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

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

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.100, 59.785, 68.818, 90.00, 93.27, 90.00
R / Rfree (%)	19.3 / 22.5

The structure of Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactoseamine 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 Galactoseamine Mimic (pdb code 5jpv). 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 Galactoseamine Mimic, PDB code: 5jpv:
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 Galactoseamine 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 Galactoseamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:19.0 occ:1.00 O A:GLU252 2.4 17.8 1.0 OD1 A:ASP242 2.4 19.9 1.0 O A:HOH497 2.4 22.9 1.0 O A:HOH441 2.5 13.0 1.0 OD1 A:ASP253 2.6 19.8 1.0 O A:HOH488 2.6 18.6 1.0 OD2 A:ASP215 2.6 17.9 1.0 OD1 A:ASP215 2.7 20.4 1.0 CG A:ASP215 3.0 19.3 1.0 CG A:ASP242 3.2 19.0 1.0 C A:GLU252 3.4 17.9 1.0 CG A:ASP253 3.7 20.6 1.0 CA A:ASP253 3.9 18.6 1.0 CB A:ASP242 3.9 18.9 1.0 OD2 A:ASP242 4.0 18.4 1.0 N A:ASP253 4.1 18.0 1.0 N A:GLU252 4.2 17.2 1.0 O A:HOH447 4.2 21.6 1.0 O A:HOH414 4.2 23.0 1.0 CB A:ASP253 4.3 18.8 1.0 CA A:GLU252 4.4 17.4 1.0 CA A:ASP242 4.5 18.8 1.0 O A:HOH526 4.5 21.2 1.0 CB A:ASP215 4.6 19.9 1.0 OD2 A:ASP253 4.6 22.3 1.0 OD2 A:ASP265 4.7 15.8 1.0 O A:HOH403 4.7 19.2 1.0 O A:ASP215 4.8 21.2 1.0 O A:HOH410 4.8 24.9 1.0 CZ2 A:TRP220 5.0 20.1 1.0

Calcium binding site 2 out of 6 in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactoseamine 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 Galactoseamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:17.1 occ:1.00 OE2 A:GLU252 2.3 18.0 1.0 OD1 A:ASP265 2.4 14.9 1.0 OD1 A:ASP241 2.5 16.9 1.0 OD1 A:ASN264 2.5 16.9 1.0 O4 A:LBT301 2.5 19.1 1.0 O A:ASP265 2.5 15.6 1.0 O3 A:LBT301 2.6 18.1 1.0 OE1 A:GLN239 2.6 20.8 1.0 CD A:GLU252 3.3 18.6 1.0 C4 A:LBT301 3.4 21.1 1.0 CG A:ASP265 3.4 15.8 1.0 CG A:ASP241 3.4 19.8 1.0 C3 A:LBT301 3.5 21.2 1.0 CG A:ASN264 3.5 14.9 1.0 CD A:GLN239 3.5 21.5 1.0 C A:ASP265 3.6 16.0 1.0 OE1 A:GLU252 3.8 18.9 1.0 ND2 A:ASN264 3.8 14.2 1.0 N A:ASP265 3.8 14.9 1.0 OD2 A:ASP241 3.9 18.2 1.0 NE2 A:GLN239 4.0 21.1 1.0 OD2 A:ASP265 4.0 15.8 1.0 CA A:ASP265 4.1 15.8 1.0 C2 A:LBT301 4.1 22.7 1.0 N A:ASP241 4.2 18.8 1.0 CB A:ASP265 4.3 15.4 1.0 CG A:GLU252 4.6 18.2 1.0 CB A:ASP241 4.6 19.3 1.0 CG A:GLN239 4.7 20.5 1.0 CB A:GLU252 4.7 17.6 1.0 N A:ASP266 4.8 16.3 1.0 C A:ASN264 4.8 15.2 1.0 CB A:TRP243 4.8 18.8 1.0 CB A:ASN264 4.8 15.2 1.0 C5 A:LBT301 4.8 22.1 1.0 N A:ASP242 4.8 18.9 1.0 N A:TRP243 4.9 18.3 1.0 CA A:ASP241 4.9 19.2 1.0 O2 A:LBT301 5.0 23.1 1.0 CA A:ASN264 5.0 14.9 1.0

Calcium binding site 3 out of 6 in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactoseamine 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 Galactoseamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:21.9 occ:1.00 OE1 A:GLU196 2.3 20.3 1.0 O A:HOH428 2.3 26.7 1.0 O A:VAL190 2.4 18.5 1.0 O A:HOH493 2.4 22.5 1.0 O A:HOH448 2.5 28.0 1.0 OE2 A:GLU277 2.5 23.5 1.0 OE1 A:GLU277 2.7 22.2 1.0 CD A:GLU277 2.9 23.9 1.0 OE2 A:GLU196 3.0 21.5 1.0 CD A:GLU196 3.0 22.0 1.0 C A:VAL190 3.6 18.5 1.0 OH A:TYR165 4.2 19.0 1.0 CA A:VAL190 4.4 18.0 1.0 N A:VAL190 4.4 17.8 1.0 CB A:VAL190 4.5 17.9 1.0 CG A:GLU277 4.5 23.1 1.0 CG A:GLU196 4.5 20.9 1.0 O A:HOH419 4.5 35.7 1.0 N A:VAL191 4.6 18.9 1.0 OG1 A:THR192 4.6 21.3 1.0 OG A:SER163 4.6 27.1 1.0 CA A:VAL191 4.7 19.1 1.0 OE1 A:GLU279 4.7 32.3 1.0 O A:HOH424 4.8 32.0 1.0 CG1 A:VAL190 4.9 17.0 1.0 N A:THR192 4.9 19.5 1.0 CE2 A:TYR165 4.9 18.7 1.0 CZ A:TYR165 5.0 18.4 1.0

