Calcium in PDB 4c4n: Crystal Structure of the Sonic Hedgehog-Heparin Complex

The structure of Crystal Structure of the Sonic Hedgehog-Heparin Complex, PDB code: 4c4n was solved by D.M.Whalen, T.Malinauskas, R.J.C.Gilbert, C.Siebold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.00 / 2.36
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.680, 61.600, 62.320, 90.00, 90.00, 90.00
R / Rfree (%)	20.076 / 23.227

The structure of Crystal Structure of the Sonic Hedgehog-Heparin Complex also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Sonic Hedgehog-Heparin Complex (pdb code 4c4n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Sonic Hedgehog-Heparin Complex, PDB code: 4c4n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Sonic Hedgehog-Heparin Complex


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 the Sonic Hedgehog-Heparin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1192 b:57.9 occ:1.00 OD1 A:ASP130 2.2 67.4 1.0 OE2 A:GLU91 2.4 69.3 1.0 OE1 A:GLU127 2.4 66.2 1.0 O A:HOH2020 2.4 50.5 1.0 OE2 A:GLU127 2.6 69.0 1.0 OD2 A:ASP132 2.7 86.5 1.0 CD A:GLU127 2.8 64.6 1.0 CG A:ASP130 3.3 67.9 1.0 NE2 A:HIS134 3.4 0.3 1.0 CD A:GLU91 3.4 71.1 1.0 CG A:ASP132 3.7 92.4 1.0 CG A:GLU91 3.8 75.0 1.0 CB A:ASP130 3.9 62.9 1.0 CD2 A:HIS134 4.1 0.4 1.0 CA A:ASP130 4.2 61.2 1.0 CE1 A:HIS134 4.2 0.8 1.0 OD2 A:ASP130 4.3 72.8 1.0 OD1 A:ASP96 4.3 54.3 1.0 CA A:CA1193 4.3 57.4 1.0 CB A:ASP132 4.3 95.7 1.0 CG A:GLU127 4.3 60.9 1.0 OE1 A:GLU91 4.5 69.2 1.0 OD1 A:ASP132 4.7 94.2 1.0 OE2 A:GLU90 4.7 76.2 1.0 O A:TRP129 4.7 51.4 1.0 N A:GLU131 4.9 70.8 1.0 N A:ASP132 4.9 86.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Sonic Hedgehog-Heparin Complex


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 the Sonic Hedgehog-Heparin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1193 b:57.4 occ:1.00 O A:THR126 2.2 56.5 1.0 OD2 A:ASP96 2.2 56.5 1.0 OE2 A:GLU127 2.3 69.0 1.0 OE1 A:GLU90 2.5 74.3 1.0 OE2 A:GLU91 2.5 69.3 1.0 OE2 A:GLU90 2.6 76.2 1.0 OD1 A:ASP96 2.7 54.3 1.0 OE1 A:GLU91 2.7 69.2 1.0 CG A:ASP96 2.8 51.6 1.0 CD A:GLU90 2.8 76.9 1.0 CD A:GLU91 3.0 71.1 1.0 C A:THR126 3.4 53.1 1.0 CD A:GLU127 3.5 64.6 1.0 CA A:GLU127 4.0 50.6 1.0 CG A:GLU127 4.0 60.9 1.0 N A:GLU127 4.1 49.5 1.0 CA A:CA1192 4.3 57.9 1.0 CB A:ASP96 4.3 49.1 1.0 CG A:GLU90 4.3 84.3 1.0 N A:GLU90 4.4 73.9 1.0 N A:ASP89 4.4 62.4 1.0 CG A:GLU91 4.5 75.0 1.0 O A:HOH2020 4.5 50.5 1.0 CA A:THR126 4.5 52.7 1.0 OE1 A:GLU127 4.5 66.2 1.0 CB A:GLU127 4.6 54.0 1.0 CA A:ASP89 4.7 64.2 1.0 CB A:LYS88 4.8 65.3 1.0 CD A:LYS88 4.8 74.8 1.0 CG A:LYS88 5.0 73.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Sonic Hedgehog-Heparin Complex


