Calcium in PDB 3n1f: Crystal Structure of Ihhn Bound to CDOFN3

The structure of Crystal Structure of Ihhn Bound to CDOFN3, PDB code: 3n1f 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)	25.31 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	71.758, 98.198, 144.105, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 18.9

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

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Ihhn Bound to CDOFN3 (pdb code 3n1f). 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 Ihhn Bound to CDOFN3, PDB code: 3n1f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Ihhn 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 Ihhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5 b:17.8 occ:1.00 OE2 A:GLU131 2.3 18.9 1.0 O A:THR130 2.4 17.1 1.0 OE2 A:GLU94 2.4 19.8 1.0 OD2 A:ASP100 2.4 18.0 1.0 OD1 A:ASP100 2.5 19.7 1.0 OE1 A:GLU94 2.5 16.7 1.0 OE2 A:GLU95 2.5 20.1 1.0 OE1 A:GLU95 2.7 18.2 1.0 CD A:GLU94 2.8 15.5 1.0 CG A:ASP100 2.8 17.3 1.0 CD A:GLU95 2.9 18.6 1.0 HA A:GLU131 3.2 22.0 1.0 CD A:GLU131 3.5 19.1 1.0 C A:THR130 3.5 14.9 1.0 H A:GLU94 3.8 21.8 1.0 HG2 A:GLU131 3.8 20.6 1.0 O A:HOH1 3.9 18.7 1.0 CA A:CA6 3.9 19.3 1.0 HD11 D:ILE920 4.0 23.0 1.0 H A:ASP93 4.0 20.2 1.0 CA A:GLU131 4.0 18.3 1.0 HA A:ASP93 4.1 18.4 1.0 O D:HOH8 4.1 19.4 1.0 CG A:GLU131 4.1 17.1 1.0 N A:GLU131 4.2 17.6 1.0 CG A:GLU94 4.3 17.2 1.0 O A:HOH4 4.3 20.0 1.0 H A:GLU95 4.3 20.3 1.0 CB A:ASP100 4.3 17.1 1.0 CG A:GLU95 4.4 20.9 1.0 N A:ASP93 4.4 16.8 1.0 N A:GLU94 4.4 18.1 1.0 HG2 A:GLU94 4.5 20.7 1.0 HA A:THR130 4.5 17.6 1.0 OE1 A:GLU131 4.5 19.5 1.0 H A:GLY132 4.6 21.1 1.0 HG3 A:GLU95 4.6 25.1 1.0 CB A:GLU131 4.6 19.5 1.0 CA A:THR130 4.7 14.7 1.0 CA A:ASP93 4.7 15.3 1.0 HD12 D:ILE920 4.7 23.0 1.0 HB2 A:ASP100 4.7 20.6 1.0 HB3 A:ASP100 4.7 20.6 1.0 CD1 D:ILE920 4.8 19.2 1.0 HG3 A:GLU94 4.8 20.7 1.0 HG2 A:GLU95 4.8 25.1 1.0 CB A:LYS92 4.8 18.2 1.0 CD A:LYS92 5.0 16.5 1.0 HB A:THR130 5.0 22.6 1.0 HA A:ASP100 5.0 22.7 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Ihhn 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 Ihhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca6 b:19.3 occ:1.00 OD1 A:ASP134 2.3 17.4 1.0 OE2 A:GLU95 2.3 20.1 1.0 OD2 A:ASP136 2.4 19.5 1.0 O A:HOH1 2.4 18.7 1.0 O D:HOH8 2.5 19.4 1.0 OE1 A:GLU131 2.6 19.5 1.0 OE2 A:GLU131 2.6 18.9 1.0 CD A:GLU131 2.9 19.1 1.0 O A:HOH195 3.1 21.2 1.0 CG A:ASP134 3.4 20.7 1.0 HB2 A:ASP136 3.4 20.6 1.0 CD A:GLU95 3.5 18.6 1.0 CG A:ASP136 3.5 18.6 1.0 HA A:ASP134 3.5 22.6 1.0 HG2 A:GLU95 3.6 25.1 1.0 HB2 A:ASP134 3.7 24.8 1.0 H A:ASP136 3.8 23.0 1.0 CA A:CA5 3.9 17.8 1.0 CG A:GLU95 3.9 20.9 1.0 CB A:ASP134 3.9 20.6 1.0 CB