Calcium in PDB 6rym: Structure of Carbohydrate Recognition Domain with Glcnac Bound

The structure of Structure of Carbohydrate Recognition Domain with Glcnac Bound, PDB code: 6rym was solved by A.K.Shrive, T.J.Greenhough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.11 / 1.46
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	50.225, 50.225, 51.925, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 18.4

The binding sites of Calcium atom in the Structure of Carbohydrate Recognition Domain with Glcnac Bound (pdb code 6rym). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Carbohydrate Recognition Domain with Glcnac Bound, PDB code: 6rym:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Carbohydrate Recognition Domain with Glcnac Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Carbohydrate Recognition Domain with Glcnac Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:12.0 occ:1.00 OD1 A:ASP338 2.3 13.8 1.0 O4 A:NAG404 2.4 13.3 0.5 OE1 A:GLU325 2.4 13.6 1.0 O3 A:NAG404 2.4 13.7 0.5 OD1 A:ASN337 2.4 12.2 1.0 OD1 A:ASN317 2.4 17.6 1.0 O A:ASP338 2.5 10.7 1.0 O4 A:NDG403 2.5 13.2 0.5 OE1 A:GLU315 2.6 13.3 1.0 O3 A:NDG403 2.8 14.0 0.5 C4 A:NAG404 3.2 15.2 0.5 C3 A:NAG404 3.3 14.8 0.5 CD A:GLU325 3.4 13.0 1.0 CG A:ASP338 3.4 13.0 1.0 C4 A:NDG403 3.4 15.1 0.5 CD A:GLU315 3.4 12.9 1.0 CG A:ASN337 3.4 10.1 1.0 CG A:ASN317 3.4 20.6 1.0 C A:ASP338 3.5 9.2 1.0 C3 A:NDG403 3.5 14.7 0.5 N A:ASP338 3.7 10.0 1.0 OE2 A:GLU315 3.7 13.4 1.0 OE2 A:GLU325 3.7 14.4 1.0 ND2 A:ASN337 3.9 11.1 1.0 ND2 A:ASN317 3.9 21.1 1.0 CA A:ASP338 4.0 10.4 1.0 OD2 A:ASP338 4.2 13.1 1.0 CB A:ASP338 4.2 11.3 1.0 N A:ASN317 4.3 20.0 1.0 O A:SER319 4.5 28.5 1.0 C A:ASN337 4.5 10.5 1.0 CG A:GLU325 4.6 12.8 1.0 CB A:ASN317 4.7 20.6 1.0 C2 A:NAG404 4.7 15.5 0.5 C5 A:NAG404 4.7 16.4 0.5 CG A:GLU315 4.7 13.6 1.0 N A:VAL339 4.7 9.8 1.0 CB A:ASN337 4.7 9.6 1.0 N A:ASN318 4.8 22.1 1.0 N A:SER319 4.8 25.6 1.0 CB A:GLU325 4.8 12.2 1.0 C5 A:NDG403 4.8 15.7 0.5 CA A:ASN337 4.8 9.3 1.0 C2 A:NDG403 4.9 15.2 0.5 CA A:ASN317 4.9 22.3 1.0 C A:SER319 5.0 27.6 1.0

Calcium binding site 2 out of 2 in the Structure of Carbohydrate Recognition Domain with Glcnac Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Carbohydrate Recognition Domain with Glcnac Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:22.8 occ:1.00 OD2 A:ASP291 2.3 19.3 1.0 O A:HOH528 2.3 21.1 1.0 OE2 A:GLU295 2.6 32.7 1.0 OE1 A:GLU295 2.6 30.0 1.0 O A:GLU325 2.6 15.6 1.0 OD1 A:ASN318 2.7 24.4 1.0 OD1 A:ASP291 2.7 17.1 1.0 OD1 A:ASN326 2.8 18.8 1.0 CG A:ASP291 2.8 17.0 1.0 CD A:GLU295 2.9 31.8 1.0 CG A:ASN318 3.4 24.3 1.0 C A:GLU325 3.5 13.2 1.0 CA A:ASN326 3.8 12.2 1.0 CG A:ASN326 3.9 15.5 1.0 CB A:ASN318 4.0 23.8 1.0 N A:ASN326 4.1 12.2 1.0 ND2 A:ASN318 4.2 25.2 1.0 CB A:ASN326 4.3 12.9 1.0 CB A:ASP291 4.3 15.3 1.0 CG A:GLU295 4.4 30.2 1.0 N A:GLU325 4.4 14.1 1.0 O A:HOH541 4.4 26.4 1.0 CZ A:PHE298 4.5 13.2 1.0 CA A:ASN318 4.6 24.2 1.0 CA A:GLU325 4.6 13.6 1.0 N A:GLY296 4.6 25.8 1.0 OD2 A:ASP338 4.6 13.1 1.0 O A:HOH629 4.7 27.5 1.0 O A:ASP291 4.8 16.7 1.0 CA A:GLU295 4.9 28.8 1.0 C A:ASN326 5.0 10.5 1.0

J.M.Paterson, A.J.Shaw, I.Burns, A.W.Dodds, A.Prasad, K.B.Reid, T.J.Greenhough, A.K.Shrive. Atomic-Resolution Crystal Structures of the Immune Protein Conglutinin From Cow Reveal Specific Interactions of Its Binding Site Withn-Acetylglucosamine. J.Biol.Chem. V. 294 17155 2019.
ISSN: ESSN 1083-351X
PubMed: 31562242
DOI: 10.1074/JBC.RA119.010271