Zinc in PDB 2vme: Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum

The structure of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum, PDB code: 2vme was solved by K.S.Aragao, M.Satre, A.Imberty, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.80 / 2.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	287.885, 56.281, 123.674, 90.00, 109.10, 90.00
R / Rfree (%)	18.1 / 23.8

The structure of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	6 atoms

The binding sites of Zinc atom in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum (pdb code 2vme). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum, PDB code: 2vme:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:14.3 occ:1.00 OD1 A:ASP68 2.0 13.3 0.5 OD2 A:ASP68 2.0 10.9 0.5 OD2 B:ASP68 2.0 16.3 0.5 OD1 B:ASP68 2.0 18.6 0.5 OD1 C:ASP68 2.0 14.3 0.5 OD2 C:ASP68 2.0 15.6 0.5 CG A:ASP68 2.2 14.9 0.5 CG B:ASP68 2.3 17.3 0.5 CG C:ASP68 2.3 15.0 0.5 O A:HOH2034 3.6 25.3 1.0 CB A:ASP68 3.7 18.3 0.5 CB B:ASP68 3.8 18.6 0.5 CB C:ASP68 3.9 16.1 0.5 CB A:SER69 4.5 22.1 1.0 N B:SER69 4.5 20.1 1.0 CB B:SER69 4.5 20.5 1.0 N A:SER69 4.6 21.4 1.0 CA A:ASP68 4.7 20.1 1.0 CB C:SER69 4.7 20.9 1.0 CA B:ASP68 4.7 19.6 1.0 N C:SER69 4.7 19.9 1.0 N A:ASP68 4.8 20.5 1.0 CA C:ASP68 4.8 17.8 1.0 C A:ASP68 4.9 21.0 1.0 C B:ASP68 4.9 19.9 1.0 N C:ASP68 4.9 17.6 1.0 N B:ASP68 5.0 19.7 1.0

Zinc binding site 2 out of 2 in the Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Wild-Type Discoidin II From Dictyostelium Discoideum within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:16.7 occ:1.00 OD1 E:ASP68 2.0 16.5 0.5 OD2 D:ASP68 2.0 16.4 0.5 OD1 F:ASP68 2.0 17.8 0.5 OD2 F:ASP68 2.0 19.9 0.5 OD2 E:ASP68 2.0 11.9 0.5 OD1 D:ASP68 2.0 16.0 0.5 CG D:ASP68 2.2 18.8 0.5 CG E:ASP68 2.2 15.0 0.5 CG F:ASP68 2.3 20.9 0.5 CB E:ASP68 3.7 17.7 0.5 CB D:ASP68 3.7 22.2 0.5 CB F:ASP68 3.8 23.4 0.5 N E:SER69 4.5 21.3 1.0 N F:SER69 4.6 25.9 1.0 CB E:SER69 4.6 22.6 1.0 N D:SER69 4.6 25.5 1.0 CA E:ASP68 4.7 19.1 1.0 CA F:ASP68 4.7 24.3 1.0 CB F:SER69 4.7 26.4 1.0 CA D:ASP68 4.7 23.3 1.0 CB D:SER69 4.7 25.9 1.0 N F:ASP68 4.8 24.2 1.0 N E:ASP68 4.8 19.8 1.0 C F:ASP68 4.9 25.9 1.0 C D:ASP68 4.9 24.6 1.0 C E:ASP68 4.9 20.1 1.0 N D:ASP68 4.9 23.7 1.0

K.S.Aragao, M.Satre, A.Imberty, A.Varrot. Structure Determination of Discoidin II From Dictyostelium Discoideum and Carbohydrate Binding Properties of the Lectin Domain. Proteins V. 73 43 2008.
ISSN: ISSN 0887-3585
PubMed: 18384150
DOI: 10.1002/PROT.22038