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 the Sonic Hedgehog-Heparin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1193 b:41.0 occ:1.00 OE2 B:GLU127 2.3 47.4 1.0 OD2 B:ASP96 2.3 42.1 1.0 OE2 B:GLU90 2.4 46.1 1.0 O B:THR126 2.4 40.4 1.0 OE1 B:GLU90 2.5 42.4 1.0 OE1 B:GLU91 2.6 39.1 1.0 OE2 B:GLU91 2.6 39.6 1.0 OD1 B:ASP96 2.7 41.7 1.0 CD B:GLU90 2.8 45.5 1.0 CG B:ASP96 2.9 42.7 1.0 CD B:GLU91 2.9 40.2 1.0 CD B:GLU127 3.5 47.8 1.0 C B:THR126 3.6 43.7 1.0 CG B:GLU127 4.1 47.4 1.0 CA B:GLU127 4.1 41.5 1.0 O B:HOH2015 4.1 37.1 1.0 CA B:CA1194 4.2 42.4 1.0 CG B:GLU90 4.2 46.3 1.0 N B:GLU127 4.3 43.2 1.0 CB B:ASP96 4.4 40.0 1.0 CG B:GLU91 4.4 42.4 1.0 N B:GLU90 4.4 44.9 1.0 O B:HOH2013 4.5 36.3 1.0 OE1 B:GLU127 4.5 46.1 1.0 O B:HOH2016 4.6 38.1 1.0 N B:ASP89 4.6 44.1 1.0 CB B:GLU127 4.7 45.4 1.0 CA B:THR126 4.7 44.8 1.0 CA B:ASP89 4.8 44.1 1.0 CD B:LYS88 4.9 52.1 1.0 N B:GLU91 5.0 45.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Sonic Hedgehog-Heparin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Sonic Hedgehog-Heparin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1194 b:42.4 occ:1.00 OD1 B:ASP130 2.2 40.9 1.0 OE2 B:GLU91 2.3 39.6 1.0 OD2 B:ASP132 2.4 57.7 1.0 O B:HOH2015 2.5 37.1 1.0 OE1 B:GLU127 2.5 46.1 1.0 O B:HOH2016 2.5 38.1 1.0 OE2 B:GLU127 2.6 47.4 1.0 CD B:GLU127 2.9 47.8 1.0 O B:HOH2014 3.0 46.5 1.0 CG B:ASP130 3.4 42.4 1.0 CD B:GLU91 3.5 40.2 1.0 CG B:ASP132 3.5 58.5 1.0 CB B:ASP130 4.0 41.4 1.0 CG B:GLU91 4.0 42.4 1.0 CB B:ASP132 4.1 58.0 1.0 CA B:CA1193 4.2 41.0 1.0 CA B:ASP130 4.3 41.1 1.0 OD2 B:ASP130 4.3 42.6 1.0 CG B:GLU127 4.4 47.4 1.0 OD1 B:ASP96 4.4 41.7 1.0 OD1 B:ASP132 4.5 57.8 1.0 OE1 B:GLU91 4.5 39.1 1.0 OE2 B:GLU90 4.6 46.1 1.0 N B:ASP132 4.7 53.2 1.0 ND1 B:HIS134 4.8 65.8 1.0 N B:GLU131 4.8 45.6 1.0 O B:TRP129 4.8 40.2 1.0

D.M.Whalen, T.Malinauskas, R.J.C.Gilbert, C.Siebold. Structural Insights Into Proteoglycan-Shaped Hedgehog Signaling. Proc.Natl.Acad.Sci.Usa V. 110 16420 2013.
ISSN: ISSN 0027-8424
PubMed: 24062467
DOI: 10.1073/PNAS.1310097110