Calcium in PDB 5jq1: Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic

The structure of Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic, PDB code: 5jq1 was solved by S.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.37 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.080, 59.490, 68.650, 90.00, 93.18, 90.00
R / Rfree (%)	18.7 / 22.2

The structure of Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic (pdb code 5jq1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic, PDB code: 5jq1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:25.6 occ:1.00 O A:HOH1125 2.4 19.8 1.0 OD1 A:ASP242 2.4 21.6 1.0 O A:GLU252 2.5 24.7 1.0 OD2 A:ASP215 2.5 25.3 1.0 OD1 A:ASP253 2.6 22.9 1.0 O A:HOH1133 2.7 23.7 1.0 OD1 A:ASP215 2.7 24.2 1.0 CG A:ASP215 2.9 27.1 1.0 CG A:ASP242 3.3 23.4 1.0 C A:GLU252 3.4 25.7 1.0 CG A:ASP253 3.6 25.2 1.0 CA A:ASP253 3.8 21.1 1.0 CB A:ASP242 3.9 22.8 1.0 N A:ASP253 4.0 22.1 1.0 OD2 A:ASP242 4.1 25.0 1.0 N A:GLU252 4.2 20.4 1.0 CB A:ASP253 4.2 22.7 1.0 O A:HOH1162 4.4 25.5 1.0 O A:HOH1105 4.4 26.0 1.0 CB A:ASP215 4.4 25.1 1.0 CA A:GLU252 4.5 19.9 1.0 CA A:ASP242 4.5 21.7 1.0 OD2 A:ASP253 4.6 23.6 1.0 OD2 A:ASP265 4.6 21.0 1.0 O A:HOH1106 4.7 25.8 1.0 O A:HOH1104 4.8 27.1 1.0 CZ2 A:TRP220 4.8 26.7 1.0 O A:ASP215 4.9 25.6 1.0 C A:ASP253 5.0 25.0 1.0

Calcium binding site 2 out of 6 in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:23.1 occ:1.00 H15 A:ZPF1004 1.7 21.2 0.0 H14 A:ZPF1004 1.8 23.9 0.0 OD1 A:ASP265 2.4 18.9 1.0 OE2 A:GLU252 2.4 23.1 1.0 O5 A:ZPF1004 2.5 24.1 1.0 OD1 A:ASN264 2.5 21.4 1.0 OE1 A:GLN239 2.5 22.9 1.0 OD1 A:ASP241 2.5 23.1 1.0 O A:ASP265 2.6 23.1 1.0 O6 A:ZPF1004 2.6 21.4 1.0 CG A:ASP265 3.4 19.5 1.0 CD A:GLU252 3.4 22.1 1.0 C5 A:ZPF1004 3.4 25.8 1.0 C4 A:ZPF1004 3.4 23.4 1.0 CD A:GLN239 3.4 32.9 1.0 CG A:ASN264 3.5 23.7 1.0 CG A:ASP241 3.5 28.2 1.0 C A:ASP265 3.6 23.0 1.0 H3 A:ZPF1004 3.7 25.9 0.0 H1 A:ZPF1004 3.7 26.9 0.0 ND2 A:ASN264 3.8 19.7 1.0 N A:ASP265 3.8 21.7 1.0 OE1 A:GLU252 3.8 26.2 1.0 OD2 A:ASP241 3.9 27.7 1.0 NE2 A:GLN239 3.9 26.1 1.0 OD2 A:ASP265 4.1 21.0 1.0 CA A:ASP265 4.2 20.5 1.0 C3 A:ZPF1004 4.2 27.1 1.0 N A:ASP241 4.2 22.6 1.0 H2 A:ZPF1004 4.2 23.6 0.0 CB A:ASP265 4.3 21.6 1.0 CG A:GLN239 4.6 24.6 1.0 CG A:GLU252 4.6 20.9 1.0 CB A:ASP241 4.7 24.5 1.0 CB A:GLU252 4.7 20.4 1.0 C A:ASN264 4.8 23.1 1.0 CB A:ASN264 4.8 18.8 1.0 N A:ASP266 4.8 19.6 1.0 N A:ASP242 4.8 22.3 1.0 CB A:TRP243 4.8 24.6 1.0 C6 A:ZPF1004 4.8 29.3 1.0 CA A:ASP241 4.9 22.6 1.0 N A:TRP243 4.9 24.2 1.0 CA A:ASN264 5.0 19.7 1.0 H11 A:ZPF1004 5.0 32.1 0.0

