Calcium in PDB 6yau: Crystal Structure of Asgpr 1 in Complex with Gn-A.

The structure of Crystal Structure of Asgpr 1 in Complex with Gn-A., PDB code: 6yau was solved by H.A.Schreuder, A.Liesum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.25 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	114.75, 32.53, 39.65, 90, 93.82, 90
R / Rfree (%)	17.2 / 21.9

The binding sites of Calcium atom in the Crystal Structure of Asgpr 1 in Complex with Gn-A. (pdb code 6yau). 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 1 in Complex with Gn-A., PDB code: 6yau:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Asgpr 1 in Complex with Gn-A.


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 1 in Complex with Gn-A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:14.2 occ:0.95 O A:HOH1120 2.3 14.6 1.0 OD2 A:ASP215 2.4 17.6 1.0 OD1 A:ASP215 2.4 17.2 1.0 OD1 A:ASP242 2.4 18.5 1.0 OD1 A:ASP253 2.5 15.3 1.0 O A:HOH1179 2.5 30.3 1.0 O A:HOH1148 2.5 27.8 1.0 O A:GLU252 2.6 13.8 1.0 CG A:ASP215 2.7 17.3 1.0 CG A:ASP242 3.3 20.7 1.0 C A:GLU252 3.5 14.9 1.0 CG A:ASP253 3.7 14.8 1.0 CA A:ASP253 3.8 10.1 1.0 O A:HOH1151 3.9 29.3 1.0 CB A:ASP242 4.0 11.2 1.0 N A:ASP253 4.2 11.0 1.0 OD2 A:ASP242 4.2 18.7 1.0 CB A:ASP253 4.2 11.4 1.0 CB A:ASP215 4.3 13.7 1.0 N A:GLU252 4.4 12.5 1.0 O A:HOH1102 4.4 27.2 1.0 O A:ASP215 4.4 16.6 1.0 CA A:ASP242 4.5 10.7 1.0 CZ2 A:TRP220 4.5 13.1 1.0 OD2 A:ASP265 4.6 12.5 1.0 CA A:GLU252 4.6 11.8 1.0 OD2 A:ASP253 4.7 17.9 1.0 O A:HOH1104 4.7 18.2 1.0 CE2 A:TRP220 4.9 14.7 1.0 O A:HOH1106 4.9 31.1 1.0 C A:ASP215 5.0 17.6 1.0 C A:ASP253 5.0 13.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Asgpr 1 in Complex with Gn-A.


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 1 in Complex with Gn-A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:13.6 occ:1.00 OD1 A:ASP265 2.3 12.5 1.0 OE2 A:GLU252 2.4 13.3 1.0 OD1 A:ASP241 2.4 15.1 1.0 OD1 A:ASN264 2.5 12.2 1.0 OE1 A:GLN239 2.5 12.7 1.0 O A:ASP265 2.5 10.6 1.0 O25 A:OJB1004 2.5 13.0 0.9 O26 A:OJB1004 2.6 12.6 0.9 C20 A:OJB1004 3.4 13.7 0.9 CG A:ASP241 3.4 17.2 1.0 CG A:ASN264 3.4 18.0 1.0 CD A:GLU252 3.4 19.3 1.0 CD A:GLN239 3.4 18.6 1.0 CG A:ASP265 3.4 15.5 1.0 C21 A:OJB1004 3.5 12.5 0.9 C A:ASP265 3.6 11.5 1.0 ND2 A:ASN264 3.7 9.1 1.0 OD2 A:ASP241 3.8 14.8 1.0 N A:ASP265 3.8 8.6 1.0 OE1 A:GLU252 3.8 14.9 1.0 NE2 A:GLN239 3.9 19.9 1.0 CA A:ASP265 4.1 7.4 1.0 N A:ASP241 4.2 14.2 1.0 OD2 A:ASP265 4.2 12.5 1.0 C22 A:OJB1004 4.3 14.7 0.9 CB A:ASP265 4.3 8.5 1.0 CB A:ASP241 4.6 13.7 1.0 CG A:GLN239 4.6 11.6 1.0 CG A:GLU252 4.6 14.4 1.0 CB A:ASN264 4.7 12.6 1.0 C A:ASN264 4.7 10.3 1.0 CB A:GLU252 4.7 12.3 1.0 CB A:TRP243 4.7 13.3 1.0 N A:ASP266 4.8 10.5 1.0 C19 A:OJB1004 4.8 14.7 0.9 N A:ASP242 4.8 12.7 1.0 CA A:ASP241 4.8 13.1 1.0 N A:TRP243 4.9 9.4 1.0 CA A:ASN264 4.9 10.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Asgpr 1 in Complex with Gn-A.


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 1 in Complex with Gn-A. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:19.0 occ:0.92 OE1 A:GLU196 2.3 20.2 1.0 O A:HOH1133 2.4 27.2 1.0 OE2 A:GLU277 2.4 22.7 1.0 O A:VAL190 2.4 16.8 1.0 O A:HOH1130 2.5 26.1 1.0 O A:HOH1216 2.5 28.0 1.0 OE1 A:GLU277 2.7 20.0 1.0 CD A:GLU277 2.9 21.9 1.0 OE2 A:GLU196 2.9 20.5 1.0 CD A:GLU196 2.9 22.6 1.0 C A:VAL190 3.6 17.5 1.0 OH A:TYR165 4.2 20.0 1.0 CA A:VAL190 4.4 15.0 1.0 N A:VAL190 4.4 15.0 1.0 CG A:GLU196 4.4 19.5 1.0 CG A:GLU277 4.4 19.5 1.0 O A:HOH1267 4.4 56.8 1.0 CB A:VAL190 4.4 18.2 1.0 OG A:SER163 4.5 28.4 1.0 OG1 A:THR192 4.5 24.6 1.0 O A:HOH1159 4.6 34.4 1.0 OE1 A:GLU279 4.6 40.9 1.0 N A:VAL191 4.6 15.6 1.0 O A:HOH1207 4.8 32.2 1.0 CA A:VAL191 4.8 16.2 1.0 CG1 A:VAL190 4.8 18.4 1.0 N A:THR192 4.9 21.6 1.0 CE2 A:TYR165 4.9 17.7 1.0 CZ A:TYR165 5.0 21.6 1.0

A.Mishra, T.R.Castaneda, E.Bader, B.Elshorst, S.Cummings, P.Scherer, D.S.Bangari, C.Loewe, H.Schreuder, C.Poverlein, M.Helms, S.Jones, G.Zech, T.Licher, M.Wagner, M.Schudok, M.De Hoop, A.T.Plowright, J.Atzrodt, A.Kannt, I.Laitinen, V.Derdau. Triantennary Galnac Molecular Imaging Probes For Monitoring Hepatocyte Function in A Rat Model of Nonalcoholic Steatohepatitis. Adv Sci V. 7 02997 2020.
ISSN: ESSN 2198-3844
PubMed: 33344141
DOI: 10.1002/ADVS.202002997