Calcium in PDB 6ryn: Structure of Conglutinin Carbohydrate Recognition Domain with Glcnac- Alpha-1-Phosphate Bound

The structure of Structure of Conglutinin Carbohydrate Recognition Domain with Glcnac- Alpha-1-Phosphate Bound, PDB code: 6ryn 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)	50.00 / 1.00
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	50.278, 50.278, 52.192, 90.00, 90.00, 90.00
R / Rfree (%)	12.4 / 14

The binding sites of Calcium atom in the Structure of Conglutinin Carbohydrate Recognition Domain with Glcnac- Alpha-1-Phosphate Bound (pdb code 6ryn). 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 Conglutinin Carbohydrate Recognition Domain with Glcnac- Alpha-1-Phosphate Bound, PDB code: 6ryn:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Conglutinin Carbohydrate Recognition Domain with Glcnac- Alpha-1-Phosphate 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 Conglutinin Carbohydrate Recognition Domain with Glcnac- Alpha-1-Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:11.0 occ:1.00 OD1 A:ASP338 2.3 11.2 1.0 OD1 A:ASN337 2.4 9.8 1.0 OD1 A:ASN317 2.4 15.7 1.0 OE1 A:GLU325 2.4 12.2 1.0 O4' A:GN1403 2.5 11.7 1.0 O A:ASP338 2.5 9.9 1.0 OE1 A:GLU315 2.6 11.4 1.0 O3' A:GN1403 2.6 11.8 1.0 C4' A:GN1403 3.3 12.2 1.0 CG A:ASP338 3.4 10.6 1.0 CD A:GLU315 3.4 10.4 1.0 CG A:ASN337 3.4 8.7 1.0 CD A:GLU325 3.4 11.7 1.0 C3' A:GN1403 3.4 11.7 1.0 CG A:ASN317 3.4 19.6 1.0 C A:ASP338 3.5 8.8 1.0 N A:ASP338 3.6 8.6 1.0 OE2 A:GLU315 3.7 11.0 1.0 OE2 A:GLU325 3.8 12.9 1.0 ND2 A:ASN337 3.9 10.2 1.0 O A:HOH555 3.9 24.2 1.0 CA A:ASP338 3.9 8.9 1.0 N A:ASN317 4.2 20.8 1.0 ND2 A:ASN317 4.2 23.6 1.0 CB A:ASP338 4.2 9.9 1.0 OD2 A:ASP338 4.3 12.8 1.0 CB A:ASN317 4.4 22.6 1.0 C A:ASN337 4.4 7.8 1.0 CG A:GLU315 4.6 10.8 1.0 CG A:GLU325 4.7 12.1 1.0 CB A:ASN337 4.7 7.6 1.0 N A:VAL339 4.7 8.3 1.0 C5' A:GN1403 4.8 12.4 1.0 CA A:ASN337 4.8 7.5 1.0 C2' A:GN1403 4.8 12.1 1.0 CB A:GLU325 4.8 11.3 1.0 CA A:ASN317 4.9 30.8 1.0

Calcium binding site 2 out of 2 in the Structure of Conglutinin Carbohydrate Recognition Domain with Glcnac- Alpha-1-Phosphate 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 Conglutinin Carbohydrate Recognition Domain with Glcnac- Alpha-1-Phosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:36.7 occ:1.00 O A:HOH552 2.1 26.9 1.0 OD2 A:ASP291 2.3 22.1 1.0 OE2 A:GLU295 2.8 57.3 1.0 OD1 A:ASP291 2.8 19.5 1.0 OE1 A:GLU295 2.8 58.0 1.0 CG A:ASP291 2.9 17.7 1.0 O A:GLU325 2.9 14.3 1.0 CD A:GLU295 3.1 49.7 1.0 OD1 A:ASN326 3.2 22.2 1.0 C A:GLU325 3.7 11.2 1.0 CA A:ASN326 3.9 10.4 1.0 CG A:ASN326 4.2 15.5 1.0 N A:ASN326 4.2 10.3 1.0 CB A:ASP291 4.4 15.3 1.0 CZ A:PHE298 4.5 15.4 1.0 CG A:GLU295 4.5 48.2 1.0 N A:GLY296 4.5 30.2 1.0 N A:GLU325 4.5 15.9 1.0 CB A:ASN326 4.6 12.1 1.0 OD2 A:ASP338 4.6 12.8 1.0 O A:HOH557 4.7 34.6 1.0 CA A:GLU325 4.7 11.8 1.0 CA A:GLU295 4.9 39.1 1.0 C A:ASN326 5.0 8.9 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