Nickel in PDB 6g48: Sporosarcina Pasteurii Urease Inhibited By Silver

All present enzymatic activity of Sporosarcina Pasteurii Urease Inhibited By Silver:
3.5.1.5;

The structure of Sporosarcina Pasteurii Urease Inhibited By Silver, PDB code: 6g48 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)	45.43 / 1.91
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.088, 131.088, 189.059, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.9

The structure of Sporosarcina Pasteurii Urease Inhibited By Silver also contains other interesting chemical elements:

Silver

(Ag)

2 atoms

The binding sites of Nickel atom in the Sporosarcina Pasteurii Urease Inhibited By Silver (pdb code 6g48). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Sporosarcina Pasteurii Urease Inhibited By Silver, PDB code: 6g48:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Sporosarcina Pasteurii Urease Inhibited By Silver


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Sporosarcina Pasteurii Urease Inhibited By Silver within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:30.4 occ:1.00 OQ2 C:KCX220 2.0 30.3 1.0 ND1 C:HIS249 2.0 29.4 1.0 NE2 C:HIS275 2.1 27.7 1.0 O C:OH603 2.1 26.6 1.0 O C:HOH701 2.2 25.5 1.0 CE1 C:HIS249 2.9 31.6 1.0 CE1 C:HIS275 3.0 28.1 1.0 CD2 C:HIS275 3.1 28.8 1.0 CG C:HIS249 3.1 33.5 1.0 CX C:KCX220 3.1 30.9 1.0 O C:GLY280 3.3 29.6 1.0 OQ1 C:KCX220 3.4 31.3 1.0 O C:HOH703 3.5 29.5 1.0 CB C:HIS249 3.5 29.6 1.0 NE2 C:HIS222 3.6 28.7 1.0 O C:HOH704 3.6 27.6 1.0 NI C:NI602 3.7 29.8 1.0 CE1 C:HIS137 3.9 27.1 1.0 CD2 C:HIS222 4.0 26.9 1.0 NE2 C:HIS249 4.1 31.7 1.0 ND1 C:HIS275 4.1 26.6 1.0 CD2 C:HIS249 4.2 31.4 1.0 CG C:HIS275 4.2 27.6 1.0 NE2 C:HIS137 4.2 26.4 1.0 NZ C:KCX220 4.3 32.1 1.0 O2 C:SO4612 4.3 36.8 1.0 C C:GLY280 4.3 31.4 1.0 OD2 C:ASP363 4.4 31.6 1.0 CE1 C:HIS222 4.5 29.5 1.0 CE C:KCX220 4.7 30.3 1.0 CA C:HIS249 4.8 29.5 1.0 CA C:GLY281 5.0 30.1 1.0 O C:ALA170 5.0 28.2 1.0

Nickel binding site 2 out of 2 in the Sporosarcina Pasteurii Urease Inhibited By Silver


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Sporosarcina Pasteurii Urease Inhibited By Silver within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni602 b:29.8 occ:1.00 NE2 C:HIS137 2.0 26.4 1.0 NE2 C:HIS139 2.1 26.1 1.0 O C:HOH704 2.1 27.6 1.0 OQ1 C:KCX220 2.2 31.3 1.0 O C:OH603 2.2 26.6 1.0 OD1 C:ASP363 2.2 27.5 1.0 CD2 C:HIS137 3.0 26.8 1.0 CE1 C:HIS139 3.0 25.2 1.0 CE1 C:HIS137 3.0 27.1 1.0 CG C:ASP363 3.0 31.5 1.0 CX C:KCX220 3.1 30.9 1.0 CD2 C:HIS139 3.2 25.3 1.0 OD2 C:ASP363 3.3 31.6 1.0 OQ2 C:KCX220 3.4 30.3 1.0 O C:HOH701 3.5 25.5 1.0 NI C:NI601 3.7 30.4 1.0 O C:HOH703 3.7 29.5 1.0 ND1 C:HIS137 4.1 27.5 1.0 CG2 C:THR172 4.1 26.2 1.0 CG C:HIS137 4.1 26.0 1.0 ND1 C:HIS139 4.2 26.1 1.0 CB C:ALA366 4.2 28.5 0.5 CB C:ALA366 4.2 28.5 0.5 O C:ALA170 4.2 28.2 1.0 NZ C:KCX220 4.2 32.1 1.0 CG C:HIS139 4.3 25.8 1.0 CB C:ASP363 4.3 26.8 1.0 CA C:ASP363 4.6 26.6 1.0 NE2 C:HIS275 4.8 27.7 1.0 CD2 C:HIS275 4.8 28.8 1.0 N C:THR172 5.0 26.1 1.0

L.Mazzei, M.Cianci, A.Gonzalez Vara, S.Ciurli. The Structure of Urease Inactivated By Ag(I): A New Paradigm For Enzyme Inhibition By Heavy Metals. Dalton Trans V. 47 8240 2018.
ISSN: ESSN 1477-9234
PubMed: 29845996
DOI: 10.1039/C8DT01190G