Calcium in PDB 3d1m: Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo

The structure of Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo, PDB code: 3d1m was solved by J.S.Mclellan, D.J.Leahy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.56 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.179, 98.582, 144.047, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.9

The structure of Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo (pdb code 3d1m). 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 Sonic Hedgehog Bound to the Third Fniii Domain of Cdo, PDB code: 3d1m:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo


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 Sonic Hedgehog Bound to the Third Fniii Domain of Cdo within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca190 b:19.2 occ:1.00 O A:THR126 2.4 30.4 1.0 OE2 A:GLU127 2.4 32.1 1.0 OE2 A:GLU90 2.4 30.9 1.0 OD2 A:ASP96 2.5 29.7 1.0 OD1 A:ASP96 2.5 31.3 1.0 OE1 A:GLU90 2.5 32.2 1.0 OE2 A:GLU91 2.6 33.4 1.0 OE1 A:GLU91 2.7 30.4 1.0 CG A:ASP96 2.8 32.3 1.0 CD A:GLU90 2.8 31.5 1.0 CD A:GLU91 3.0 30.9 1.0 C A:THR126 3.5 31.8 1.0 CD A:GLU127 3.5 33.1 1.0 O A:HOH214 3.9 22.2 1.0 CA A:GLU127 3.9 32.2 1.0 CA A:CA2 4.0 21.4 1.0 CG A:GLU127 4.2 32.5 1.0 N A:GLU127 4.2 31.8 1.0 O D:HOH24 4.2 19.5 1.0 CG A:GLU90 4.3 31.1 1.0 CB A:ASP96 4.3 30.7 1.0 N A:ASP89 4.4 30.8 1.0 CG A:GLU91 4.5 29.4 1.0 O A:HOH203 4.5 22.4 1.0 N A:GLU90 4.5 30.2 1.0 OE1 A:GLU127 4.5 32.4 1.0 CB A:GLU127 4.6 31.4 1.0 CA A:THR126 4.7 31.6 1.0 CD1 D:ILE920 4.7 30.5 1.0 CA A:ASP89 4.7 31.2 1.0 CB A:LYS88 4.8 31.6 1.0 CD A:LYS88 4.8 30.2 1.0 CG A:LYS88 5.0 31.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo


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 Sonic Hedgehog Bound to the Third Fniii Domain of Cdo within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:21.4 occ:1.00 OD1 A:ASP130 2.3 31.8 1.0 OE2 A:GLU91 2.3 33.4 1.0 OD2 A:ASP132 2.4 30.5 1.0 O A:HOH214 2.4 22.2 1.0 O D:HOH24 2.5 19.5 1.0 OE1 A:GLU127 2.6 32.4 1.0 OE2 A:GLU127 2.6 32.1 1.0 CD A:GLU127 3.0 33.1 1.0 O A:HOH193 3.1 22.9 1.0 CG A:ASP130 3.4 31.9 1.0 CD A:GLU91 3.5 30.9 1.0 CG A:ASP132 3.5 30.8 1.0 CB A:ASP130 3.9 31.7 1.0 CA A:CA190 4.0 19.2 1.0 CG A:GLU91 4.0 29.4 1.0 CB A:ASP132 4.0 29.4 1.0 OE2 A:GLU90 4.1 30.9 1.0 CE1 A:HIS134 4.1 33.9 1.0 CA A:ASP130 4.2 30.8 1.0 OD1 A:ASP96 4.4 31.3 1.0 OD2 A:ASP130 4.4 31.9 1.0 CG A:GLU127 4.5 32.5 1.0 OE1 A:GLU91 4.5 30.4 1.0 N A:ASP132 4.6 30.2 1.0 OD1 A:ASP132 4.6 31.8 1.0 O D:VAL918 4.6 27.7 1.0 O A:TRP129 4.7 32.5 1.0 N A:GLU131 4.8 30.2 1.0 ND1 A:HIS134 4.9 33.8 1.0 CA A:ASP132 5.0 29.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo


