Calcium in PDB 3n1q: Crystal Structure of Dhhn Bound to CDOFN3

The structure of Crystal Structure of Dhhn Bound to CDOFN3, PDB code: 3n1q was solved by J.M.Kavran, D.J.Leahy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.73 / 2.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.715, 100.265, 97.260, 90.00, 98.98, 90.00
R / Rfree (%)	23.7 / 28.8

The structure of Crystal Structure of Dhhn Bound to CDOFN3 also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of Dhhn Bound to CDOFN3 (pdb code 3n1q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Dhhn Bound to CDOFN3, PDB code: 3n1q:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Dhhn Bound to CDOFN3


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 Dhhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca191 b:33.1 occ:1.00 OD2 B:ASP132 2.7 35.8 1.0 OE2 B:GLU127 2.8 27.9 1.0 OE2 B:GLU91 2.8 24.8 1.0 OD1 B:ASP130 2.9 24.8 1.0 OE1 B:GLU127 2.9 27.6 1.0 CD B:GLU127 3.2 27.2 1.0 CD B:GLU91 3.5 24.7 1.0 CG B:ASP130 3.8 24.5 1.0 CG B:ASP132 3.8 35.7 1.0 CA B:ASP130 3.8 24.4 1.0 CB B:ASP130 3.9 24.2 1.0 CA B:CA192 4.0 23.6 1.0 CG B:GLU91 4.2 26.1 1.0 O B:TRP129 4.2 36.3 1.0 OE1 B:GLU91 4.3 24.5 1.0 OD1 B:ASP96 4.3 27.9 1.0 N B:GLU131 4.3 21.3 1.0 CB B:ALA95 4.5 40.1 1.0 OD1 B:ASP132 4.5 36.2 1.0 CB B:ASP132 4.5 35.4 1.0 C B:ASP130 4.7 24.8 1.0 N B:ASP132 4.7 36.3 1.0 CG B:GLU127 4.7 25.8 1.0 N B:ASP130 4.8 24.6 1.0 OE2 B:GLU90 4.8 20.6 1.0 C B:TRP129 4.9 36.9 1.0 OD2 B:ASP130 4.9 24.6 1.0 NE2 B:HIS134 4.9 26.6 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Dhhn Bound to CDOFN3


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 Dhhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca192 b:23.6 occ:1.00 OE2 B:GLU91 2.7 24.8 1.0 O B:THR126 2.7 25.8 1.0 OE1 B:GLU90 2.8 20.2 1.0 OD2 B:ASP96 2.8 26.2 1.0 OD1 B:ASP96 2.8 27.9 1.0 OE2 B:GLU90 2.9 20.6 1.0 OE2 B:GLU127 3.0 27.9 1.0 CD B:GLU90 3.2 20.8 1.0 CG B:ASP96 3.2 27.5 1.0 OE1 B:GLU91 3.3 24.5 1.0 CD B:GLU91 3.3 24.7 1.0 CD B:GLU127 3.4 27.2 1.0 C B:THR126 3.6 24.9 1.0 CG B:GLU127 4.0 25.8 1.0 CA B:CA191 4.0 33.1 1.0 CA B:GLU127 4.0 25.6 1.0 OE1 B:GLU127 4.0 27.6 1.0 N B:GLU127 4.2 25.5 1.0 N B:ASP89 4.6 27.9 1.0 CB B:GLU127 4.6 25.3 1.0 N B:GLU90 4.6 21.9 1.0 CG B:GLU90 4.6 21.1 1.0 CD1 C:ILE920 4.6 31.4 1.0 CB B:ASP96 4.7 27.6 1.0 CA B:THR126 4.7 24.2 1.0 CA B:ASP89 4.8 28.7 1.0 CD B:LYS88 4.8 20.6 1.0 CG B:GLU91 4.8 26.1 1.0 CB B:LYS88 4.9 20.7 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Dhhn Bound to CDOFN3


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 Dhhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca191 b:25.1 occ:1.00 OE2 A:GLU91 2.7 36.3 1.0 OE2 A:GLU127 2.8 37.9 1.0 OD1 A:ASP130 2.8 49.4 1.0 OE1 A:GLU127 3.0 38.7 1.0 OD2 A:ASP132 3.1 38.7 1.0 CD A:GLU127 3.2 38.3 1.0 CG A:ASP132 3.5 37.9 1.0 CD A:GLU91 3.6 36.5 1.0 CG A:ASP130 3.8 49.6 1.0 CG A:GLU91 3.9 36.9 1.0 NE2 A:HIS134 3.9 33.6 1.0 OD1 A:ASP132 3.9 37.0 1.0 OE2 A:GLU90 4.0 33.4 1.0 CA A:CA192 4.1 22.9 1.0 CB A:ASP132 4.1 37.5 1.0 O D:VAL918 4.4 35.0 1.0 CD2 A:HIS134 4.5 32.6 1.0 CB A:ASP130 4.5 49.1 1.0 OD2 A:ASP130 4.5 50.0 1.0 CA A:ASP130 4.7 49.6 1.0 CG A:GLU127 4.8 37.8 1.0 OE1 A:GLU91 4.8 36.9 1.0 O A:TRP129 4.8 23.8 1.0 N A:ASP132 4.9 38.4 1.0 CE1 A:HIS134 4.9 32.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Dhhn Bound to CDOFN3


