Calcium in PDB 8urf: Crystal Structure of Human ASGR2 Crd (Carbohydrate Recognition Domain) Bound to 8G8 Fab

The structure of Crystal Structure of Human ASGR2 Crd (Carbohydrate Recognition Domain) Bound to 8G8 Fab, PDB code: 8urf was solved by P.Sampathumar, Y.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.54 / 1.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	102.41, 102.41, 358.985, 90, 90, 120
R / Rfree (%)	16.6 / 20.4

The structure of Crystal Structure of Human ASGR2 Crd (Carbohydrate Recognition Domain) Bound to 8G8 Fab also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Human ASGR2 Crd (Carbohydrate Recognition Domain) Bound to 8G8 Fab (pdb code 8urf). 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 Human ASGR2 Crd (Carbohydrate Recognition Domain) Bound to 8G8 Fab, PDB code: 8urf:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Human ASGR2 Crd (Carbohydrate Recognition Domain) Bound to 8G8 Fab


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 Human ASGR2 Crd (Carbohydrate Recognition Domain) Bound to 8G8 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:39.4 occ:1.00 OD1 A:ASN266 2.3 40.9 1.0 OD2 A:ASP239 2.4 40.0 1.0 O A:HOH509 2.4 35.7 1.0 OD1 A:ASP277 2.4 46.5 1.0 O A:GLU276 2.4 40.1 1.0 O A:HOH562 2.5 41.2 1.0 OD1 A:ASP239 2.6 40.3 1.0 CG A:ASP239 2.8 42.1 1.0 CG A:ASN266 3.3 47.0 1.0 C A:GLU276 3.4 40.0 1.0 CG A:ASP277 3.5 45.0 1.0 O A:HOH577 3.6 59.7 1.0 CA A:ASP277 3.7 34.9 1.0 CB A:ASN266 4.0 38.2 1.0 N A:ASP277 4.0 36.5 1.0 CB A:ASP277 4.0 36.8 1.0 OG A:SER275 4.2 47.2 1.0 CA A:ASN266 4.3 37.1 1.0 ND2 A:ASN266 4.3 45.2 1.0 CB A:ASP239 4.3 39.2 1.0 OD2 A:ASP277 4.5 46.5 1.0 O A:HOH581 4.5 41.9 1.0 OD2 A:ASP289 4.5 33.6 1.0 N A:GLU276 4.6 38.0 1.0 CA A:GLU276 4.6 36.0 1.0 CZ2 A:TRP244 4.7 35.9 1.0 CB A:SER275 4.7 52.2 1.0 O A:HOH557 4.8 45.9 1.0 CH2 A:TRP244 4.8 35.7 1.0 O A:HOH538 4.8 49.2 1.0 O A:HOH514 4.9 61.2 1.0 C A:ASP277 4.9 39.0 1.0 C A:SER275 4.9 46.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Human ASGR2 Crd (Carbohydrate Recognition Domain) Bound to 8G8 Fab


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 Human ASGR2 Crd (Carbohydrate Recognition Domain) Bound to 8G8 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:33.4 occ:1.00 OD1 A:ASP289 2.3 32.0 1.0 OD1 A:ASN288 2.3 30.6 1.0 OE1 A:GLU276 2.4 35.0 1.0 O3 A:GOL404 2.4 35.9 1.0 O A:ASP289 2.5 32.3 1.0 OD1 A:ASP265 2.5 35.5 1.0 OE1 A:GLN263 2.5 35.7 1.0 O2 A:GOL404 2.5 33.1 1.0 CG A:ASP289 3.3 32.0 1.0 CD A:GLN263 3.3 36.2 1.0 CD A:GLU276 3.4 44.2 1.0 CG A:ASN288 3.4 33.7 1.0 C3 A:GOL404 3.4 33.1 1.0 CG A:ASP265 3.4 35.3 1.0 C2 A:GOL404 3.5 35.9 1.0 C A:ASP289 3.5 33.7 1.0 NE2 A:GLN263 3.7 32.4 1.0 OD2 A:ASP265 3.7 37.2 1.0 ND2 A:ASN288 3.8 35.5 1.0 OE2 A:GLU276 3.8 35.3 1.0 N A:ASP289 3.8 33.3 1.0 CA A:ASP289 4.1 31.9 1.0 OD2 A:ASP289 4.1 33.6 1.0 C1 A:GOL404 4.2 38.0 1.0 CB A:ASP289 4.3 34.2 1.0 N A:ASP265 4.3 38.5 1.0 CB A:GLU276 4.6 35.0 1.0 CG A:GLU276 4.6 36.9 1.0 CG A:GLN263 4.6 30.6 1.0 C A:ASN288 4.6 32.9 1.0 CB A:ASN288 4.6 28.9 1.0 CB A:ASP265 4.7 36.7 1.0 N A:ASP290 4.7 31.4 1.0 CA A:ASN288 4.8 30.6 1.0 N A:ASN266 4.8 35.8 1.0 CA A:ASP265 4.9 38.6 1.0 N A:TRP267 5.0 37.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Human ASGR2 Crd (Carbohydrate Recognition Domain) Bound to 8G8 Fab


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 Human ASGR2 Crd (Carbohydrate Recognition Domain) Bound to 8G8 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:33.6 occ:1.00 OD1 A:ASN216 2.3 39.9 1.0 O A:VAL214 2.3 31.7 1.0 OE2 A:GLU220 2.4 35.5 1.0 O A:HOH541 2.4 34.5 1.0 OE2 A:GLU301 2.5 40.0 1.0 O A:HOH559 2.5 40.5 1.0 OE1 A:GLU301 2.6 40.3 1.0 OE1 A:GLU220 2.6 31.8 1.0 CD A:GLU220 2.8 38.9 1.0 CD A:GLU301 2.9 45.1 1.0 CG A:ASN216 3.5 33.2 1.0 C A:VAL214 3.5 32.9 1.0 N A:ASN216 4.2 31.9 1.0 OH A:TYR189 4.3 36.2 1.0 CA A:VAL214 4.3 31.1 1.0 CB A:ASN216 4.3 36.7 1.0 N A:VAL214 4.4 33.4 1.0 CG A:GLU220 4.4 33.1 1.0 CB A:VAL214 4.4 31.2 1.0 CG A:GLU301 4.4 41.7 1.0 ND2 A:ASN216 4.5 33.8 1.0 N A:ILE215 4.5 30.5 1.0 CA A:ILE215 4.6 28.6 1.0 O A:HOH510 4.6 37.8 1.0 O A:HOH545 4.7 58.5 1.0 NH2 A:ARG303 4.7 95.0 1.0 CG1 A:VAL214 4.8 34.4 1.0 C A:ILE215 4.8 33.1 1.0 O A:HOH544 4.9 51.0 1.0 CG2 A:VAL213 4.9 29.1 1.0 O A:HOH501 4.9 61.1 1.0 OG A:SER187 4.9 51.0 1.0 CA A:ASN216 4.9 33.6 1.0

P.Sampathkumar, H.Jung, H.Chen, Z.Zhang, N.Suen, Y.Yang, Z.Huang, T.Lopez, R.Benisch, S.J.Lee, J.Ye, W.C.Yeh, Y.Li. Targeted Protein Degradation Systems to Enhance Wnt Signaling. Elife V. 13 2024.
ISSN: ESSN 2050-084X
PubMed: 38847394
DOI: 10.7554/ELIFE.93908