Nickel in PDB 6obe: Ricin A Chain Bound to Vhh Antibody V6H8

All present enzymatic activity of Ricin A Chain Bound to Vhh Antibody V6H8:
3.2.2.22;

The structure of Ricin A Chain Bound to Vhh Antibody V6H8, PDB code: 6obe was solved by M.J.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.12 / 1.73
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.371, 90.371, 204.015, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 20.8

The binding sites of Nickel atom in the Ricin A Chain Bound to Vhh Antibody V6H8 (pdb code 6obe). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Ricin A Chain Bound to Vhh Antibody V6H8, PDB code: 6obe:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Ricin A Chain Bound to Vhh Antibody V6H8


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ricin A Chain Bound to Vhh Antibody V6H8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:14.8 occ:1.00 N3 A:IMD306 2.0 19.0 1.0 OXT A:PHE267 2.0 20.1 1.0 ND1 A:HIS40 2.1 15.8 1.0 C A:PHE267 2.9 25.6 1.0 C2 A:IMD306 3.0 20.4 1.0 CE1 A:HIS40 3.0 15.8 1.0 C4 A:IMD306 3.0 17.7 1.0 O A:PHE267 3.1 26.1 1.0 CG A:HIS40 3.1 15.9 1.0 CB A:HIS40 3.5 15.3 1.0 CA A:HIS40 3.6 17.1 1.0 O A:GLN223 4.1 22.9 1.0 N1 A:IMD306 4.1 21.3 1.0 NE2 A:HIS40 4.1 14.8 1.0 C5 A:IMD306 4.2 17.6 1.0 N A:HIS40 4.2 12.9 1.0 CD2 A:HIS40 4.2 15.9 1.0 CA A:PHE267 4.3 25.9 1.0 O A:SER264 4.4 18.8 1.0 C A:GLN223 4.4 18.8 1.0 O A:SER265 4.5 17.9 1.0 N A:PHE267 4.6 23.8 1.0 CA A:GLN223 4.7 17.5 1.0 C A:HIS40 4.8 13.2 1.0 O A:ASN222 4.9 25.8 1.0 C A:SER265 4.9 14.5 1.0 CA A:SER265 5.0 15.7 1.0

Nickel binding site 2 out of 2 in the Ricin A Chain Bound to Vhh Antibody V6H8


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Ricin A Chain Bound to Vhh Antibody V6H8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:15.9 occ:0.50 OE2 A:GLU102 2.0 17.1 1.0 NE2 A:HIS106 2.1 18.5 1.0 CD A:GLU102 2.9 19.4 1.0 CE1 A:HIS106 3.0 26.7 1.0 OE1 A:GLU102 3.1 17.3 1.0 CD2 A:HIS106 3.1 15.6 1.0 CD1 A:ILE53 3.8 21.6 0.3 O A:HOH495 4.1 30.8 1.0 ND1 A:HIS106 4.1 20.1 1.0 CG A:HIS106 4.2 16.1 1.0 CG A:GLU102 4.3 20.5 1.0 OG1 A:THR105 4.7 15.2 1.0 O A:HOH614 4.7 38.2 1.0 O A:GLU102 4.7 13.3 1.0

M.J.Rudolph, M.J.Rudolph. N/A N/A.