Calcium in PDB 1dv8: Crystal Structure of the Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor

The structure of Crystal Structure of the Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor, PDB code: 1dv8 was solved by M.Meier, M.D.Bider, V.N.Malashkevich, M.Spiess, P.Burkhard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.35 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.720, 32.460, 40.820, 90.00, 91.29, 90.00
R / Rfree (%)	19.5 / 24.7

The structure of Crystal Structure of the Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor (pdb code 1dv8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor, PDB code: 1dv8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor


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 Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:14.8 occ:1.00 O A:HOH14 2.2 25.6 1.0 O A:HOH3 2.2 4.7 1.0 OD1 A:ASP242 2.3 14.4 1.0 O A:HOH10 2.3 6.6 1.0 OD1 A:ASP253 2.4 21.8 1.0 OD2 A:ASP215 2.4 14.3 1.0 O A:GLU252 2.5 12.4 1.0 OD1 A:ASP215 2.7 9.9 1.0 CG A:ASP215 2.9 12.3 1.0 CG A:ASP242 3.2 16.2 1.0 C A:GLU252 3.4 14.7 1.0 CG A:ASP253 3.5 20.0 1.0 CA A:ASP253 3.8 15.4 1.0 N A:ASP253 3.9 14.2 1.0 OD2 A:ASP242 3.9 17.7 1.0 CB A:ASP242 4.1 15.1 1.0 O A:HOH18 4.1 19.1 1.0 O A:HOH2 4.1 12.1 1.0 CB A:ASP253 4.1 16.5 1.0 N A:GLU252 4.2 14.8 1.0 O A:HOH92 4.3 39.0 0.5 CB A:ASP215 4.4 11.2 1.0 CA A:GLU252 4.4 15.0 1.0 OD2 A:ASP253 4.5 21.2 1.0 O A:HOH12 4.6 18.6 1.0 CA A:ASP242 4.7 17.8 1.0 O A:ASP215 4.7 13.6 1.0 O A:HOH6 4.8 16.5 1.0 OD2 A:ASP265 4.8 14.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor


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 Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:14.3 occ:1.00 OD1 A:ASP265 2.3 12.8 1.0 OE2 A:GLU252 2.4 13.8 1.0 O A:ASP265 2.4 15.6 1.0 OD1 A:ASN264 2.4 15.1 1.0 OD1 A:ASP241 2.5 15.6 1.0 OE1 A:GLN239 2.7 19.5 1.0 O A:HOH13 2.8 15.2 1.0 O A:HOH11 3.0 18.6 1.0 CG A:ASP241 3.3 18.9 1.0 CD A:GLU252 3.3 15.3 1.0 CG A:ASP265 3.4 13.2 1.0 CG A:ASN264 3.4 14.2 1.0 CD A:GLN239 3.5 18.5 1.0 C A:ASP265 3.6 14.6 1.0 OE1 A:GLU252 3.7 16.0 1.0 OD2 A:ASP241 3.7 18.4 1.0 N A:ASP265 3.8 16.0 1.0 ND2 A:ASN264 3.8 15.0 1.0 NE2 A:GLN239 3.8 17.1 1.0 CA A:ASP265 4.1 15.1 1.0 OD2 A:ASP265 4.1 14.2 1.0 N A:ASP241 4.2 19.6 1.0 CB A:ASP265 4.4 13.6 1.0 CB A:ASP241 4.5 18.1 1.0 CG A:GLU252 4.6 14.6 1.0 N A:ASP242 4.7 17.1 1.0 N A:ASP266 4.7 14.1 1.0 CG A:GLN239 4.7 20.3 1.0 C A:ASN264 4.7 16.0 1.0 CB A:GLU252 4.7 13.4 1.0 CA A:ASP241 4.7 18.9 1.0 CB A:TRP243 4.8 20.2 1.0 CB A:ASN264 4.8 14.0 1.0 N A:TRP243 4.8 18.5 1.0 C A:ASP241 4.9 17.5 1.0 CA A:ASN264 5.0 14.9 1.0 CA A:ASP266 5.0 13.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:18.9 occ:1.00 O A:HOH84 2.1 28.1 1.0 OE1 A:GLU196 2.2 22.2 1.0 O A:VAL190 2.2 20.0 1.0 O A:HOH46 2.5 25.4 1.0 O A:HOH20 2.5 19.4 1.0 OE2 A:GLU277 2.5 24.0 1.0 OE1 A:GLU277 2.7 25.5 1.0 OE2 A:GLU196 2.7 20.2 1.0 CD A:GLU196 2.8 21.3 1.0 CD A:GLU277 3.0 25.6 1.0 C A:VAL190 3.4 19.2 1.0 CB A:VAL190 4.1 17.8 1.0 CA A:VAL190 4.1 16.9 1.0 OH A:TYR165 4.2 20.2 1.0 N A:VAL190 4.3 16.3 1.0 CG A:GLU196 4.3 21.4 1.0 N A:VAL191 4.4 19.9 1.0 CG A:GLU277 4.5 23.1 1.0 O A:HOH103 4.5 41.6 1.0 CG1 A:VAL190 4.5 19.9 1.0 CA A:VAL191 4.6 22.1 1.0 OG1 A:THR192 4.6 28.6 1.0 N A:THR192 4.7 25.8 1.0 OG A:SER163 4.7 37.2 1.0 OE1 A:GLU279 4.7 36.3 1.0 CE2 A:TYR165 5.0 21.4 1.0

M.Meier, M.D.Bider, V.N.Malashkevich, M.Spiess, P.Burkhard. Crystal Structure of the Carbohydrate Recognition Domain of the H1 Subunit of the Asialoglycoprotein Receptor. J.Mol.Biol. V. 300 857 2000.
ISSN: ISSN 0022-2836
PubMed: 10891274
DOI: 10.1006/JMBI.2000.3853