Nickel in PDB 1ejv: Crystal Structure of the H320Q Variant of Klebsiella Aerogenes Urease

All present enzymatic activity of Crystal Structure of the H320Q Variant of Klebsiella Aerogenes Urease:
3.5.1.5;

The structure of Crystal Structure of the H320Q Variant of Klebsiella Aerogenes Urease, PDB code: 1ejv was solved by M.A.Pearson, I.S.Park, R.A.Schaller, L.O.Michel, P.A.Karplus, R.P.Hausinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.40
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	170.800, 170.800, 170.800, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / n/a

The binding sites of Nickel atom in the Crystal Structure of the H320Q Variant of Klebsiella Aerogenes Urease (pdb code 1ejv). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the H320Q Variant of Klebsiella Aerogenes Urease, PDB code: 1ejv:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of the H320Q Variant of Klebsiella Aerogenes Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the H320Q Variant of Klebsiella Aerogenes Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni4774 b:17.8 occ:1.00 O C:HOH501 1.9 3.9 1.0 ND1 C:HIS1246 2.0 5.1 1.0 OQ1 C:KCX1217 2.1 4.4 1.0 NE2 C:HIS1272 2.2 2.9 1.0 O C:HOH500 2.2 27.8 1.0 CE1 C:HIS1246 2.8 10.7 1.0 CX C:KCX1217 3.1 7.6 1.0 CE1 C:HIS1272 3.1 2.0 1.0 CG C:HIS1246 3.1 5.1 1.0 CD2 C:HIS1272 3.2 5.0 1.0 O C:GLY1277 3.3 10.5 1.0 OQ2 C:KCX1217 3.4 9.3 1.0 CB C:HIS1246 3.6 3.7 1.0 NE2 C:HIS1219 3.6 13.3 1.0 NI C:NI4775 3.7 15.6 1.0 CD2 C:HIS1219 4.0 10.2 1.0 O C:HOH502 4.0 17.3 1.0 NE2 C:HIS1246 4.0 6.3 1.0 CD2 C:HIS1246 4.2 6.4 1.0 ND1 C:HIS1272 4.2 2.7 1.0 O C:HOH170 4.2 46.4 1.0 NZ C:KCX1217 4.2 8.3 1.0 CE1 C:HIS1134 4.2 4.3 1.0 CG C:HIS1272 4.3 3.9 1.0 C C:GLY1277 4.4 10.4 1.0 NE2 C:HIS1134 4.5 4.5 1.0 CE1 C:HIS1219 4.6 11.2 1.0 CE C:KCX1217 4.8 7.7 1.0 CA C:HIS1246 4.8 2.0 1.0 OD2 C:ASP1360 4.8 4.5 1.0 CA C:GLY1278 4.9 7.0 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of the H320Q Variant of Klebsiella Aerogenes Urease


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the H320Q Variant of Klebsiella Aerogenes Urease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni4775 b:15.6 occ:1.00 O C:HOH500 2.1 27.8 1.0 NE2 C:HIS1134 2.1 4.5 1.0 NE2 C:HIS1136 2.2 8.8 1.0 OD1 C:ASP1360 2.2 8.0 1.0 OQ2 C:KCX1217 2.3 9.3 1.0 CG C:ASP1360 3.0 5.8 1.0 CE1 C:HIS1134 3.0 4.3 1.0 O C:HOH502 3.1 17.3 1.0 CE1 C:HIS1136 3.1 9.8 1.0 CD2 C:HIS1134 3.2 2.7 1.0 CD2 C:HIS1136 3.2 8.6 1.0 CX C:KCX1217 3.3 7.6 1.0 OD2 C:ASP1360 3.4 4.5 1.0 O C:HOH501 3.4 3.9 1.0 OQ1 C:KCX1217 3.6 4.4 1.0 NI C:NI4774 3.7 17.8 1.0 ND1 C:HIS1134 4.1 3.7 1.0 CB C:ASP1360 4.2 4.9 1.0 CG C:HIS1134 4.3 2.2 1.0 ND1 C:HIS1136 4.3 7.7 1.0 CG C:HIS1136 4.3 9.9 1.0 CG2 C:THR1169 4.3 2.9 1.0 O C:ALA1363 4.3 10.9 1.0 NZ C:KCX1217 4.4 8.3 1.0 CB C:ALA1363 4.4 4.1 1.0 CA C:ASP1360 4.5 6.2 1.0 O C:HOH170 4.6 46.4 1.0 O C:ALA1167 4.6 2.0 1.0 CD2 C:HIS1272 4.9 5.0 1.0 NE2 C:HIS1272 4.9 2.9 1.0

M.A.Pearson, I.S.Park, R.A.Schaller, L.O.Michel, P.A.Karplus, R.P.Hausinger. Kinetic and Structural Characterization of Urease Active Site Variants. Biochemistry V. 39 8575 2000.
ISSN: ISSN 0006-2960
PubMed: 10913264
DOI: 10.1021/BI000613O