Nickel in PDB 6qdy: The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Its Substrate Urea

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

The structure of The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Its Substrate Urea, PDB code: 6qdy was solved by L.Mazzei, M.Cianci, S.Benini, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.54 / 1.42
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.565, 131.565, 188.683, 90.00, 90.00, 120.00
R / Rfree (%)	9.5 / 11.9

The structure of The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Its Substrate Urea also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Nickel atom in the The Crystal Structure of Sporosarcina Pasteurii Urease in Complex with Its Substrate Urea (pdb code 6qdy). 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 Its Substrate Urea, PDB code: 6qdy:
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 Its Substrate Urea


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 Its Substrate Urea within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni601 b:8.9 occ:1.00 OQ2 C:KCX220 2.0 8.9 1.0 F C:F610 2.0 9.1 1.0 NE2 C:HIS275 2.0 8.8 1.0 ND1 C:HIS249 2.1 7.8 1.0 O C:URE611 2.2 9.2 1.0 C C:URE611 2.8 10.6 1.0 CE1 C:HIS249 3.0 8.1 1.0 CD2 C:HIS275 3.0 8.9 1.0 CX C:KCX220 3.0 9.0 1.0 CE1 C:HIS275 3.0 8.8 1.0 CG C:HIS249 3.1 8.0 1.0 O C:GLY280 3.2 10.3 1.0 OQ1 C:KCX220 3.4 8.4 1.0 CB C:HIS249 3.5 7.6 1.0 N1 C:URE611 3.5 11.2 1.0 NI C:NI602 3.6 8.3 1.0 NE2 C:HIS222 3.7 8.5 1.0 N2 C:URE611 3.7 8.4 1.0 CE1 C:HIS137 4.0 8.1 1.0 CD2 C:HIS222 4.0 8.6 1.0 NE2 C:HIS249 4.1 8.6 1.0 ND1 C:HIS275 4.1 8.6 1.0 CG C:HIS275 4.1 8.4 1.0 NZ C:KCX220 4.2 8.8 1.0 C C:GLY280 4.2 10.1 1.0 CD2 C:HIS249 4.2 8.9 1.0 NE2 C:HIS137 4.3 7.5 1.0 OD2 C:ASP363 4.4 9.3 1.0 CE1 C:HIS222 4.6 8.5 1.0 CE C:KCX220 4.7 9.2 1.0 CA C:HIS249 4.8 7.7 1.0 CA C:GLY281 4.9 9.8 1.0 N C:GLY281 4.9 9.4 1.0 OD1 C:ASP363 5.0 8.0 1.0

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


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 Its Substrate Urea within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni602 b:8.3 occ:1.00 OQ1 C:KCX220 2.0 8.4 1.0 F C:F610 2.1 9.1 1.0 NE2 C:HIS137 2.1 7.5 1.0 NE2 C:HIS139 2.1 7.8 1.0 OD1 C:ASP363 2.1 8.0 1.0 N2 C:URE611 2.3 8.4 1.0 CE1 C:HIS139 2.9 7.9 1.0 CE1 C:HIS137 3.0 8.1 1.0 CX C:KCX220 3.0 9.0 1.0 CG C:ASP363 3.0 8.2 1.0 C C:URE611 3.0 10.6 1.0 CD2 C:HIS137 3.1 7.9 1.0 CD2 C:HIS139 3.2 7.2 1.0 OD2 C:ASP363 3.3 9.3 1.0 OQ2 C:KCX220 3.4 8.9 1.0 O C:URE611 3.5 9.2 1.0 NI C:NI601 3.6 8.9 1.0 N1 C:URE611 3.9 11.2 1.0 CG2 C:THR172 4.0 8.2 1.0 O C:ALA366 4.1 9.5 1.0 NZ C:KCX220 4.1 8.8 1.0 ND1 C:HIS137 4.1 8.4 1.0 ND1 C:HIS139 4.1 7.5 1.0 CG C:HIS137 4.2 7.9 1.0 CG C:HIS139 4.3 6.9 1.0 O C:ALA170 4.4 8.3 1.0 CB C:ASP363 4.4 8.6 1.0 CB C:ALA366 4.5 9.0 1.0 CA C:ASP363 4.7 7.8 1.0 NE2 C:HIS275 4.8 8.8 1.0 CD2 C:HIS275 4.8 8.9 1.0 N C:THR172 4.9 7.8 1.0

L.Mazzei, M.Cianci, S.Benini, S.Ciurli. The Structure of the Elusive Urease-Urea Complex Unveils the Mechanism of A Paradigmatic Nickel-Dependent Enzyme. Angew.Chem.Int.Ed.Engl. V. 58 7415 2019.
ISSN: ESSN 1521-3773
PubMed: 30969470
DOI: 10.1002/ANIE.201903565