Calcium binding site 3 out of 6 in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:27.3 occ:1.00 O A:VAL190 2.3 24.8 1.0 OE1 A:GLU196 2.4 26.8 1.0 OE2 A:GLU277 2.4 26.4 1.0 OE1 A:GLU277 2.6 26.8 1.0 CD A:GLU277 2.9 33.7 1.0 OE2 A:GLU196 2.9 29.9 1.0 CD A:GLU196 3.0 33.0 1.0 C A:VAL190 3.6 25.7 1.0 OH A:TYR165 4.2 28.0 1.0 N A:VAL190 4.4 22.5 1.0 CA A:VAL190 4.4 22.4 1.0 CG A:GLU277 4.4 29.1 1.0 CG A:GLU196 4.5 26.0 1.0 CB A:VAL190 4.5 26.4 1.0 OG A:SER163 4.5 40.2 1.0 OG1 A:THR192 4.5 28.1 1.0 N A:VAL191 4.6 21.7 1.0 OE1 A:GLU279 4.7 34.2 1.0 CA A:VAL191 4.7 22.3 1.0 O A:HOH1136 4.8 37.7 1.0 N A:THR192 4.9 24.6 1.0 CG1 A:VAL190 4.9 25.9 1.0 CE2 A:TYR165 4.9 25.0 1.0

Calcium binding site 4 out of 6 in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:25.8 occ:1.00 O B:HOH1141 2.4 26.0 1.0 OD1 B:ASP242 2.5 26.3 1.0 O B:HOH1162 2.5 22.6 1.0 OD2 B:ASP215 2.5 23.7 1.0 O B:GLU252 2.6 24.6 1.0 OD1 B:ASP215 2.6 26.9 1.0 OD1 B:ASP253 2.6 26.1 1.0 O B:HOH1160 2.6 23.0 1.0 CG B:ASP215 2.9 29.2 1.0 CG B:ASP242 3.3 26.9 1.0 C B:GLU252 3.5 26.2 1.0 CG B:ASP253 3.7 26.4 1.0 CA B:ASP253 3.8 20.3 1.0 CB B:ASP242 3.9 23.4 1.0 N B:ASP253 4.1 20.7 1.0 OD2 B:ASP242 4.1 30.2 1.0 CB B:ASP253 4.2 20.7 1.0 N B:GLU252 4.3 20.0 1.0 O B:HOH1138 4.3 24.9 1.0 O B:HOH1127 4.3 26.4 1.0 CB B:ASP215 4.4 23.2 1.0 O B:HOH1179 4.4 27.3 1.0 O B:HOH1124 4.5 28.1 1.0 CA B:ASP242 4.5 22.3 1.0 CA B:GLU252 4.5 21.0 1.0 OD2 B:ASP253 4.6 27.6 1.0 OD2 B:ASP265 4.7 27.9 1.0 O B:HOH1103 4.8 24.6 1.0 O B:HOH1104 4.8 22.6 1.0 CZ2 B:TRP220 4.8 28.4 1.0 O B:ASP215 4.8 25.8 1.0 C B:ASP253 5.0 24.3 1.0

