Cadmium in PDB 6f0d: Crystal Structure of A Llama Vhh Antibody BCD090-M2 Against Human ERBB3 in Space Group P1 with Cadmium Ions

The structure of Crystal Structure of A Llama Vhh Antibody BCD090-M2 Against Human ERBB3 in Space Group P1 with Cadmium Ions, PDB code: 6f0d was solved by I.E.Eliseev, A.N.Yudenko, V.V.Vysochinskaya, A.A.Svirina, A.V.Evstratyeva, M.S.Drozhzhachih, E.A.Krendeleva, A.K.Vladimirova, T.A.Nemankin, V.M.Ekimova, A.B.Ulitin, M.I.Lomovskaya, P.A.Yakovlev, F.V.Moiseenko, O.B.Chakchir, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.34 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.766, 41.526, 46.487, 89.99, 67.92, 76.06
R / Rfree (%)	17.4 / 21.8

The binding sites of Cadmium atom in the Crystal Structure of A Llama Vhh Antibody BCD090-M2 Against Human ERBB3 in Space Group P1 with Cadmium Ions (pdb code 6f0d). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of A Llama Vhh Antibody BCD090-M2 Against Human ERBB3 in Space Group P1 with Cadmium Ions, PDB code: 6f0d:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in the Crystal Structure of A Llama Vhh Antibody BCD090-M2 Against Human ERBB3 in Space Group P1 with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of A Llama Vhh Antibody BCD090-M2 Against Human ERBB3 in Space Group P1 with Cadmium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:16.5 occ:1.00 OD1 A:ASP100 2.0 20.4 1.0 OD1 A:ASP116 2.4 12.2 1.0 O A:HOH325 2.5 16.4 1.0 O A:GLU114 2.5 13.7 1.0 OD2 A:ASP116 2.9 18.2 1.0 CG A:ASP116 3.0 14.5 1.0 CG A:ASP100 3.1 18.1 1.0 C A:GLU114 3.7 15.4 1.0 OD2 A:ASP100 3.7 20.3 1.0 CB A:ASP100 4.3 13.2 1.0 CB A:ASP116 4.4 11.1 1.0 N A:LEU101 4.5 11.3 1.0 OG A:SER105 4.5 22.2 1.0 N A:ASP116 4.5 13.0 1.0 CA A:ASP100 4.5 15.5 1.0 C A:TYR115 4.5 12.6 1.0 CA A:TYR115 4.6 13.7 1.0 CA A:GLU114 4.6 8.8 1.0 O A:LEU101 4.6 15.3 1.0 CB A:SER105 4.6 20.6 1.0 N A:TYR115 4.6 9.2 1.0 O A:HOH309 4.7 24.2 1.0 CA A:ASP116 4.8 11.2 1.0 OE1 A:GLU114 4.8 15.1 1.0 CB A:GLU114 4.8 10.5 1.0 C A:ASP100 4.9 14.7 1.0

Cadmium binding site 2 out of 2 in the Crystal Structure of A Llama Vhh Antibody BCD090-M2 Against Human ERBB3 in Space Group P1 with Cadmium Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of A Llama Vhh Antibody BCD090-M2 Against Human ERBB3 in Space Group P1 with Cadmium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:14.4 occ:1.00 O A:GLY1 2.6 18.7 1.0 N A:GLY1 2.6 21.1 1.0 CA A:GLY1 3.0 20.9 1.0 C A:GLY1 3.1 30.6 1.0 NE2 A:GLN2 3.9 25.5 1.0 N A:GLN2 4.2 30.4 1.0 CD A:GLN2 4.7 33.2 1.0

I.E.Eliseev, A.N.Yudenko, V.V.Vysochinskaya, A.A.Svirina, A.V.Evstratyeva, M.S.Drozhzhachih, E.A.Krendeleva, A.K.Vladimirova, T.A.Nemankin, V.M.Ekimova, A.B.Ulitin, M.I.Lomovskaya, P.A.Yakovlev, A.S.Bukatin, N.A.Knyazev, F.V.Moiseenko, O.B.Chakchir. Crystal Structures of A Llama Vhh Antibody BCD090-M2 Targeting Human ERBB3 Receptor. F1000RES V. 7 57 2018.
ISSN: ISSN 2046-1402
PubMed: 30430004
DOI: 10.12688/F1000RESEARCH.13612.1