10.2 1.0 CD2 C:HIS137 3.1 9.9 1.0 CG C:ASP363 3.1 10.4 1.0 CBC C:FLC1572 3.1 14.4 1.0 CD2 C:HIS139 3.2 8.7 1.0 OQ1 C:KCX220 3.4 10.6 1.0 OD2 C:ASP363 3.4 11.5 1.0 OB2 C:FLC1572 3.4 13.5 1.0 NI C:NI600 3.5 11.1 1.0 CG2 C:THR172 4.1 10.5 1.0 ND1 C:HIS139 4.1 9.4 1.0 NZ C:KCX220 4.2 9.5 1.0 CB C:ALA366 4.2 11.5 1.0 ND1 C:HIS137 4.2 10.4 1.0 CG C:HIS137 4.2 8.6 1.0 CG C:HIS139 4.3 8.4 1.0 CB C:ASP363 4.4 11.5 1.0 CB C:FLC1572 4.5 16.6 1.0 O C:ALA170 4.5 11.2 1.0 OA1 C:FLC1572 4.6 17.5 1.0 CA C:ASP363 4.7 10.5 1.0 OHB C:FLC1572 4.8 19.1 1.0 NE2 C:HIS275 4.8 10.8 1.0 CD2 C:HIS275 4.8 10.3 1.0 N C:THR172 4.9 9.8 1.0 CA C:FLC1572 5.0 19.7 1.0

S.Benini, P.Kosikowska, M.Cianci, L.Mazzei, A.G.Vara, L.Berlicki, S.Ciurli. The Crystal Structure of Sporosarcina Pasteurii Urease in A Complex with Citrate Provides New Hints For Inhibitor Design. J.Biol.Inorg.Chem. V. 18 391 2013.
ISSN: ISSN 0949-8257
PubMed: 23412551
DOI: 10.1007/S00775-013-0983-7