Calcium in PDB 4c4m: Crystal Structure of the Sonic Hedgehog-Chondroitin-4-Sulphate Complex

The structure of Crystal Structure of the Sonic Hedgehog-Chondroitin-4-Sulphate Complex, PDB code: 4c4m 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)	43.828 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.350, 55.660, 71.100, 90.00, 90.00, 90.00
R / Rfree (%)	16.02 / 19.34

The structure of Crystal Structure of the Sonic Hedgehog-Chondroitin-4-Sulphate Complex also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Sonic Hedgehog-Chondroitin-4-Sulphate Complex (pdb code 4c4m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Sonic Hedgehog-Chondroitin-4-Sulphate Complex, PDB code: 4c4m:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the Sonic Hedgehog-Chondroitin-4-Sulphate 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-Chondroitin-4-Sulphate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1194 b:18.7 occ:1.00 O A:HOH2077 2.3 30.3 1.0 OE2 A:GLU91 2.3 15.6 1.0 OD1 A:ASP130 2.4 16.0 1.0 O A:HOH2076 2.5 19.0 1.0 OE1 A:GLU127 2.5 19.7 1.0 OD2 A:ASP132 2.7 41.9 1.0 OE2 A:GLU127 2.7 18.1 1.0 O A:HOH2103 2.9 18.8 1.0 CD A:GLU127 3.0 20.4 1.0 CG A:ASP130 3.4 11.7 1.0 CD A:GLU91 3.5 17.6 1.0 CG A:ASP132 3.8 40.4 1.0 CG A:GLU91 4.0 16.4 1.0 CA A:CA1195 4.1 12.0 1.0 CB A:ASP130 4.1 9.0 1.0 CA A:ASP130 4.3 10.8 1.0 CB A:ASP132 4.3 30.1 1.0 OD2 A:ASP130 4.3 15.6 1.0 O A:HOH2075 4.4 34.4 1.0 OD1 A:ASP96 4.4 10.8 1.0 CG A:GLU127 4.5 20.1 1.0 OE1 A:GLU91 4.5 14.5 1.0 OE2 A:GLU90 4.7 19.8 1.0 O A:TRP129 4.7 12.0 1.0 ND1 A:HIS134 4.8 37.2 1.0 OD1 A:ASP132 4.9 39.5 1.0 N A:GLU131 4.9 14.0 1.0 N A:ASP132 4.9 20.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the Sonic Hedgehog-Chondroitin-4-Sulphate 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-Chondroitin-4-Sulphate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1195 b:12.0 occ:1.00 OE2 A:GLU127 2.3 18.1 1.0 OD2 A:ASP96 2.4 13.6 1.0 O A:THR126 2.4 11.9 1.0 OE2 A:GLU90 2.5 19.8 1.0 OD1 A:ASP96 2.5 10.8 1.0 OE2 A:GLU91 2.5 15.6 1.0 OE1 A:GLU90 2.6 19.2 1.0 OE1 A:GLU91 2.7 14.5 1.0 CD A:GLU90 2.8 20.4 1.0 CG A:ASP96 2.8 12.1 1.0 CD A:GLU91 3.0 17.6 1.0 CD A:GLU127 3.5 20.4 1.0 C A:THR126 3.6 10.1 1.0 CA A:GLU127 4.1 9.9 1.0 O A:HOH2076 4.1 19.0 1.0 CA A:CA1194 4.1 18.7 1.0 CG A:GLU127 4.1 20.1 1.0 CG A:GLU90 4.2 17.4 1.0 N A:GLU127 4.3 8.3 1.0 CB A:ASP96 4.3 9.0 1.0 O A:HOH2073 4.4 17.4 1.0 OE1 A:GLU127 4.4 19.7 1.0 CG A:GLU91 4.5 16.4 1.0 N A:GLU90 4.5 18.5 1.0 O A:HOH2075 4.5 34.4 1.0 O A:HOH2077 4.6 30.3 1.0 N A:ASP89 4.6 14.4 1.0 CA A:THR126 4.7 9.0 1.0 CB A:GLU127 4.7 13.9 1.0 CA A:ASP89 4.8 15.7 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