Calcium in PDB 2vmd: Structure of the Complex of Discoidin II From Dictyostelium Discoideum with Beta-Methyl-Galactose

The structure of Structure of the Complex of Discoidin II From Dictyostelium Discoideum with Beta-Methyl-Galactose, PDB code: 2vmd 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)	36.74 / 1.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	81.140, 81.140, 259.280, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 22.7

The structure of Structure of the Complex of Discoidin II From Dictyostelium Discoideum with Beta-Methyl-Galactose also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Structure of the Complex of Discoidin II From Dictyostelium Discoideum with Beta-Methyl-Galactose (pdb code 2vmd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Structure of the Complex of Discoidin II From Dictyostelium Discoideum with Beta-Methyl-Galactose, PDB code: 2vmd:

Calcium binding site 1 out of 1 in the Structure of the Complex of Discoidin II From Dictyostelium Discoideum with Beta-Methyl-Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Complex of Discoidin II From Dictyostelium Discoideum with Beta-Methyl-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:27.7 occ:1.00 O A:SER40 2.3 24.9 1.0 O A:HOH2065 2.3 29.2 1.0 O A:HOH2064 2.3 25.9 1.0 OD1 A:ASN39 2.5 20.1 1.0 OD1 A:ASP47 2.5 18.4 1.0 O A:HOH2051 2.5 29.6 1.0 O A:HOH2056 2.7 28.7 1.0 CG A:ASP47 3.4 21.4 1.0 C A:SER40 3.4 27.1 1.0 CG A:ASN39 3.5 20.8 1.0 OD2 A:ASP47 3.6 23.0 1.0 N A:SER40 3.9 23.2 1.0 ND2 A:ASN39 4.1 19.3 1.0 CA A:SER40 4.1 25.9 1.0 C A:ASN39 4.3 22.6 1.0 O A:GLY48 4.4 18.9 1.0 N A:LYS41 4.5 29.2 1.0 OE2 A:GLU50 4.5 21.6 1.0 O A:HOH2031 4.5 29.9 1.0 CB A:ASN39 4.5 19.3 1.0 CB A:SER40 4.6 26.4 1.0 N A:ASP47 4.7 22.6 1.0 O A:ASP42 4.7 39.2 1.0 CA A:LYS41 4.7 32.9 1.0 O A:ASN39 4.8 22.0 1.0 CB A:ASP47 4.8 21.2 1.0 CA A:ASN39 4.8 21.5 1.0 O A:ARG45 5.0 29.2 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