Calcium in PDB 9g76: Crystal Structure of Asgpr with Bound Galnac

The structure of Crystal Structure of Asgpr with Bound Galnac, PDB code: 9g76 was solved by H.A.Schreuder, A.Hofmeister, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.68 / 1.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.082, 32.641, 40.702, 90, 91.89, 90
R / Rfree (%)	19.9 / 23.3

The binding sites of Calcium atom in the Crystal Structure of Asgpr with Bound Galnac (pdb code 9g76). 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 Asgpr with Bound Galnac, PDB code: 9g76:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Asgpr with Bound Galnac


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 Asgpr with Bound Galnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:9.1 occ:1.00 O A:HOH1107 2.3 23.9 1.0 OD1 A:ASP253 2.4 9.6 1.0 O A:GLU252 2.4 7.9 1.0 OD1 A:ASP242 2.4 10.3 1.0 OD2 A:ASP215 2.4 12.4 1.0 O A:HOH1116 2.4 8.7 1.0 OD1 A:ASP215 2.6 10.2 1.0 CG A:ASP215 2.9 9.9 1.0 O A:HOH1256 3.3 88.0 1.0 CG A:ASP242 3.3 11.0 1.0 C A:GLU252 3.4 8.1 1.0 CG A:ASP253 3.5 11.8 1.0 CA A:ASP253 3.8 8.3 1.0 C2 A:GOL1004 3.8 8.5 0.5 N A:ASP253 4.0 8.0 1.0 CB A:ASP242 4.0 9.7 1.0 C3 A:GOL1004 4.1 9.6 0.5 CB A:ASP253 4.1 9.3 1.0 N A:GLU252 4.2 8.2 1.0 OD2 A:ASP242 4.2 10.7 1.0 O A:HOH1154 4.3 19.0 1.0 O2 A:GOL1004 4.3 10.1 0.5 CB A:ASP215 4.4 8.9 1.0 CA A:GLU252 4.4 7.6 1.0 OD2 A:ASP253 4.5 12.9 1.0 O A:HOH1275 4.5 13.2 1.0 CA A:ASP242 4.5 8.3 1.0 O A:ASP215 4.6 9.7 1.0 O A:HOH1205 4.6 14.3 1.0 OD2 A:ASP265 4.6 7.9 1.0 O3 A:GOL1004 4.6 13.0 0.5 O1 A:GOL1004 4.7 8.6 0.5 O A:HOH1115 4.7 18.4 1.0 CZ2 A:TRP220 4.8 10.9 1.0 C1 A:GOL1004 4.9 10.1 0.5 C A:ASP253 5.0 8.6 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Asgpr with Bound Galnac


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 Asgpr with Bound Galnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:8.6 occ:1.00 OE2 A:GLU252 2.3 10.1 1.0 OD1 A:ASP265 2.4 7.3 1.0 OD1 A:ASP241 2.4 8.4 1.0 OD1 A:ASN264 2.5 9.0 1.0 O A:ASP265 2.5 7.0 1.0 OE1 A:GLN239 2.5 10.6 1.0 O3 A:NGA1006 2.6 8.1 0.4 O4 A:NGA1006 2.6 7.8 0.4 O4 A:A2G1005 2.6 9.7 0.6 O3 A:A2G1005 2.6 10.2 0.6 CD A:GLU252 3.4 9.5 1.0 C4 A:NGA1006 3.4 8.7 0.4 C4 A:A2G1005 3.4 11.3 0.6 CG A:ASP265 3.4 8.9 1.0 CG A:ASP241 3.4 11.6 1.0 CG A:ASN264 3.5 8.9 1.0 CD A:GLN239 3.5 15.4 1.0 C3 A:NGA1006 3.5 8.5 0.4 C3 A:A2G1005 3.5 11.0 0.6 C A:ASP265 3.6 6.8 1.0 OE1 A:GLU252 3.8 11.1 1.0 OD2 A:ASP241 3.8 11.1 1.0 N A:ASP265 3.8 7.3 1.0 ND2 A:ASN264 3.8 8.7 1.0 NE2 A:GLN239 4.0 18.9 1.0 CA A:ASP265 4.1 7.0 1.0 OD2 A:ASP265 4.2 7.9 1.0 C2 A:A2G1005 4.2 11.9 0.6 C2 A:NGA1006 4.3 8.9 0.4 N A:ASP241 4.3 9.8 1.0 CB A:ASP265 4.3 7.3 1.0 CG A:GLU252 4.6 7.1 1.0 CB A:ASP241 4.6 10.3 1.0 CB A:GLU252 4.6 7.2 1.0 CG A:GLN239 4.7 13.6 1.0 N A:ASP266 4.7 6.5 1.0 CB A:TRP243 4.8 11.5 1.0 CB A:ASN264 4.8 9.6 1.0 N A:ASP242 4.8 9.1 1.0 C5 A:NGA1006 4.8 9.1 0.4 C A:ASN264 4.8 7.8 1.0 C5 A:A2G1005 4.8 12.5 0.6 CA A:ASP241 4.8 9.8 1.0 N A:TRP243 4.9 8.8 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Asgpr with Bound Galnac


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 Asgpr with Bound Galnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:13.7 occ:1.00 OE2 A:GLU277 2.4 15.2 1.0 O A:VAL190 2.4 13.2 1.0 O A:HOH1194 2.4 19.9 1.0 O A:HOH1226 2.4 20.1 1.0 OE1 A:GLU196 2.4 14.1 1.0 O A:HOH1131 2.5 19.2 1.0 OE1 A:GLU277 2.7 12.7 1.0 CD A:GLU277 2.9 14.8 1.0 OE2 A:GLU196 2.9 15.3 1.0 CD A:GLU196 3.0 13.1 1.0 C A:VAL190 3.6 12.0 1.0 OH A:TYR165 4.2 13.7 1.0 CA A:VAL190 4.3 11.5 1.0 N A:VAL190 4.3 10.4 1.0 CB A:VAL190 4.4 11.9 1.0 CG A:GLU277 4.4 12.0 1.0 O A:HOH1201 4.4 29.3 1.0 O A:HOH1307 4.5 52.5 1.0 CG A:GLU196 4.5 13.5 1.0 N A:VAL191 4.6 11.9 1.0 OG1 A:THR192 4.6 17.5 1.0 OG A:SER163 4.6 20.6 1.0 OE1 A:GLU279 4.6 32.1 1.0 O A:HOH1216 4.7 26.8 1.0 CA A:VAL191 4.7 12.4 1.0 CG1 A:VAL190 4.8 12.6 1.0 N A:THR192 4.8 13.9 1.0 O A:HOH1173 5.0 25.0 1.0

A.Hofmeister, K.Jahn-Hofmann, B.Brunner, M.Helms, C.Metz-Weidmann, C.Poeverlein, G.Zech, Z.Li, G.Hessler, H.Schreuder, B.Elshorst, A.Krack, M.Kurz, C.Heubel, S.Scheidler. Trivalent Sirna-Conjugates with Guanosine As Asgpr-Binder Show Potent Knock-Down in Vivo. J.Med.Chem. 2025.
ISSN: ISSN 0022-2623
PubMed: 40052708
DOI: 10.1021/ACS.JMEDCHEM.4C02275