Zinc in PDB 6ocd: Ricin A Chain Bound to Vhh Antibody V6D4

All present enzymatic activity of Ricin A Chain Bound to Vhh Antibody V6D4:
3.2.2.22;

The structure of Ricin A Chain Bound to Vhh Antibody V6D4, PDB code: 6ocd 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)	46.45 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.937, 78.605, 103.890, 90.00, 96.46, 90.00
R / Rfree (%)	18.9 / 22.8

The structure of Ricin A Chain Bound to Vhh Antibody V6D4 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Ricin A Chain Bound to Vhh Antibody V6D4 (pdb code 6ocd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Ricin A Chain Bound to Vhh Antibody V6D4, PDB code: 6ocd:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Ricin A Chain Bound to Vhh Antibody V6D4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ricin A Chain Bound to Vhh Antibody V6D4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:31.5 occ:1.00 OE2 A:GLU102 2.0 38.5 1.0 N3 A:IMD303 2.2 42.7 1.0 NE2 A:HIS106 2.2 50.0 1.0 CD A:GLU102 2.8 45.4 1.0 C2 A:IMD303 3.0 51.4 1.0 OE1 A:GLU102 3.1 37.7 1.0 CD2 A:HIS106 3.1 32.6 1.0 C4 A:IMD303 3.2 53.2 1.0 CE1 A:HIS106 3.3 46.5 1.0 O A:HOH456 4.1 41.0 1.0 CG A:GLU102 4.2 47.5 1.0 N1 A:IMD303 4.2 62.7 1.0 CG A:HIS106 4.3 34.5 1.0 C5 A:IMD303 4.3 61.5 1.0 ND1 A:HIS106 4.3 42.3 1.0 O A:GLU102 4.4 34.9 1.0 OG1 A:THR105 4.7 37.7 1.0

Zinc binding site 2 out of 3 in the Ricin A Chain Bound to Vhh Antibody V6D4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ricin A Chain Bound to Vhh Antibody V6D4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:32.7 occ:1.00 OE2 C:GLU102 2.0 37.7 1.0 NE2 C:HIS106 2.3 37.8 1.0 CD C:GLU102 2.8 47.3 1.0 OE1 C:GLU102 3.0 34.8 1.0 CD2 C:HIS106 3.1 30.8 1.0 CE1 C:HIS106 3.3 42.0 1.0 O C:HOH435 3.8 42.8 1.0 CG C:GLU102 4.2 44.8 1.0 CG C:HIS106 4.3 36.5 1.0 O C:GLU102 4.4 32.3 1.0 ND1 C:HIS106 4.4 41.8 1.0 OG1 C:THR105 4.6 38.9 1.0

Zinc binding site 3 out of 3 in the Ricin A Chain Bound to Vhh Antibody V6D4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ricin A Chain Bound to Vhh Antibody V6D4 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:44.8 occ:1.00 ND1 C:HIS40 2.3 40.4 1.0 CG C:HIS40 3.2 37.1 1.0 CE1 C:HIS40 3.2 44.1 1.0 CB C:HIS40 3.5 35.6 1.0 CA C:HIS40 3.7 32.0 1.0 NE2 C:HIS40 4.4 38.7 1.0 CD2 C:HIS40 4.4 36.0 1.0 O C:HOH472 4.6 50.2 1.0 N C:HIS40 4.6 33.0 1.0 C C:HIS40 4.7 33.7 1.0 O C:HOH413 4.7 36.6 1.0 O C:GLN223 4.8 32.9 1.0

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