Calcium in PDB 6pws: Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside

The structure of Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside, PDB code: 6pws was solved by W.I.Weis, H.Feinberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.53 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.553, 45.915, 69.273, 90.00, 90.00, 90.00
R / Rfree (%)	11.5 / 12.8

The binding sites of Calcium atom in the Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside (pdb code 6pws). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside, PDB code: 6pws:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:4.7 occ:1.00 OD1 A:ASP272 2.4 4.5 1.0 OE1 A:GLU259 2.4 5.5 1.0 OD1 A:ASN253 2.4 5.3 1.0 OD1 A:ASN271 2.5 5.3 1.0 O3 A:MMA303 2.5 5.6 0.5 O A:ASP272 2.5 4.8 1.0 OE1 A:GLU251 2.5 5.2 1.0 O4 A:MMA303 2.5 5.8 0.5 O3 A:MMA303 2.6 5.1 0.5 O4 A:MMA303 2.6 7.7 0.5 HO4 A:MMA303 3.0 7.0 0.5 HO3 A:MMA303 3.1 6.7 0.5 HO4 A:MMA303 3.2 9.2 0.5 HO3 A:MMA303 3.2 6.2 0.5 CD A:GLU251 3.4 4.9 1.0 C4 A:MMA303 3.4 6.0 0.5 C3 A:MMA303 3.4 6.8 0.5 CG A:ASP272 3.4 4.3 1.0 CD A:GLU259 3.4 5.6 1.0 C3 A:MMA303 3.4 7.8 0.5 CG A:ASN253 3.4 5.6 1.0 H A:ASN253 3.4 5.8 1.0 C4 A:MMA303 3.4 7.4 0.5 CG A:ASN271 3.5 5.3 1.0 C A:ASP272 3.5 4.2 1.0 H3 A:MMA303 3.6 9.4 0.5 HD21 A:ASN271 3.6 8.4 1.0 H4 A:MMA303 3.6 8.9 0.5 H A:ASP272 3.6 5.0 1.0 H4 A:MMA303 3.6 7.1 0.5 H3 A:MMA303 3.6 8.2 0.5 HD21 A:ASN253 3.6 7.9 1.0 OE2 A:GLU251 3.7 5.9 1.0 OE2 A:GLU259 3.8 7.2 1.0 N A:ASP272 3.9 4.2 1.0 ND2 A:ASN253 3.9 6.6 1.0 ND2 A:ASN271 3.9 7.0 1.0 H A:ALA255 4.0 7.1 1.0 CA A:ASP272 4.1 4.2 1.0 HB3 A:ALA255 4.1 9.3 1.0 OD2 A:ASP272 4.2 4.9 1.0 N A:ASN253 4.2 4.8 1.0 CB A:ASP272 4.3 4.3 1.0 HA A:PRO252 4.3 5.4 1.0 H A:ASP254 4.3 6.0 1.0 HB2 A:ALA255 4.3 9.3 1.0 HB2 A:GLU259 4.4 5.8 1.0 HA A:ALA273 4.5 6.0 1.0 HB3 A:GLU259 4.5 5.8 1.0 HA A:ASN271 4.5 5.3 1.0 HB3 A:GLU251 4.6 5.7 1.0 CG A:GLU251 4.6 5.0 1.0 CB A:ASN253 4.6 5.6 1.0 C A:ASN271 4.6 4.1 1.0 CG A:GLU259 4.6 5.2 1.0 CB A:ALA255 4.7 7.7 1.0 N A:ALA273 4.7 4.6 1.0 C2 A:MMA303 4.7 11.3 0.5 HD22 A:ASN253 4.7 7.9 1.0 HG3 A:GLU251 4.7 6.0 1.0 CB