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 Dhhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca192 b:22.9 occ:1.00 OE1 A:GLU90 2.7 32.7 1.0 O A:THR126 2.8 21.5 1.0 OD2 A:ASP96 2.8 32.2 1.0 OE2 A:GLU91 2.9 36.3 1.0 OE2 A:GLU90 2.9 33.4 1.0 OD1 A:ASP96 2.9 33.2 1.0 OE2 A:GLU127 3.0 37.9 1.0 CD A:GLU90 3.1 33.2 1.0 OE1 A:GLU91 3.2 36.9 1.0 CD A:GLU91 3.2 36.5 1.0 CG A:ASP96 3.2 33.0 1.0 C A:THR126 3.7 20.7 1.0 CD A:GLU127 3.9 38.3 1.0 N A:ASP89 4.0 37.7 1.0 CA A:CA191 4.1 25.1 1.0 N A:GLU90 4.1 34.4 1.0 CA A:ASP89 4.3 38.6 1.0 CA A:GLU127 4.4 36.5 1.0 CG A:GLU91 4.4 36.9 1.0 N A:GLU127 4.4 36.4 1.0 CG A:GLU90 4.5 33.8 1.0 CG A:GLU127 4.5 37.8 1.0 CB A:LYS88 4.6 20.1 1.0 CA A:THR126 4.6 19.7 1.0 OE1 A:GLU127 4.7 38.7 1.0 C A:ASP89 4.7 39.0 1.0 CB A:ASP96 4.7 34.1 1.0 CG A:LYS88 4.8 20.1 1.0 CD A:LYS88 4.9 19.7 1.0 C A:LYS88 5.0 21.5 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Dhhn Bound to CDOFN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Dhhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca192 b:19.8 occ:1.00 O E:THR126 2.7 26.4 1.0 OE2 E:GLU91 2.7 22.3 1.0 OD2 E:ASP96 2.8 24.1 1.0 OD1 E:ASP96 2.9 25.9 1.0 OE1 E:GLU90 2.9 25.8 1.0 OE2 E:GLU90 2.9 15.4 1.0 OE2 E:GLU127 3.1 34.0 1.0 CG E:ASP96 3.1 25.0 1.0 OE1 E:GLU91 3.1 20.3 1.0 CD E:GLU90 3.2 26.4 1.0 CD E:GLU127 3.2 33.2 1.0 CD E:GLU91 3.3 21.3 1.0 C E:THR126 3.5 26.3 1.0 CG E:GLU127 3.6 33.1 1.0 CA E:GLU127 3.6 31.7 1.0 OE1 E:GLU127 3.8 33.1 1.0 N E:GLU127 3.9 31.0 1.0 CA E:CA191 4.1 47.1 1.0 CB E:GLU127 4.2 33.0 1.0 O E:HOH1 4.4 29.4 1.0 N E:ASP89 4.5 23.1 1.0 CB E:ASP96 4.6 25.3 1.0 CA E:THR126 4.6 25.6 1.0 CD1 F:ILE920 4.7 18.4 1.0 N E:GLU90 4.7 25.1 1.0 CG E:GLU90 4.7 15.2 1.0 N E:GLY128 4.8 27.7 1.0 C E:GLU127 4.8 32.0 1.0 CA E:ASP89 4.8 22.9 1.0 CB E:LYS88 4.8 21.3 1.0 CG E:GLU91 4.8 21.2 1.0 CD E:LYS88 4.9 21.2 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Dhhn Bound to CDOFN3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Dhhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca191 b:47.1 occ:1.00 OE2 E:GLU91 2.8 22.3 1.0 OD1 E:ASP130 2.8 28.3 1.0 OE2 E:GLU127 2.9 34.0 1.0 OD2 E:ASP132 2.9 34.9 1.0 OE1 E:GLU127 3.0 33.1 1.0 CD E:GLU127 3.3 33.2 1.0 O E:HOH1 3.3 29.4 1.0 CD E:GLU91 3.3 21.3 1.0 CA E:ASP130 3.5 28.2 1.0 CG E:ASP130 3.6 29.3 1.0 CB E:ASP130 3.7 29.3 1.0 CG E:GLU91 3.8 21.2 1.0 O E:TRP129 3.9 24.1 1.0 CG E:ASP132 4.0 36.6 1.0 OD1 E:ASP96 4.0 25.9 1.0 CA E:CA192 4.1 19.8 1.0 OE1 E:GLU91 4.1 20.3 1.0 N E:GLU131 4.2 47.7 1.0 C E:ASP130 4.4 28.7 1.0 N E:ASP130 4.5 28.5 1.0 C E:TRP129 4.6 24.8 1.0 CB E:ASP132 4.6 37.8 1.0 N E:ASP132 4.7 37.5 1.0 OD2 E:ASP130 4.8 30.7 1.0 CG E:GLU127 4.8 33.1 1.0 OD1 E:ASP132 4.8 36.4 1.0 CB E:ALA95 4.8 26.9 1.0 OE2 E:GLU90 4.9 15.4 1.0

J.M.Kavran, M.D.Ward, O.O.Oladosu, S.Mulepati, D.J.Leahy. All Mammalian Hedgehog Proteins Interact with Cdo and Boc in A Conserved Manner. J.Biol.Chem. 2010.
ISSN: ESSN 1083-351X
PubMed: 20519495
DOI: 10.1074/JBC.M110.131680