Nickel in PDB 5g4h: 1.50 A Resolution Catechol (1,2-Dihydroxybenzene) Inhibited Sporosarcina Pasteurii Urease

All present enzymatic activity of 1.50 A Resolution Catechol (1,2-Dihydroxybenzene) Inhibited Sporosarcina Pasteurii Urease:
3.5.1.5;

The structure of 1.50 A Resolution Catechol (1,2-Dihydroxybenzene) Inhibited Sporosarcina Pasteurii Urease, PDB code: 5g4h 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)	113.69 / 1.50
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.276, 131.276, 189.017, 90.00, 90.00, 120.00
R / Rfree (%)	12.1 / 15.4

The binding sites of Nickel atom in the 1.50 A Resolution Catechol (1,2-Dihydroxybenzene) Inhibited Sporosarcina Pasteurii Urease (pdb code 5g4h). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 1.50 A Resolution Catechol (1,2-Dihydroxybenzene) Inhibited Sporosarcina Pasteurii Urease, PDB code: 5g4h:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the 1.50 A Resolution Catechol (1,2-Dihydroxybenzene) 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 1.50 A Resolution Catechol (1,2-Dihydroxybenzene) Inhibited Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni600 b:26.3 occ:1.00 O C:OH1573 1.9 25.4 1.0 OQ2 C:KCX220 2.0 22.7 1.0 ND1 C:HIS249 2.0 20.5 1.0 NE2 C:HIS275 2.1 23.3 1.0 O C:HOH2176 2.2 26.8 1.0 CE1 C:HIS249 3.0 22.8 1.0 CX C:KCX220 3.1 21.7 1.0 CD2 C:HIS275 3.1 21.8 1.0 CE1 C:HIS275 3.1 28.9 1.0 CG C:HIS249 3.1 21.6 1.0 OQ1 C:KCX220 3.4 19.1 1.0 O C:GLY280 3.4 25.9 1.0 CB C:HIS249 3.5 21.6 1.0 NI C:NI601 3.6 22.0 1.0 O C:HOH2248 3.6 35.6 1.0 NE2 C:HIS222 3.6 21.7 1.0 O C:HOH2153 3.7 26.2 1.0 CD2 C:HIS222 3.9 19.9 1.0 CE1 C:HIS137 4.0 20.8 1.0 NE2 C:HIS249 4.1 22.6 1.0 NE2 C:HIS137 4.2 21.1 1.0 ND1 C:HIS275 4.2 23.1 1.0 CD2 C:HIS249 4.2 22.7 1.0 CG C:HIS275 4.2 22.1 1.0 NZ C:KCX220 4.2 19.8 1.0 OD2 C:ASP363 4.3 23.4 1.0 C C:GLY280 4.4 22.7 1.0 O1 C:SO41572 4.5 34.2 0.8 CE1 C:HIS222 4.7 19.7 1.0 CE C:KCX220 4.8 21.0 1.0 CA C:HIS249 4.8 20.0 1.0 OD1 C:ASP363 4.9 20.1 1.0

Nickel binding site 2 out of 2 in the 1.50 A Resolution Catechol (1,2-Dihydroxybenzene) 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 1.50 A Resolution Catechol (1,2-Dihydroxybenzene) Inhibited Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:22.0 occ:1.00 O C:OH1573 2.0 25.4 1.0 OQ1 C:KCX220 2.1 19.1 1.0 NE2 C:HIS139 2.1 17.1 1.0 NE2 C:HIS137 2.1 21.1 1.0 OD1 C:ASP363 2.1 20.1 1.0 O C:HOH2153 2.2 26.2 1.0 CE1 C:HIS139 2.9 19.1 1.0 CG C:ASP363 3.0 20.6 1.0 CD2 C:HIS137 3.0 21.3 1.0 CX C:KCX220 3.1 21.7 1.0 CE1 C:HIS137 3.1 20.8 1.0 CD2 C:HIS139 3.2 18.4 1.0 OD2 C:ASP363 3.3 23.4 1.0 OQ2 C:KCX220 3.4 22.7 1.0 NI C:NI600 3.6 26.3 1.0 O C:HOH2176 3.6 26.8 1.0 O C:HOH2248 4.0 35.6 1.0 CG2 C:THR172 4.1 18.5 1.0 CB C:ALA366 4.1 18.4 0.5 ND1 C:HIS139 4.1 17.9 1.0 NZ C:KCX220 4.2 19.8 1.0 CG C:HIS137 4.2 18.7 1.0 ND1 C:HIS137 4.2 20.5 1.0 CG C:HIS139 4.3 17.4 1.0 CB C:ASP363 4.3 21.0 1.0 O C:ALA170 4.3 18.8 1.0 CB C:ALA366 4.4 22.3 0.5 CA C:ASP363 4.6 20.3 1.0 O C:ALA366 4.6 35.3 0.5 NE2 C:HIS275 4.8 23.3 1.0 CD2 C:HIS275 4.9 21.8 1.0 N C:THR172 4.9 18.0 1.0

L.Mazzei, M.Cianci, F.Musiani, G.Lente, M.Palombo, S.Ciurli. Inactivation of Urease By Catechol: Kinetics and Structure. J.Inorg.Biochem. V. 166 182 2016.
ISSN: ISSN 0162-0134
PubMed: 27888701
DOI: 10.1016/J.JINORGBIO.2016.11.016