Calcium in PDB 9g7d: Crystal Structure of Asgpr with Bound Imp

The structure of Crystal Structure of Asgpr with Bound Imp, PDB code: 9g7d 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)	56.85 / 1.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.775, 32.689, 40.819, 90, 91.98, 90
R / Rfree (%)	18.2 / 23.1

The binding sites of Calcium atom in the Crystal Structure of Asgpr with Bound Imp (pdb code 9g7d). 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 Imp, PDB code: 9g7d:
Jump to Calcium binding site number: 1; 2; 3;

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


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 Imp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:13.0 occ:1.00 O A:HOH1141 2.3 11.2 1.0 O A:HOH1186 2.4 13.6 1.0 OD1 A:ASP253 2.4 16.6 1.0 OD1 A:ASP242 2.4 15.4 1.0 OD2 A:ASP215 2.5 13.7 1.0 O A:GLU252 2.5 10.8 1.0 OD1 A:ASP215 2.6 10.7 1.0 O A:HOH1175 2.6 20.5 1.0 CG A:ASP215 2.9 12.1 1.0 CG A:ASP242 3.3 15.5 1.0 C A:GLU252 3.4 10.1 1.0 CG A:ASP253 3.5 15.7 1.0 CA A:ASP253 3.8 9.6 1.0 N A:ASP253 4.0 9.5 1.0 CB A:ASP242 4.0 12.2 1.0 OD2 A:ASP242 4.1 18.0 1.0 CB A:ASP253 4.1 10.0 1.0 N A:GLU252 4.2 9.6 1.0 O A:HOH1127 4.4 17.3 1.0 O A:HOH1272 4.4 15.0 1.0 CB A:ASP215 4.4 11.2 1.0 O A:HOH1162 4.4 55.1 0.5 O A:HOH1173 4.4 9.7 1.0 OD2 A:ASP253 4.4 18.0 1.0 CA A:GLU252 4.5 9.8 1.0 O A:HOH1105 4.6 10.1 1.0 CA A:ASP242 4.6 11.8 1.0 OD2 A:ASP265 4.6 12.6 1.0 O A:ASP215 4.7 11.5 1.0 CZ2 A:TRP220 4.8 13.4 1.0 O A:HOH1109 4.8 17.2 1.0

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


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 Imp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:11.9 occ:0.93 OD1 A:ASP265 2.3 9.1 1.0 OE2 A:GLU252 2.4 12.6 1.0 OD1 A:ASP241 2.5 10.4 1.0 OD1 A:ASN264 2.5 13.0 1.0 OE1 A:GLN239 2.6 15.4 1.0 O A:ASP265 2.6 9.6 1.0 O2' A:IMP1004 2.7 11.7 0.7 O3' A:IMP1004 2.7 9.9 0.7 CD A:GLU252 3.4 13.6 1.0 CG A:ASP265 3.4 11.2 1.0 CG A:ASP241 3.4 13.1 1.0 CG A:ASN264 3.5 12.3 1.0 CD A:GLN239 3.5 15.7 1.0 C3' A:IMP1004 3.6 12.1 0.7 C2' A:IMP1004 3.6 12.5 0.7 C A:ASP265 3.7 9.6 1.0 ND2 A:ASN264 3.8 10.6 1.0 OD2 A:ASP241 3.8 15.0 1.0 N A:ASP265 3.8 10.6 1.0 OE1 A:GLU252 3.9 12.9 1.0 NE2 A:GLN239 4.0 14.9 1.0 OD2 A:ASP265 4.1 12.6 1.0 C4' A:IMP1004 4.1 14.2 0.7 CA A:ASP265 4.1 9.5 1.0 N A:ASP241 4.2 14.3 1.0 CB A:ASP265 4.3 8.1 1.0 CG A:GLU252 4.6 13.1 1.0 CB A:GLU252 4.6 10.5 1.0 CG A:GLN239 4.6 15.9 1.0 CB A:ASP241 4.6 11.5 1.0 CB A:ASN264 4.8 11.4 1.0 C A:ASN264 4.8 11.3 1.0 N A:ASP242 4.8 11.9 1.0 CB A:TRP243 4.8 13.3 1.0 N A:ASP266 4.8 9.6 1.0 C1' A:IMP1004 4.8 14.2 0.7 CA A:ASP241 4.9 12.8 1.0 N A:TRP243 4.9 12.2 1.0 CA A:ASN264 5.0 11.9 1.0

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


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 Imp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:18.6 occ:1.00 OE1 A:GLU196 2.2 20.9 1.0 O A:VAL190 2.3 14.7 1.0 O A:HOH1132 2.4 22.5 1.0 OE2 A:GLU277 2.5 20.3 1.0 O A:HOH1146 2.5 14.6 1.0 O A:HOH1232 2.7 23.5 1.0 OE1 A:GLU277 2.7 18.4 1.0 OE2 A:GLU196 2.9 25.1 1.0 CD A:GLU196 2.9 23.7 1.0 CD A:GLU277 2.9 20.2 1.0 C A:VAL190 3.6 13.9 1.0 OH A:TYR165 4.2 16.7 1.0 CB A:VAL190 4.3 11.2 1.0 CA A:VAL190 4.3 11.6 1.0 N A:VAL190 4.3 10.6 1.0 CG A:GLU196 4.4 23.1 1.0 CG A:GLU277 4.4 18.2 1.0 OG1 A:THR192 4.5 22.3 1.0 O A:HOH1284 4.5 44.1 1.0 N A:VAL191 4.6 14.6 1.0 OG A:SER163 4.6 25.4 1.0 O A:HOH1208 4.6 36.3 1.0 CA A:VAL191 4.8 16.7 1.0 OE1 A:GLU279 4.8 34.1 1.0 CG1 A:VAL190 4.8 11.3 1.0 O A:HOH1200 4.9 26.1 1.0 N A:THR192 4.9 19.4 1.0 O A:HOH1150 5.0 24.2 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