A:ASP136 4.0 17.2 1.0 HG3 A:GLU95 4.0 25.1 1.0 OE2 A:GLU94 4.1 19.8 1.0 H A:GLU135 4.2 26.1 1.0 NE2 A:HIS138 4.2 19.5 1.0 HE2 A:HIS139 4.2 23.5 1.0 CA A:ASP134 4.2 18.8 1.0 OD2 A:ASP134 4.4 19.1 1.0 OD1 A:ASP100 4.4 19.7 1.0 CG A:GLU131 4.4 17.1 1.0 OE1 A:GLU95 4.5 18.2 1.0 N A:ASP136 4.6 19.2 1.0 OD1 A:ASP136 4.6 19.9 1.0 HA A:GLU131 4.6 22.0 1.0 O D:VAL918 4.6 18.6 1.0 HB3 A:ASP136 4.6 20.6 1.0 HD2 A:HIS138 4.7 23.5 1.0 O A:TRP133 4.7 22.6 1.0 HB3 A:GLU131 4.7 23.4 1.0 N A:GLU135 4.8 21.7 1.0 CD2 A:HIS138 4.8 19.5 1.0 HG2 A:GLU131 4.8 20.6 1.0 HG3 A:GLU131 4.8 20.6 1.0 HB3 A:ASP134 4.9 24.8 1.0 HB3 A:ALA99 4.9 25.9 1.0 CA A:ASP136 4.9 16.7 1.0 NE2 A:HIS139 5.0 19.6 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Ihhn 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 Ihhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca8 b:28.0 occ:1.00 O A:HOH716 2.3 33.6 1.0 O A:HOH657 2.3 30.1 1.0 OD1 B:ASN96 2.4 21.4 1.0 OD1 A:ASN96 2.4 19.4 1.0 O B:HOH194 2.4 21.6 1.0 O B:HOH343 2.7 37.1 1.0 O B:HOH240 2.8 33.7 1.0 CG A:ASN96 3.4 16.9 1.0 CG B:ASN96 3.4 17.2 1.0 HA B:ASN96 3.6 23.5 1.0 HA A:ASN96 3.6 23.7 1.0 HB3 A:ASN96 3.9 25.3 1.0 HB3 B:ASN96 4.0 20.4 1.0 O C:HOH149 4.0 32.3 1.0 CB A:ASN96 4.1 21.0 1.0 O D:HOH198 4.2 26.7 1.0 CB B:ASN96 4.2 17.0 1.0 OD2 B:ASP93 4.2 25.9 1.0 O D:HOH249 4.3 29.5 1.0 OD2 A:ASP93 4.3 25.0 1.0 O C:HOH129 4.4 29.8 1.0 CA B:ASN96 4.4 19.6 1.0 CA A:ASN96 4.4 19.8 1.0 O B:HOH216 4.4 27.0 1.0 ND2 B:ASN96 4.4 24.2 1.0 ND2 A:ASN96 4.4 23.6 1.0 HD22 B:ASN96 4.5 29.0 1.0 HD21 A:ASN96 4.5 28.4 1.0 O A:HOH208 4.5 25.4 1.0 O B:ASP93 4.6 20.8 1.0 HB3 B:ASP93 4.7 22.6 1.0 OD2 D:ASP874 4.8 36.8 1.0 O C:HOH522 4.8 39.6 1.0 O A:ASP93 4.8 18.1 1.0 HB3 A:ASP93 4.9 21.6 1.0 H B:ASN96 5.0 21.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Ihhn 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 Ihhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:19.2 occ:1.00 OE2 B:GLU95 2.3 16.9 1.0 OD1 B:ASP134 2.3 20.2 1.0 OD2 B:ASP136 2.4 16.9 1.0 O B:HOH2 2.4 19.2 1.0 OE1 B:GLU131 2.5 16.6 1.0 OE2 B:GLU131 2.5 16.1 1.0 O C:HOH11 2.5 18.1 1.0 CD B:GLU131 2.9 18.1 1.0 O B:HOH200 3.1 19.3 1.0 HB2 B:ASP136 3.4 23.0 1.0 CG B:ASP134 3.4 21.2 1.0 CD B:GLU95 3.4 16.6 1.0 CG B:ASP136 3.5 18.5 1.0 HA B:ASP134 3.6 22.2 1.0 HB2 B:ASP134 3.6 22.0 1.0 HG2 B:GLU95 3.7 20.5 1.0 H B:ASP136 3.8 22.6 1.0 CA B:CA4 3.9 18.2 1.0 CB B:ASP134 3.9 18.3 1.0 CB B:ASP136 4.0 19.2 1.0 CG B:GLU95 4.0 17.0 1.0 OE2 B:GLU94 4.0 17.1 1.0 HG3 B:GLU95 4.1 20.5 1.0 NE2 B:HIS138 4.1 18.2 1.0 HE2 B:HIS139 4.2 22.4 1.0 CA B:ASP134 4.3 18.5 1.0 H B:GLU135 4.3 23.3 1.0 CG B:GLU131 4.4 16.1 1.0 OD1 B:ASP100 4.4 18.9 1.0 OD2 B:ASP134 4.4 19.3 1.0 OE1 B:GLU95 