Nickel in PDB 4gy7: Crystallographic Structure Analysis of Urease From Jack Bean (Canavalia Ensiformis) at 1.49 A Resolution

All present enzymatic activity of Crystallographic Structure Analysis of Urease From Jack Bean (Canavalia Ensiformis) at 1.49 A Resolution:
3.5.1.5;

The structure of Crystallographic Structure Analysis of Urease From Jack Bean (Canavalia Ensiformis) at 1.49 A Resolution, PDB code: 4gy7 was solved by A.Begum, S.Banumathi, M.I.Choudhary, C.Betzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.49
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	140.664, 140.664, 198.109, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 16.5

The structure of Crystallographic Structure Analysis of Urease From Jack Bean (Canavalia Ensiformis) at 1.49 A Resolution also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Nickel atom in the Crystallographic Structure Analysis of Urease From Jack Bean (Canavalia Ensiformis) at 1.49 A Resolution (pdb code 4gy7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystallographic Structure Analysis of Urease From Jack Bean (Canavalia Ensiformis) at 1.49 A Resolution, PDB code: 4gy7:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystallographic Structure Analysis of Urease From Jack Bean (Canavalia Ensiformis) at 1.49 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystallographic Structure Analysis of Urease From Jack Bean (Canavalia Ensiformis) at 1.49 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:10.5 occ:0.91 O3 A:PO4903 2.0 10.4 0.9 OQ2 A:KCX490 2.1 9.1 1.0 NE2 A:HIS545 2.1 10.7 1.0 ND1 A:HIS519 2.1 10.8 1.0 O1 A:PO4903 2.2 12.8 0.8 P A:PO4903 2.5 22.7 0.5 CE1 A:HIS519 2.9 10.7 1.0 CE1 A:HIS545 3.0 11.7 1.0 CX A:KCX490 3.1 11.4 1.0 CD2 A:HIS545 3.1 10.1 1.0 CG A:HIS519 3.2 8.5 1.0 O A:GLY550 3.4 13.2 1.0 OQ1 A:KCX490 3.4 9.9 1.0 O4 A:PO4903 3.5 23.9 0.7 NI A:NI902 3.6 9.8 1.0 CB A:HIS519 3.6 9.3 1.0 NE2 A:HIS492 3.7 12.0 1.0 O2 A:PO4903 3.7 13.4 0.8 NE2 A:HIS519 4.1 10.5 1.0 CD2 A:HIS492 4.1 12.1 1.0 ND1 A:HIS545 4.1 11.0 1.0 CE1 A:HIS407 4.2 9.4 1.0 CG A:HIS545 4.2 10.5 1.0 NZ A:KCX490 4.2 9.7 1.0 CD2 A:HIS519 4.2 9.9 1.0 OD2 A:ASP633 4.4 12.5 1.0 C A:GLY550 4.4 13.3 1.0 NE2 A:HIS407 4.4 10.6 1.0 CE1 A:HIS492 4.7 11.1 1.0 CE A:KCX490 4.7 10.1 1.0 CA A:HIS519 4.9 9.1 1.0 OD1 A:ASP633 4.9 9.3 1.0

Nickel binding site 2 out of 2 in the Crystallographic Structure Analysis of Urease From Jack Bean (Canavalia Ensiformis) at 1.49 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystallographic Structure Analysis of Urease From Jack Bean (Canavalia Ensiformis) at 1.49 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni902 b:9.8 occ:1.00 OQ1 A:KCX490 2.0 9.9 1.0 OD1 A:ASP633 2.1 9.3 1.0 NE2 A:HIS409 2.1 8.1 1.0 O3 A:PO4903 2.1 10.4 0.9 NE2 A:HIS407 2.1 10.6 1.0 O2 A:PO4903 2.3 13.4 0.8 P A:PO4903 2.7 22.7 0.5 CE1 A:HIS409 2.9 9.4 1.0 CG A:ASP633 3.0 11.1 1.0 CE1 A:HIS407 3.0 9.4 1.0 CX A:KCX490 3.0 11.4 1.0 CD2 A:HIS407 3.1 9.7 1.0 CD2 A:HIS409 3.1 8.3 1.0 OD2 A:ASP633 3.3 12.5 1.0 OQ2 A:KCX490 3.4 9.1 1.0 NI A:NI901 3.6 10.5 0.9 O1 A:PO4903 3.8 12.8 0.8 O4 A:PO4903 3.8 23.9 0.7 ND1 A:HIS409 4.1 8.3 1.0 NZ A:KCX490 4.1 9.7 1.0 ND1 A:HIS407 4.1 9.3 1.0 CG A:HIS409 4.2 9.2 1.0 CG A:HIS407 4.2 9.8 1.0 CG2 A:THR442 4.3 11.0 1.0 O A:ALA636 4.3 17.5 1.0 CB A:ASP633 4.3 10.3 1.0 CB A:ALA636 4.5 12.8 1.0 O A:ALA440 4.5 10.9 1.0 CA A:ASP633 4.6 9.9 1.0 NE2 A:HIS545 4.8 10.7 1.0 CD2 A:HIS545 4.8 10.1 1.0

A.Begum, S.Banumathi, M.I.Choudhary, C.Betzel. Crystallographic Structure Analysis of Urease From Jack Bean (Canavalia Ensiformis) at 1.49 A Resolution To Be Published.