Nickel in PDB 5fsd: 1.75 A Resolution 2,5-Dihydroxybenzensulfonate Inhibited Sporosarcina Pasteurii Urease

All present enzymatic activity of 1.75 A Resolution 2,5-Dihydroxybenzensulfonate Inhibited Sporosarcina Pasteurii Urease:
3.5.1.5;

The structure of 1.75 A Resolution 2,5-Dihydroxybenzensulfonate Inhibited Sporosarcina Pasteurii Urease, PDB code: 5fsd 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)	113.72 / 1.75
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.312, 131.312, 188.920, 90.00, 90.00, 120.00
R / Rfree (%)	13.4 / 17

The binding sites of Nickel atom in the 1.75 A Resolution 2,5-Dihydroxybenzensulfonate Inhibited Sporosarcina Pasteurii Urease (pdb code 5fsd). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 1.75 A Resolution 2,5-Dihydroxybenzensulfonate Inhibited Sporosarcina Pasteurii Urease, PDB code: 5fsd:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the 1.75 A Resolution 2,5-Dihydroxybenzensulfonate Inhibited Sporosarcina Pasteurii Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of 1.75 A Resolution 2,5-Dihydroxybenzensulfonate Inhibited Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni600 b:36.4 occ:1.00 O C:OH1584 1.9 30.0 1.0 OQ2 C:KCX220 2.0 28.7 1.0 ND1 C:HIS249 2.1 26.1 1.0 NE2 C:HIS275 2.1 28.0 1.0 O C:HOH2165 2.3 33.0 1.0 CE1 C:HIS249 3.0 29.3 1.0 CE1 C:HIS275 3.0 29.2 1.0 CX C:KCX220 3.1 32.2 1.0 CG C:HIS249 3.1 27.1 1.0 CD2 C:HIS275 3.2 29.0 1.0 OQ1 C:KCX220 3.4 26.2 1.0 CB C:HIS249 3.4 22.2 1.0 O C:GLY280 3.5 32.2 1.0 NI C:NI601 3.5 29.1 1.0 O C:HOH2243 3.6 47.1 1.0 O C:HOH2143 3.6 34.2 1.0 NE2 C:HIS222 3.6 26.9 1.0 CD2 C:HIS222 3.9 25.2 1.0 CE1 C:HIS137 4.0 26.2 1.0 NE2 C:HIS249 4.1 30.9 1.0 NE2 C:HIS137 4.2 25.4 1.0 ND1 C:HIS275 4.2 28.6 1.0 CD2 C:HIS249 4.2 25.7 1.0 CG C:HIS275 4.3 29.7 1.0 OD2 C:ASP363 4.3 31.4 1.0 NZ C:KCX220 4.3 25.7 1.0 C C:GLY280 4.5 34.1 1.0 O1 C:SO41583 4.6 53.2 1.0 CE1 C:HIS222 4.6 24.9 1.0 CE C:KCX220 4.8 24.4 1.0 CA C:HIS249 4.8 22.8 1.0 OD1 C:ASP363 5.0 28.8 1.0

Nickel binding site 2 out of 2 in the 1.75 A Resolution 2,5-Dihydroxybenzensulfonate Inhibited Sporosarcina Pasteurii Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of 1.75 A Resolution 2,5-Dihydroxybenzensulfonate Inhibited Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:29.1 occ:1.00 O C:OH1584 2.1 30.0 1.0 OQ1 C:KCX220 2.1 26.2 1.0 NE2 C:HIS137 2.2 25.4 1.0 NE2 C:HIS139 2.2 21.5 1.0 OD1 C:ASP363 2.2 28.8 1.0 O C:HOH2143 2.2 34.2 1.0 CE1 C:HIS139 3.0 24.6 1.0 CG C:ASP363 3.0 30.0 1.0 CD2 C:HIS137 3.1 27.4 1.0 CX C:KCX220 3.1 32.2 1.0 CE1 C:HIS137 3.2 26.2 1.0 CD2 C:HIS139 3.3 22.4 1.0 OD2 C:ASP363 3.3 31.4 1.0 OQ2 C:KCX220 3.4 28.7 1.0 O C:HOH2165 3.5 33.0 1.0 NI C:NI600 3.5 36.4 1.0 CB C:ALA366 4.1 24.6 0.5 CG2 C:THR172 4.1 23.4 1.0 NZ C:KCX220 4.2 25.7 1.0 ND1 C:HIS139 4.2 22.8 1.0 CG C:HIS137 4.2 23.9 1.0 O C:HOH2243 4.3 47.1 1.0 ND1 C:HIS137 4.3 26.4 1.0 CG C:HIS139 4.3 21.2 1.0 O C:ALA170 4.4 22.7 1.0 CB C:ASP363 4.4 26.2 1.0 O C:ALA366 4.4 38.7 0.5 CB C:ALA366 4.4 29.9 0.5 CA C:ASP363 4.6 25.3 1.0 NE2 C:HIS275 4.8 28.0 1.0 N C:THR172 4.9 22.4 1.0 CD2 C:HIS275 4.9 29.0 1.0

L.Mazzei, M.Cianci, F.Musiani, S.Ciurli. Inactivation of Urease By 1,4-Benzoquinone: Chemistry at the Protein Surface. Dalton Trans V. 45 5455 2016.
ISSN: ISSN 1477-9226
PubMed: 26961812
DOI: 10.1039/C6DT00652C