Nickel in PDB 5fse: 2.07 A Resolution 1,4-Benzoquinone Inhibited Sporosarcina Pasteurii Urease

All present enzymatic activity of 2.07 A Resolution 1,4-Benzoquinone Inhibited Sporosarcina Pasteurii Urease:
3.5.1.5;

The structure of 2.07 A Resolution 1,4-Benzoquinone Inhibited Sporosarcina Pasteurii Urease, PDB code: 5fse 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)	114.17 / 2.07
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.834, 131.834, 188.580, 90.00, 90.00, 120.00
R / Rfree (%)	14.5 / 19.2

The binding sites of Nickel atom in the 2.07 A Resolution 1,4-Benzoquinone Inhibited Sporosarcina Pasteurii Urease (pdb code 5fse). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the 2.07 A Resolution 1,4-Benzoquinone Inhibited Sporosarcina Pasteurii Urease, PDB code: 5fse:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the 2.07 A Resolution 1,4-Benzoquinone 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 2.07 A Resolution 1,4-Benzoquinone Inhibited Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni600 b:35.5 occ:1.00 O C:OH1580 2.0 31.6 1.0 OQ2 C:KCX220 2.0 27.3 1.0 NE2 C:HIS275 2.2 30.1 1.0 ND1 C:HIS249 2.2 29.6 1.0 O C:HOH2111 2.4 28.6 1.0 CX C:KCX220 3.1 28.7 1.0 CE1 C:HIS275 3.1 31.8 1.0 CE1 C:HIS249 3.2 27.9 1.0 CG C:HIS249 3.2 29.4 1.0 CD2 C:HIS275 3.2 28.3 1.0 OQ1 C:KCX220 3.4 26.5 1.0 CB C:HIS249 3.4 27.1 1.0 NE2 C:HIS222 3.5 28.2 1.0 O C:HOH2172 3.5 36.8 1.0 NI C:NI601 3.5 29.5 1.0 O C:GLY280 3.5 34.4 1.0 O C:HOH2094 3.6 35.1 1.0 CE1 C:HIS137 3.9 24.5 1.0 CD2 C:HIS222 3.9 26.8 1.0 NE2 C:HIS137 4.1 25.2 1.0 ND1 C:HIS275 4.2 29.2 1.0 OD2 C:ASP363 4.2 31.4 1.0 NE2 C:HIS249 4.3 31.9 1.0 NZ C:KCX220 4.3 26.7 1.0 CG C:HIS275 4.3 29.7 1.0 CD2 C:HIS249 4.3 29.4 1.0 CE1 C:HIS222 4.4 25.8 1.0 C C:GLY280 4.6 34.3 1.0 O1 C:SO41579 4.8 63.1 1.0 CA C:HIS249 4.8 25.2 1.0 CE C:KCX220 4.8 26.0 1.0

Nickel binding site 2 out of 2 in the 2.07 A Resolution 1,4-Benzoquinone 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 2.07 A Resolution 1,4-Benzoquinone Inhibited Sporosarcina Pasteurii Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:29.5 occ:1.00 NE2 C:HIS137 2.1 25.2 1.0 OQ1 C:KCX220 2.1 26.5 1.0 O C:OH1580 2.1 31.6 1.0 O C:HOH2094 2.3 35.1 1.0 NE2 C:HIS139 2.3 23.6 1.0 OD1 C:ASP363 2.3 27.7 1.0 CE1 C:HIS137 3.0 24.5 1.0 CX C:KCX220 3.1 28.7 1.0 CD2 C:HIS137 3.1 25.1 1.0 CG C:ASP363 3.1 30.8 1.0 CE1 C:HIS139 3.1 22.9 1.0 OD2 C:ASP363 3.2 31.4 1.0 OQ2 C:KCX220 3.2 27.3 1.0 CD2 C:HIS139 3.4 23.5 1.0 NI C:NI600 3.5 35.5 1.0 O C:HOH2111 3.5 28.6 1.0 CB C:ALA366 4.0 26.8 0.5 ND1 C:HIS137 4.1 24.6 1.0 O C:HOH2172 4.2 36.8 1.0 CG C:HIS137 4.2 24.6 1.0 NZ C:KCX220 4.2 26.7 1.0 CG2 C:THR172 4.2 22.7 1.0 ND1 C:HIS139 4.3 23.6 1.0 O C:ALA366 4.3 39.8 0.5 CB C:ASP363 4.4 27.8 1.0 O C:ALA170 4.4 20.8 1.0 CG C:HIS139 4.5 21.8 1.0 CA C:ASP363 4.7 26.0 1.0 CB C:ALA366 4.7 31.3 0.5 NE2 C:HIS275 4.8 30.1 1.0 CD2 C:HIS275 4.9 28.3 1.0 NE2 C:HIS222 4.9 28.2 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