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 Sonic Hedgehog Bound to the Third Fniii Domain of Cdo within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:19.4 occ:1.00 O B:THR126 2.3 29.6 1.0 OE2 B:GLU127 2.4 28.7 1.0 OD2 B:ASP96 2.4 28.1 1.0 OE2 B:GLU90 2.4 27.9 1.0 OD1 B:ASP96 2.5 29.4 1.0 OE1 B:GLU90 2.5 29.9 1.0 OE2 B:GLU91 2.5 27.5 1.0 OE1 B:GLU91 2.6 27.8 1.0 CD B:GLU90 2.8 27.7 1.0 CG B:ASP96 2.8 29.2 1.0 CD B:GLU91 2.9 26.8 1.0 C B:THR126 3.5 29.0 1.0 CD B:GLU127 3.5 27.0 1.0 CA B:CA4 4.0 22.3 1.0 O B:HOH221 4.0 19.8 1.0 CA B:GLU127 4.1 27.8 1.0 O C:HOH276 4.2 18.9 1.0 CG B:GLU127 4.2 25.5 1.0 N B:GLU127 4.2 29.0 1.0 CG B:GLU90 4.2 26.0 1.0 CB B:ASP96 4.3 27.3 1.0 O B:HOH222 4.4 20.5 1.0 CG B:GLU91 4.4 28.0 1.0 N B:ASP89 4.4 27.4 1.0 N B:GLU90 4.5 27.1 1.0 OE1 B:GLU127 4.5 28.3 1.0 CA B:THR126 4.7 28.4 1.0 CB B:GLU127 4.7 27.8 1.0 CD1 C:ILE920 4.7 30.9 1.0 CA B:ASP89 4.7 28.1 1.0 CB B:LYS88 4.8 26.8 1.0 CG B:LYS88 5.0 28.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Sonic Hedgehog Bound to the Third Fniii Domain of Cdo


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 Sonic Hedgehog Bound to the Third Fniii Domain of Cdo within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4 b:22.3 occ:1.00 OD1 B:ASP130 2.3 27.8 1.0 OE2 B:GLU91 2.4 27.5 1.0 OD2 B:ASP132 2.4 27.5 1.0 O B:HOH221 2.4 19.8 1.0 O C:HOH276 2.5 18.9 1.0 OE1 B:GLU127 2.6 28.3 1.0 OE2 B:GLU127 2.6 28.7 1.0 CD B:GLU127 2.9 27.0 1.0 O B:HOH197 3.0 21.4 1.0 CG B:ASP130 3.4 27.4 1.0 CD B:GLU91 3.5 26.8 1.0 CG B:ASP132 3.5 26.7 1.0 CA B:CA3 4.0 19.4 1.0 CB B:ASP130 4.0 28.0 1.0 CB B:ASP132 4.0 26.4 1.0 CG B:GLU91 4.0 28.0 1.0 OE2 B:GLU90 4.1 27.9 1.0 NE2 B:HIS134 4.1 30.0 1.0 CA B:ASP130 4.3 27.9 1.0 OD1 B:ASP96 4.4 29.4 1.0 OD2 B:ASP130 4.4 28.8 1.0 CG B:GLU127 4.4 25.5 1.0 N B:ASP132 4.5 27.0 1.0 OE1 B:GLU91 4.5 27.8 1.0 O C:VAL918 4.6 29.1 1.0 OD1 B:ASP132 4.6 27.9 1.0 O B:TRP129 4.7 29.3 1.0 N B:GLU131 4.8 26.2 1.0 CD2 B:HIS134 4.8 29.5 1.0 CA B:ASP132 4.9 26.7 1.0

J.S.Mclellan, X.Zheng, G.Hauk, R.Ghirlando, P.A.Beachy, D.J.Leahy. The Mode of Hedgehog Binding to Ihog Homologues Is Not Conserved Across Different Phyla. Nature V. 455 979 2008.
ISSN: ISSN 0028-0836
PubMed: 18794898
DOI: 10.1038/NATURE07358