Zinc in PDB 7kd2: Ricin Bound to Vhh Antibody V11B2

All present enzymatic activity of Ricin Bound to Vhh Antibody V11B2:
3.2.2.22;

The structure of Ricin Bound to Vhh Antibody V11B2, PDB code: 7kd2 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)	26.19 / 2.55
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	77.607, 99.559, 111.283, 90, 90, 90
R / Rfree (%)	22.7 / 28

The structure of Ricin Bound to Vhh Antibody V11B2 also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Zinc atom in the Ricin Bound to Vhh Antibody V11B2 (pdb code 7kd2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Ricin Bound to Vhh Antibody V11B2, PDB code: 7kd2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:45.6 occ:1.00 O A:HOH419 3.1 26.7 1.0 ND1 A:HIS65 3.1 81.5 1.0 CE1 A:HIS65 3.7 82.1 1.0 N A:GLY15 3.9 58.7 1.0 CG A:HIS65 4.3 82.6 1.0 CA A:ALA14 4.5 61.2 1.0 C A:ALA14 4.5 61.7 1.0 CB A:HIS65 4.7 83.0 1.0 CA A:GLY15 4.7 58.2 1.0 CB A:ALA14 4.8 63.3 1.0 NE2 A:HIS65 4.9 82.6 1.0

Zinc binding site 2 out of 5 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:108.9 occ:1.00 NH2 A:ARG134 3.2 56.2 1.0 OE1 A:GLU135 3.4 78.3 1.0 O A:HOH411 3.7 43.1 1.0 OE2 A:GLU127 4.1 58.7 1.0 CZ A:ARG134 4.1 53.2 1.0 OE1 A:GLU127 4.1 64.2 1.0 CD A:GLU135 4.3 75.3 1.0 OE2 A:GLU135 4.3 73.8 1.0 NE A:ARG134 4.5 51.4 1.0 CD A:GLU127 4.6 60.2 1.0

Zinc binding site 3 out of 5 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:68.7 occ:1.00 ND1 B:HIS29 2.6 58.1 1.0 CG B:HIS29 3.5 55.4 1.0 CE1 B:HIS29 3.5 61.0 1.0 CB B:HIS29 3.7 48.8 1.0 CG B:ARG27 4.3 54.4 1.0 O B:HOH423 4.5 23.4 1.0 NE2 B:HIS29 4.6 60.7 1.0 CD2 B:HIS29 4.6 58.2 1.0

Zinc binding site 4 out of 5 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:46.8 occ:1.00 OD2 C:ASP99 2.0 99.4 1.0 OG C:SER29 2.1 99.7 1.0 ND1 C:HIS105 2.1 102.6 1.0 O C:HOH312 2.3 42.0 1.0 CG C:ASP99 3.0 91.7 1.0 CE1 C:HIS105 3.0 103.8 1.0 CG C:HIS105 3.0 95.8 1.0 CB C:SER29 3.3 90.1 1.0 CB C:HIS105 3.4 83.7 1.0 OD1 C:ASP99 3.7 93.8 1.0 CB C:ASP99 3.9 80.9 1.0 NE2 C:HIS105 4.0 102.1 1.0 CD2 C:HIS105 4.1 99.5 1.0 N C:SER29 4.3 78.2 1.0 CA C:SER29 4.4 82.6 1.0 CB C:ASP102 4.6 66.5 1.0 CD1 C:ILE28 4.8 71.5 1.0 CA C:HIS105 4.9 73.3 1.0

Zinc binding site 5 out of 5 in the Ricin Bound to Vhh Antibody V11B2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ricin Bound to Vhh Antibody V11B2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:75.2 occ:1.00 O C:HOH315 2.1 71.9 1.0 O C:HOH305 3.1 43.7 1.0 NH2 C:ARG98 3.5 47.1 1.0 CB B:SER241 3.8 38.6 1.0 NH1 C:ARG98 3.8 45.6 1.0 N B:SER241 3.9 36.7 1.0 CD B:PRO240 3.9 40.9 1.0 NE C:ARG103 4.0 49.7 1.0 CZ C:ARG98 4.1 48.7 1.0 OD2 B:ASP239 4.1 43.4 1.0 CG B:PRO240 4.2 39.2 1.0 OE1 C:GLU106 4.2 43.4 1.0 NH2 C:ARG103 4.2 45.4 1.0 CB B:PRO240 4.2 35.6 1.0 O C:HOH310 4.3 42.1 1.0 OG B:SER241 4.3 38.5 1.0 CA B:SER241 4.4 37.6 1.0 N B:PRO240 4.5 38.6 1.0 CZ C:ARG103 4.6 47.6 1.0 C B:PRO240 4.7 36.8 1.0 CA B:PRO240 4.8 34.9 1.0 CG C:ARG103 4.8 48.2 1.0 OE2 C:GLU106 4.8 43.8 1.0 CD C:GLU106 4.9 44.6 1.0 CD C:ARG103 5.0 49.9 1.0

M.J.Rudolph, A.Y.Poon, S.Kavaliauskiene, A.G.Myrann, C.Reynolds-Peterson, S.A.Davis, K.Sandvig, D.J.Vance, N.J.Mantis. Structural Analysis of Toxin-Neutralizing, Single-Domain Antibodies That Bridge Ricin'S A-B Subunit Interface. J.Mol.Biol. V. 433 67086 2021.
ISSN: ESSN 1089-8638
PubMed: 34089718
DOI: 10.1016/J.JMB.2021.167086