Calcium binding site 5 out of 6 in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:26.5 occ:1.00 H14 B:ZPF1003 1.6 29.3 0.0 OE2 B:GLU252 2.4 25.6 1.0 OD1 B:ASP265 2.4 23.1 1.0 OD1 B:ASN264 2.4 25.9 1.0 O5 B:ZPF1003 2.5 30.0 1.0 O B:ASP265 2.5 23.7 1.0 OD1 B:ASP241 2.5 26.3 1.0 O6 B:ZPF1003 2.5 25.8 1.0 OE1 B:GLN239 2.6 29.6 1.0 H15 B:ZPF1003 3.3 25.4 0.0 CD B:GLU252 3.3 28.3 1.0 C4 B:ZPF1003 3.4 28.7 1.0 C5 B:ZPF1003 3.4 31.0 1.0 CG B:ASP265 3.4 25.0 1.0 CD B:GLN239 3.4 36.4 1.0 CG B:ASP241 3.4 29.1 1.0 CG B:ASN264 3.4 29.1 1.0 H3 B:ZPF1003 3.6 30.7 0.0 C B:ASP265 3.6 24.7 1.0 H1 B:ZPF1003 3.6 31.1 0.0 OE1 B:GLU252 3.8 26.0 1.0 ND2 B:ASN264 3.8 24.3 1.0 N B:ASP265 3.8 23.4 1.0 NE2 B:GLN239 3.8 28.1 1.0 OD2 B:ASP241 3.8 25.6 1.0 C3 B:ZPF1003 4.1 31.1 1.0 CA B:ASP265 4.1 22.9 1.0 OD2 B:ASP265 4.2 27.9 1.0 H2 B:ZPF1003 4.2 28.7 0.0 N B:ASP241 4.2 22.9 1.0 CB B:ASP265 4.3 23.5 1.0 CG B:GLU252 4.6 23.9 1.0 CG B:GLN239 4.6 33.2 1.0 CB B:ASP241 4.6 24.8 1.0 CB B:GLU252 4.7 22.8 1.0 N B:ASP266 4.7 21.4 1.0 CB B:ASN264 4.8 22.2 1.0 C B:ASN264 4.8 25.8 1.0 CB B:TRP243 4.8 25.6 1.0 C6 B:ZPF1003 4.8 35.0 1.0 N B:ASP242 4.8 23.2 1.0 CA B:ASP241 4.9 23.5 1.0 N B:TRP243 4.9 24.5 1.0 O3 B:ZPF1003 5.0 35.3 1.0 CA B:ASN264 5.0 22.3 1.0

Calcium binding site 6 out of 6 in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactosamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1004 b:26.3 occ:1.00 O B:HOH1130 2.1 28.0 1.0 OE1 B:GLU196 2.2 33.4 1.0 OE2 B:GLU277 2.3 28.5 1.0 O B:HOH1167 2.4 30.2 1.0 O B:VAL190 2.4 28.0 1.0 O B:HOH1116 2.5 38.8 1.0 OE1 B:GLU277 2.7 22.7 1.0 CD B:GLU277 2.8 27.8 1.0 CD B:GLU196 3.0 39.9 1.0 OE2 B:GLU196 3.0 29.7 1.0 C B:VAL190 3.6 28.0 1.0 OH B:TYR165 4.1 26.9 1.0 O B:HOH1159 4.1 46.5 1.0 CA B:VAL190 4.3 22.6 1.0 CG B:GLU277 4.3 24.5 1.0 N B:VAL190 4.4 23.2 1.0 CB B:VAL190 4.4 26.4 1.0 CG B:GLU196 4.4 29.2 1.0 OG B:SER163 4.5 42.4 1.0 OG1 B:THR192 4.5 33.2 1.0 O B:HOH1155 4.6 36.6 1.0 N B:VAL191 4.6 25.1 1.0 OE1 B:GLU279 4.7 39.5 1.0 CG1 B:VAL190 4.8 26.7 1.0 CA B:VAL191 4.8 25.4 1.0 N B:THR192 5.0 29.1 1.0 CZ B:TYR165 5.0 26.7 1.0 CE2 B:TYR165 5.0 25.8 1.0

C.A.Sanhueza, M.M.Baksh, B.Thuma, M.D.Roy, S.Dutta, C.Preville, B.A.Chrunyk, K.Beaumont, R.Dullea, M.Ammirati, S.Liu, D.Gebhard, J.E.Finley, C.T.Salatto, A.King-Ahmad, I.Stock, K.Atkinson, B.Reidich, W.Lin, R.Kumar, M.Tu, E.Menhaji-Klotz, D.A.Price, S.Liras, M.G.Finn, V.Mascitti. Efficient Liver Targeting By Polyvalent Display of A Compact Ligand For the Asialoglycoprotein Receptor. J. Am. Chem. Soc. V. 139 3528 2017.
ISSN: ESSN 1520-5126
PubMed: 28230359
DOI: 10.1021/JACS.6B12964