Zinc 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
Calcium	(Ca)	4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Sonic Hedgehog-Heparin Complex, PDB code: 4c4n:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Sonic Hedgehog-Heparin Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1191 b:50.0 occ:1.00 OD1 A:ASP148 1.8 39.8 1.0 ND1 A:HIS183 2.1 44.7 1.0 NE2 A:HIS141 2.2 48.0 1.0 CG A:ASP148 2.6 46.0 1.0 OD2 A:ASP148 2.7 47.9 1.0 CE1 A:HIS183 3.0 44.5 1.0 CD2 A:HIS141 3.1 50.9 1.0 CG A:HIS183 3.1 42.7 1.0 CE1 A:HIS141 3.2 45.7 1.0 OE1 A:GLU177 3.3 65.6 1.0 CB A:HIS183 3.5 44.1 1.0 CB A:ASP148 4.0 44.5 1.0 CD2 A:HIS135 4.1 72.9 1.0 NE2 A:HIS183 4.2 43.2 1.0 CD2 A:HIS183 4.2 43.3 1.0 ND1 A:HIS141 4.3 45.7 1.0 CG A:HIS141 4.3 48.5 1.0 CA A:HIS183 4.3 40.6 1.0 NE2 A:HIS135 4.3 70.8 1.0 O A:HOH2032 4.4 43.6 1.0 NE2 A:HIS181 4.4 60.1 1.0 CD A:GLU177 4.5 69.7 1.0 CA A:ASP148 4.6 41.7 1.0 N A:ASP148 4.6 41.0 1.0 O A:VAL147 4.6 39.7 1.0 O A:HOH2038 4.7 57.8 1.0 C A:VAL147 4.7 38.9 1.0 OE2 A:GLU177 4.8 75.5 1.0 CD2 A:HIS181 4.8 56.0 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Sonic Hedgehog-Heparin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1192 b:42.0 occ:1.00 OD1 B:ASP148 1.7 33.6 1.0 NE2 B:HIS141 2.1 41.8 1.0 ND1 B:HIS183 2.1 44.8 1.0 O B:HOH2024 2.3 51.0 1.0 CG B:ASP148 2.6 36.6 1.0 OD2 B:ASP148 2.7 37.5 1.0 CE1 B:HIS183 3.0 43.6 1.0 CD2 B:HIS141 3.0 42.9 1.0 CE1 B:HIS141 3.1 39.7 1.0 CG B:HIS183 3.2 44.5 1.0 OE1 B:GLU177 3.5 77.2 1.0 CB B:HIS183 3.5 44.8 1.0 CB B:ASP148 4.0 37.0 1.0 NE2 B:HIS183 4.2 43.7 1.0 ND1 B:HIS141 4.2 38.3 1.0 CG B:HIS141 4.2 40.0 1.0 ND1 B:HIS135 4.2 60.8 1.0 CD2 B:HIS183 4.2 44.9 1.0 CA B:HIS183 4.3 43.5 1.0 CE1 B:HIS135 4.3 57.0 1.0 O B:VAL147 4.5 40.7 1.0 NE2 B:HIS181 4.5 56.3 1.0 N B:ASP148 4.5 38.2 1.0 CA B:ASP148 4.5 38.7 1.0 CD B:GLU177 4.6 80.8 1.0 C B:VAL147 4.6 39.5 1.0 CD2 B:HIS181 4.9 53.0 1.0 OE2 B:GLU177 5.0 92.7 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