Nickel in PDB 1e9z: Crystal Structure of Helicobacter Pylori Urease

All present enzymatic activity of Crystal Structure of Helicobacter Pylori Urease:
3.5.1.5;

The structure of Crystal Structure of Helicobacter Pylori Urease, PDB code: 1e9z was solved by N.-C.Ha, S.-T.Oh, B.-H.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	I 2 3
Cell size a, b, c (Å), α, β, γ (°)	177.910, 177.910, 177.910, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 28.4

The binding sites of Nickel atom in the Crystal Structure of Helicobacter Pylori Urease (pdb code 1e9z). 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 Helicobacter Pylori Urease, PDB code: 1e9z:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Helicobacter Pylori 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 Helicobacter Pylori Urease within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni3001 b:56.3 occ:1.00 NI B:NI3002 2.1 74.7 1.0 NE2 B:HIS274 2.6 26.0 1.0 ND1 B:HIS248 2.6 11.7 1.0 O B:HOH2027 2.6 14.6 1.0 OQ2 B:KCX219 2.7 39.5 1.0 OQ1 B:KCX219 2.9 41.8 1.0 CE1 B:HIS248 3.0 11.1 1.0 CD2 B:HIS274 3.1 25.9 1.0 CX B:KCX219 3.2 39.3 1.0 OD1 B:ASP362 3.6 31.2 1.0 NE2 B:HIS221 3.6 27.4 1.0 CE1 B:HIS274 3.8 26.2 1.0 CG B:HIS248 3.9 13.9 1.0 NE2 B:HIS136 3.9 28.9 1.0 O B:GLY279 3.9 26.8 1.0 CE1 B:HIS136 3.9 30.0 1.0 CD2 B:HIS221 4.0 26.7 1.0 NE2 B:HIS248 4.3 10.0 1.0 NE2 B:HIS138 4.3 10.5 1.0 O B:ALA169 4.4 12.5 1.0 CG B:HIS274 4.4 24.6 1.0 NZ B:KCX219 4.5 35.4 1.0 CE1 B:HIS138 4.5 9.8 1.0 CB B:HIS248 4.6 15.9 1.0 CE1 B:HIS221 4.7 25.9 1.0 CD2 B:HIS248 4.7 13.0 1.0 CG B:ASP362 4.7 30.8 1.0 ND1 B:HIS274 4.7 25.8 1.0 C B:GLY279 4.9 26.6 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Helicobacter Pylori 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 Helicobacter Pylori Urease within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni3002 b:74.7 occ:1.00 NI B:NI3001 2.1 56.3 1.0 OD1 B:ASP362 2.2 31.2 1.0 NE2 B:HIS138 2.3 10.5 1.0 NE2 B:HIS136 2.7 28.9 1.0 OQ2 B:KCX219 2.7 39.5 1.0 CE1 B:HIS138 2.9 9.8 1.0 CE1 B:HIS136 3.2 30.0 1.0 O B:HOH2027 3.3 14.6 1.0 OQ1 B:KCX219 3.4 41.8 1.0 CX B:KCX219 3.4 39.3 1.0 CG B:ASP362 3.5 30.8 1.0 CD2 B:HIS138 3.5 12.3 1.0 CD2 B:HIS136 3.7 28.6 1.0 ND1 B:HIS138 4.1 12.1 1.0 O B:ALA169 4.2 12.5 1.0 NE2 B:HIS274 4.2 26.0 1.0 OD2 B:ASP362 4.3 30.8 1.0 ND1 B:HIS136 4.3 28.3 1.0 CD2 B:HIS274 4.4 25.9 1.0 CB B:ASP362 4.4 28.1 1.0 CG B:HIS138 4.4 12.7 1.0 O B:ALA365 4.5 26.4 1.0 CG B:HIS136 4.6 26.5 1.0 ND1 B:HIS248 4.6 11.7 1.0 NZ B:KCX219 4.6 35.4 1.0 NE2 B:HIS221 4.6 27.4 1.0 CG2 B:THR171 4.7 8.0 1.0 CD2 B:HIS221 4.7 26.7 1.0 CB B:ALA365 4.8 24.9 1.0 CA B:ASP362 5.0 25.3 1.0

N.-C.Ha, S.-T.Oh, J.Y.Sung, K.-A.Cha, M.Hyung Lee, B.-H.Oh. Supramolecular Assembly and Acid Resistance of Helicobacter Pylori Urease Nat.Struct.Biol. V. 8 480 2001.
ISSN: ISSN 1072-8368
PubMed: 11373617
DOI: 10.1038/88563