Calcium in PDB 7mjr: VIP4DA2 Toxin Structure

The structure of VIP4DA2 Toxin Structure, PDB code: 7mjr was solved by T.J.Rydel, D.Duda, M.Zheng, A.Henry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.05 / 3.22
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	117.517, 221.374, 154.141, 90, 90, 90
R / Rfree (%)	19.6 / 24.1

The binding sites of Calcium atom in the VIP4DA2 Toxin Structure (pdb code 7mjr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the VIP4DA2 Toxin Structure, PDB code: 7mjr:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the VIP4DA2 Toxin Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of VIP4DA2 Toxin Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:90.3 occ:1.00 OD1 A:ASP191 2.1 86.8 1.0 OD2 A:ASP189 2.2 85.9 1.0 O A:ILE193 2.2 92.1 1.0 OD1 A:ASP187 2.4 91.4 1.0 OE1 A:GLU198 2.7 83.1 1.0 CG A:ASP191 2.9 87.9 1.0 OD2 A:ASP191 3.2 86.4 1.0 CG A:ASP189 3.2 86.9 1.0 C A:ILE193 3.2 88.0 1.0 CD A:GLU198 3.3 82.5 1.0 CG A:ASP187 3.5 91.6 1.0 N A:ILE193 3.5 88.8 1.0 CB A:ILE193 3.6 77.5 1.0 CA A:ILE193 3.6 84.8 1.0 CB A:ASP189 3.7 86.2 1.0 CG A:GLU198 3.9 77.2 1.0 CA A:CA1002 4.0 81.5 1.0 OD2 A:ASP187 4.0 88.7 1.0 OE2 A:GLU198 4.1 82.7 1.0 OD1 A:ASP189 4.2 93.1 1.0 CB A:ASP191 4.3 85.1 1.0 N A:ASP191 4.4 85.2 1.0 N A:PRO194 4.4 87.4 1.0 O A:PRO194 4.4 82.4 1.0 CG1 A:ILE193 4.6 81.2 1.0 CG2 A:ILE193 4.6 74.4 1.0 CB A:ASP187 4.6 93.0 1.0 C A:ASP191 4.6 89.7 1.0 C A:PRO194 4.6 84.8 1.0 N A:ASP189 4.6 87.6 1.0 CA A:ASP191 4.7 85.5 1.0 C A:CYS192 4.7 88.7 1.0 CA A:ASP189 4.7 83.9 1.0 N A:CYS192 4.7 89.6 1.0 CA A:PRO194 4.9 87.0 1.0 OD1 A:ASP195 4.9 89.2 1.0 O A:ASP191 4.9 89.1 1.0 CB A:GLU198 4.9 76.6 1.0 N A:ASN190 5.0 87.0 1.0 CA A:PRO228 5.0 77.7 1.0

Calcium binding site 2 out of 3 in the VIP4DA2 Toxin Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of VIP4DA2 Toxin Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:81.5 occ:1.00 OD2 A:ASP191 2.4 86.4 1.0 OD2 A:ASP240 2.4 77.4 1.0 O A:HIS230 2.4 83.2 1.0 O A:ASN227 2.4 79.2 1.0 OE2 A:GLU198 2.5 82.7 1.0 OE1 A:GLU198 2.6 83.1 1.0 CD A:GLU198 2.9 82.5 1.0 OD1 A:ASP189 3.2 93.1 1.0 CG A:ASP189 3.3 86.9 1.0 OD2 A:ASP189 3.5 85.9 1.0 CG A:ASP240 3.5 75.8 1.0 C A:HIS230 3.6 86.8 1.0 CG A:ASP191 3.6 87.9 1.0 C A:ASN227 3.6 76.8 1.0 CA A:ALA231 3.9 80.2 1.0 CA A:CA1001 4.0 90.3 1.0 CB A:ASP240 4.1 78.3 1.0 CB A:ASP189 4.1 86.2 1.0 OD1 A:ASP191 4.2 86.8 1.0 OG1 A:THR233 4.2 72.6 1.0 N A:ALA231 4.2 86.9 1.0 C A:ALA231 4.3 75.0 1.0 O A:ALA231 4.3 82.0 1.0 N A:ASN227 4.4 79.2 1.0 CA A:ASN227 4.5 75.1 1.0 CG A:GLU198 4.5 77.2 1.0 CA A:PRO228 4.5 77.7 1.0 N A:PRO228 4.5 78.0 1.0 OD1 A:ASP240 4.6 71.0 1.0 N A:HIS230 4.6 81.5 1.0 C A:PRO228 4.7 83.4 1.0 CA A:HIS230 4.7 87.6 1.0 N A:TYR229 4.7 84.5 1.0 CB A:ASP191 4.7 85.1 1.0 CB A:ASN227 4.8 81.5 1.0 OG A:SER226 4.8 75.0 1.0 CB A:SER226 4.9 72.8 1.0

Calcium binding site 3 out of 3 in the VIP4DA2 Toxin Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of VIP4DA2 Toxin Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:95.9 occ:1.00 OD2 A:ASP718 2.5 95.9 1.0 O A:THR617 2.5 100.6 1.0 OD1 A:ASP718 3.1 84.7 1.0 CG A:ASP718 3.1 89.5 1.0 O A:PHE599 3.2 109.8 1.0 O A:LYS620 3.2 107.5 1.0 C A:THR617 3.6 102.6 1.0 CA A:GLY618 3.8 104.6 1.0 OE1 A:GLU600 3.8 115.6 1.0 CG A:GLU600 3.9 104.6 1.0 N A:PHE599 3.9 90.9 1.0 C A:PHE599 3.9 106.7 1.0 CD A:GLU600 4.0 111.3 1.0 CB A:GLU600 4.1 102.0 1.0 N A:GLY618 4.1 105.5 1.0 C A:ASP598 4.1 90.4 1.0 N A:LYS619 4.2 109.5 1.0 C A:GLY618 4.3 104.9 1.0 C A:LYS620 4.3 106.1 1.0 CB A:ASP598 4.4 85.1 1.0 CA A:PHE599 4.5 95.9 1.0 CA A:ASP598 4.5 85.5 1.0 N A:LYS620 4.6 112.6 1.0 OD1 A:ASP719 4.6 80.0 1.0 CB A:ASP718 4.6 83.0 1.0 O A:ASP598 4.7 98.4 1.0 OG1 A:THR617 4.7 92.0 1.0 OE2 A:GLU600 4.8 118.0 1.0 CA A:THR617 4.8 99.2 1.0 OD2 A:ASP598 4.8 96.7 1.0 N A:GLU600 4.8 108.5 1.0 CA A:GLU600 4.9 110.9 1.0 N A:THR617 5.0 100.3 1.0 CB A:PHE599 5.0 93.4 1.0 CG A:ASP598 5.0 90.6 1.0

M.Zheng, D.Duda, T.J.Rydel, J.L.Kouadio. Structural and Functional Insights Into the First Bacillus Thuringiensis Vegetative Insecticidal Protein of the VIP4 Fold, Active Against Western Corn Rootworm To Be Published.