Cadmium in PDB 7gqs: Crystal Structure of Werner Helicase Fragment 517-945 in Complex with Adp

The structure of Crystal Structure of Werner Helicase Fragment 517-945 in Complex with Adp, PDB code: 7gqs was solved by M.Classen, J.Benz, D.Brugger, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.89 / 1.57
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.071, 90.066, 53.788, 90, 102.46, 90
R / Rfree (%)	17.5 / 21.9

The structure of Crystal Structure of Werner Helicase Fragment 517-945 in Complex with Adp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the Crystal Structure of Werner Helicase Fragment 517-945 in Complex with Adp (pdb code 7gqs). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Crystal Structure of Werner Helicase Fragment 517-945 in Complex with Adp, PDB code: 7gqs:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Crystal Structure of Werner Helicase Fragment 517-945 in Complex with Adp


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 Werner Helicase Fragment 517-945 in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:42.4 occ:1.00 O A:HOH1302 2.4 33.5 1.0 OE1 A:GLU918 2.5 35.1 1.0 O A:HOH1314 2.6 31.6 1.0 SG A:CYS727 2.6 27.4 1.0 OE2 A:GLU918 2.7 34.0 1.0 CD A:GLU918 3.0 41.4 1.0 CB A:CYS727 3.4 20.5 1.0 N A:GLY729 4.0 22.7 1.0 CA A:GLY729 4.0 32.4 1.0 O A:HOH1188 4.2 39.1 1.0 CE2 A:PHE730 4.3 29.2 1.0 CG A:GLU918 4.5 30.4 1.0 CA A:CYS727 4.6 25.6 1.0 CB A:ALA706 4.7 25.4 1.0 C A:CYS727 4.7 24.6 1.0 CD2 A:PHE730 4.8 29.7 1.0 O A:CYS727 4.8 26.9 1.0 O A:HOH1117 4.9 25.4 1.0

Cadmium binding site 2 out of 3 in the Crystal Structure of Werner Helicase Fragment 517-945 in Complex with Adp


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 Werner Helicase Fragment 517-945 in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1003 b:25.6 occ:1.00 SG A:CYS935 2.5 24.8 1.0 SG A:CYS939 2.5 23.1 1.0 SG A:CYS908 2.5 26.1 1.0 SG A:CYS936 2.5 21.5 1.0 CB A:CYS908 3.4 27.6 1.0 CB A:CYS939 3.4 25.3 1.0 CB A:CYS936 3.4 16.9 1.0 CB A:CYS935 3.5 24.0 1.0 CA A:CYS908 3.7 23.1 1.0 N A:CYS936 3.8 20.3 1.0 N A:ARG909 4.0 19.7 1.0 C A:CYS935 4.2 20.1 1.0 CA A:CYS936 4.2 19.4 1.0 C A:CYS908 4.2 25.2 1.0 N A:GLY931 4.2 33.5 1.0 N A:CYS939 4.3 20.7 1.0 N A:ARG910 4.4 21.0 1.0 CA A:CYS939 4.5 24.2 1.0 CA A:CYS935 4.5 21.4 1.0 CB A:ARG910 4.5 20.3 1.0 O A:CYS935 4.8 17.3 1.0 CG A:MET930 4.8 34.0 1.0 C A:CYS936 4.9 17.9 1.0 O A:CYS936 4.9 17.9 1.0 CA A:GLY931 4.9 27.5 1.0 O A:HOH1297 5.0 39.5 1.0 N A:CYS908 5.0 26.1 1.0

Cadmium binding site 3 out of 3 in the Crystal Structure of Werner Helicase Fragment 517-945 in Complex with Adp


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Werner Helicase Fragment 517-945 in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1004 b:35.5 occ:1.00 NE2 A:HIS558 2.2 25.7 1.0 OE2 A:GLU563 2.2 25.4 1.0 CD A:GLU563 3.1 37.5 1.0 CE1 A:HIS558 3.1 24.2 1.0 CD2 A:HIS558 3.2 24.5 1.0 CG A:GLU563 3.3 23.7 1.0 CD A:PRO530 4.2 29.5 1.0 ND1 A:HIS558 4.2 23.2 1.0 OE1 A:GLU563 4.3 34.4 1.0 CG A:HIS558 4.3 25.5 1.0 CG A:PRO530 4.5 31.2 1.0 CB A:GLU563 4.8 32.6 1.0 CB A:GLU562 5.0 32.6 1.0

K.A.Baltgalvis, K.N.Lamb, K.T.Symons, C.C.Wu, M.A.Hoffman, A.N.Snead, X.Song, T.Glaza, S.Kikuchi, J.C.Green, D.C.Rogness, B.Lam, M.E.Rodriguez-Aguirre, D.R.Woody, C.L.Eissler, S.Rodiles, S.M.Negron, S.M.Bernard, E.Tran, J.Pollock, A.Tabatabaei, V.Contreras, H.N.Williams, M.K.Pastuszka, J.J.Sigler, P.Pettazzoni, M.G.Rudolph, M.Classen, D.Brugger, C.Claiborne, J.M.Plancher, I.Cuartas, J.Seoane, L.E.Burgess, R.T.Abraham, D.S.Weinstein, G.M.Simon, M.P.Patricelli, T.M.Kinsella. Chemoproteomic Discovery of A Covalent Allosteric Inhibitor of Wrn Helicase Nature 2024.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-024-07318-Y