A:ASN271 4.7 4.8 1.0 HD22 A:ASN271 4.7 8.4 1.0 N A:ASP254 4.8 5.0 1.0 CB A:GLU259 4.8 4.8 1.0 C2 A:MMA303 4.8 8.9 0.5 C5 A:MMA303 4.8 8.4 0.5 HB2 A:ASP272 4.8 5.2 1.0 N A:ALA255 4.8 5.9 1.0 CA A:ASN253 4.8 5.2 1.0 HA A:GLU251 4.8 5.4 1.0 CA A:ASN271 4.9 4.4 1.0 C5 A:MMA303 4.9 15.7 0.5 H5 A:MMA303 4.9 10.1 0.5 HB3 A:ASN253 4.9 6.8 1.0 O2 A:MMA303 4.9 19.8 0.5 HB3 A:ASP272 5.0 5.2 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Cow C-Type Carbohydrate-Recognition Domain of CD23 in the Presence of Alpha-Methyl Mannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:4.8 occ:1.00 O A:HOH454 2.4 5.7 1.0 OE1 A:GLU231 2.4 6.3 1.0 OD1 A:ASN260 2.5 5.4 1.0 OD1 A:ASP254 2.5 5.5 1.0 O A:GLU259 2.5 5.0 1.0 OD2 A:ASP227 2.5 5.6 1.0 OE2 A:GLU231 2.6 6.3 1.0 OD1 A:ASP227 2.6 5.4 1.0 CD A:GLU231 2.8 6.2 1.0 CG A:ASP227 2.9 5.2 1.0 HA A:ASN260 3.0 5.5 1.0 CG A:ASP254 3.4 5.1 1.0 C A:GLU259 3.4 4.6 1.0 CG A:ASN260 3.6 5.0 1.0 H A:GLU259 3.6 5.9 1.0 CA A:ASN260 3.8 4.6 1.0 HB2 A:ASP254 3.8 6.5 1.0 H A:GLY232 4.0 8.0 1.0 O A:HOH491 4.0 8.1 1.0 N A:ASN260 4.0 4.4 1.0 HA A:ASP254 4.1 6.4 1.0 CB A:ASN260 4.1 4.9 1.0 CB A:ASP254 4.1 5.5 1.0 OD2 A:ASP254 4.1 6.3 1.0 HA A:GLU231 4.2 8.3 1.0 HB3 A:ASN260 4.2 5.9 1.0 HZ A:PHE234 4.2 8.5 1.0 N A:GLU259 4.2 5.0 1.0 CG A:GLU231 4.4 6.8 1.0 CB A:ASP227 4.4 5.0 1.0 CA A:GLU259 4.5 4.8 1.0 OD2 A:ASP272 4.5 4.9 1.0 O A:HOH594 4.6 7.3 1.0 CA A:ASP254 4.7 5.3 1.0 ND2 A:ASN260 4.7 5.7 1.0 HB2 A:GLU259 4.7 5.8 1.0 HG3 A:GLU231 4.7 8.2 1.0 HB2 A:ASP227 4.7 5.9 1.0 N A:GLY232 4.7 6.7 1.0 O A:ASP227 4.8 6.3 1.0 HD21 A:ASN260 4.8 6.9 1.0 HB3 A:ASP227 4.8 5.9 1.0 HG2 A:GLU231 4.8 8.2 1.0 O A:HOH407 4.8 8.0 1.0 CZ A:PHE234 4.8 7.1 1.0 HB2 A:ASP272 4.8 5.2 1.0 H A:ASN260 4.9 5.3 1.0 HB3 A:ASP254 5.0 6.5 1.0 HA2 A:GLY258 5.0 7.3 1.0 CA A:GLU231 5.0 7.0 1.0

S.A.F.Jegouzo, H.Feinberg, A.G.Morrison, A.Holder, A.May, Z.Huang, L.Jiang, Y.Lasanajak, D.F.Smith, D.Werling, K.Drickamer, W.I.Weis, M.E.Taylor. CD23 Is A Glycan-Binding Receptor in Some Mammalian Species. J.Biol.Chem. V. 294 14845 2019.
ISSN: ESSN 1083-351X
PubMed: 31488546
DOI: 10.1074/JBC.RA119.010572