Calcium binding site 4 out of 6 in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactoseamine 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 Galactoseamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:18.4 occ:1.00 O B:HOH434 2.3 17.7 1.0 O B:HOH497 2.4 24.4 1.0 O B:GLU252 2.5 17.9 1.0 OD1 B:ASP242 2.5 20.7 1.0 OD2 B:ASP215 2.6 19.8 1.0 OD1 B:ASP253 2.6 20.0 1.0 O B:HOH500 2.7 19.1 1.0 OD1 B:ASP215 2.7 19.1 1.0 CG B:ASP215 3.0 20.2 1.0 CG B:ASP242 3.3 20.7 1.0 C B:GLU252 3.4 18.5 1.0 CG B:ASP253 3.7 19.6 1.0 CA B:ASP253 3.8 18.0 1.0 CB B:ASP242 4.0 20.0 1.0 N B:ASP253 4.1 17.6 1.0 OD2 B:ASP242 4.1 20.5 1.0 O B:HOH438 4.2 21.5 1.0 O B:HOH451 4.2 25.7 1.0 N B:GLU252 4.2 19.0 1.0 CB B:ASP253 4.3 17.9 1.0 O B:HOH529 4.5 21.5 1.0 CA B:ASP242 4.5 20.2 1.0 CA B:GLU252 4.5 18.4 1.0 CB B:ASP215 4.5 19.8 1.0 O B:HOH415 4.6 28.6 1.0 OD2 B:ASP253 4.6 20.3 1.0 O B:HOH427 4.7 22.7 1.0 OD2 B:ASP265 4.8 18.8 1.0 O B:HOH425 4.8 20.1 1.0 O B:ASP215 4.8 19.7 1.0 CZ2 B:TRP220 4.9 21.9 1.0

Calcium binding site 5 out of 6 in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactoseamine 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 Galactoseamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:18.6 occ:1.00 OD1 B:ASP265 2.4 18.1 1.0 OE2 B:GLU252 2.4 21.6 1.0 OD1 B:ASN264 2.4 19.4 1.0 O3 B:LBT301 2.5 26.3 1.0 OD1 B:ASP241 2.5 19.4 1.0 O B:ASP265 2.5 16.6 1.0 O4 B:LBT301 2.5 23.1 1.0 OE1 B:GLN239 2.6 22.8 1.0 CG B:ASP265 3.3 18.1 1.0 CD B:GLU252 3.4 21.4 1.0 C4 B:LBT301 3.4 27.4 1.0 C3 B:LBT301 3.4 28.6 1.0 CD B:GLN239 3.4 24.1 1.0 CG B:ASN264 3.5 18.6 1.0 CG B:ASP241 3.5 20.5 1.0 C B:ASP265 3.6 17.6 1.0 OE1 B:GLU252 3.8 20.4 1.0 N B:ASP265 3.8 18.0 1.0 ND2 B:ASN264 3.8 17.1 1.0 NE2 B:GLN239 3.8 24.4 1.0 OD2 B:ASP241 3.9 19.7 1.0 OD2 B:ASP265 4.0 18.8 1.0 CA B:ASP265 4.1 17.8 1.0 C2 B:LBT301 4.1 30.9 1.0 N B:ASP241 4.3 21.2 1.0 CB B:ASP265 4.3 17.4 1.0 CG B:GLU252 4.6 19.2 1.0 CG B:GLN239 4.6 24.4 1.0 CB B:ASP241 4.7 21.0 1.0 CB B:GLU252 4.7 18.9 1.0 N B:ASP266 4.7 17.5 1.0 CB B:TRP243 4.8 20.8 1.0 C B:ASN264 4.8 18.7 1.0 CB B:ASN264 4.8 18.4 1.0 C5 B:LBT301 4.8 29.1 1.0 N B:ASP242 4.8 20.1 1.0 CA B:ASP241 4.9 20.9 1.0 N B:TRP243 4.9 20.1 1.0 O2 B:LBT301 5.0 29.8 1.0

Calcium binding site 6 out of 6 in the Efficient Targeting of the Asialoglycoprotein Receptor By Polyvalent Display of A Compact Galactoseamine 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 Galactoseamine Mimic within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:24.8 occ:1.00 OE1 B:GLU196 2.3 28.5 1.0 O B:HOH485 2.3 37.6 1.0 O B:VAL190 2.3 21.4 1.0 OE2 B:GLU277 2.4 23.1 1.0 O B:HOH505 2.4 23.3 1.0 O B:HOH421 2.4 27.5 1.0 OE1 B:GLU277 2.7 18.2 1.0 CD B:GLU277 2.9 20.8 1.0 CD B:GLU196 3.0 29.4 1.0 OE2 B:GLU196 3.0 28.0 1.0 C B:VAL190 3.5 21.1 1.0 OH B:TYR165 4.2 22.3 1.0 CA B:VAL190 4.3 20.0 1.0 N B:VAL190 4.3 19.4 1.0 CB B:VAL190 4.4 20.3 1.0 CG B:GLU277 4.4 20.9 1.0 CG B:GLU196 4.4 28.2 1.0 OG1 B:THR192 4.5 25.3 1.0 O B:HOH471 4.5 30.1 1.0 N B:VAL191 4.6 21.6 1.0 OG B:SER163 4.6 28.8 1.0 CA B:VAL191 4.8 22.6 1.0 OE1 B:GLU279 4.8 35.6 1.0 CG1 B:VAL190 4.8 20.5 1.0 N B:THR192 4.9 24.2 1.0 CE2 B:TYR165 4.9 22.9 1.0 CZ B:TYR165 5.0 23.1 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