4.5 16.9 1.0 HA B:GLU131 4.6 23.1 1.0 N B:ASP136 4.6 18.8 1.0 OD1 B:ASP136 4.6 19.3 1.0 HB3 B:ASP136 4.6 23.0 1.0 O C:VAL918 4.6 19.5 1.0 HD2 B:HIS138 4.7 23.9 1.0 O B:TRP133 4.7 20.6 1.0 HG3 B:GLU131 4.8 19.3 1.0 HG2 B:GLU131 4.8 19.3 1.0 HB3 B:GLU131 4.8 21.2 1.0 CD2 B:HIS138 4.8 19.9 1.0 N B:GLU135 4.8 19.4 1.0 HB3 B:ASP134 4.9 22.0 1.0 HB1 B:ALA99 4.9 18.6 1.0 CA B:ASP136 4.9 17.5 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Ihhn 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 Ihhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4 b:18.2 occ:1.00 OE2 B:GLU131 2.3 16.1 1.0 O B:THR130 2.4 16.4 1.0 OE1 B:GLU94 2.4 18.8 1.0 OE2 B:GLU94 2.5 17.1 1.0 OD2 B:ASP100 2.5 17.6 1.0 OD1 B:ASP100 2.5 18.9 1.0 OE2 B:GLU95 2.5 16.9 1.0 OE1 B:GLU95 2.6 16.9 1.0 CD B:GLU94 2.8 19.5 1.0 CG B:ASP100 2.8 20.2 1.0 CD B:GLU95 2.9 16.6 1.0 HA B:GLU131 3.1 23.1 1.0 C B:THR130 3.5 16.4 1.0 CD B:GLU131 3.6 18.1 1.0 H B:GLU94 3.7 21.4 1.0 H B:ASP93 3.9 22.0 1.0 HG2 B:GLU131 3.9 19.3 1.0 HB3 B:LYS92 3.9 23.6 1.0 O B:HOH2 3.9 19.2 1.0 CA B:CA3 3.9 19.2 1.0 CA B:GLU131 4.0 19.2 1.0 HD11 C:ILE920 4.0 24.7 1.0 HD3 B:LYS92 4.1 22.6 1.0 HA B:ASP93 4.1 24.3 1.0 O C:HOH11 4.2 18.1 1.0 H B:GLU95 4.2 19.7 1.0 N B:GLU131 4.2 18.3 1.0 CG B:GLU131 4.2 16.1 1.0 CG B:GLU94 4.2 18.6 1.0 O B:HOH7 4.3 19.0 1.0 CB B:ASP100 4.4 16.8 1.0 N B:GLU94 4.4 17.8 1.0 N B:ASP93 4.4 18.3 1.0 CG B:GLU95 4.4 17.0 1.0 HG2 B:GLU94 4.5 22.4 1.0 HA B:THR130 4.5 20.4 1.0 OE1 B:GLU131 4.5 16.6 1.0 HG2 B:LYS92 4.6 24.6 1.0 H B:GLY132 4.6 21.0 1.0 CB B:GLU131 4.7 17.7 1.0 HG3 B:GLU95 4.7 20.5 1.0 CA B:THR130 4.7 17.0 1.0 CA B:ASP93 4.7 20.3 1.0 HB3 B:ASP100 4.7 20.1 1.0 HD12 C:ILE920 4.7 24.7 1.0 HB2 B:ASP100 4.8 20.1 1.0 HG3 B:GLU94 4.8 22.4 1.0 CD1 C:ILE920 4.8 20.6 1.0 CB B:LYS92 4.8 19.6 1.0 HG2 B:GLU95 4.9 20.5 1.0 CD B:LYS92 4.9 18.8 1.0 HB B:THR130 4.9 19.4 1.0 N B:GLU95 5.0 16.4 1.0 HE3 B:LYS92 5.0 21.7 1.0 CG B:LYS92 5.0 20.5 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Ihhn 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 Ihhn Bound to CDOFN3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca7 b:28.7 occ:1.00 HD2 C:HIS893 2.1 40.7 1.0 O C:HOH718 2.3 31.6 1.0 CD2 C:HIS893 2.9 33.9 1.0 HB3 C:HIS893 3.4 29.8 1.0 CG C:HIS893 3.7 31.8 1.0 NE2 C:HIS893 3.9 40.9 1.0 CB C:HIS893 4.0 24.9 1.0 HE2 C:HIS893 4.0 49.1 1.0 HA C:HIS893 4.2 26.3 1.0 O C:HOH23 4.5 24.3 1.0 O C:HOH164 4.5 28.8 1.0 CA C:HIS893 4.7 21.9 1.0 HB2 C:HIS893 4.8 29.8 1.0 ND1 C:HIS893 4.9 38.4 1.0 CE1 C:HIS893 4.9 33.1 1.0

J.M.Kavran, M.D.Ward, O.O.Oladosu, S.Mulepati, D.J.Leahy. All Mammalian Hedgehog Proteins Interact with Cell Adhesion Molecule, Down-Regulated By Oncogenes (Cdo) and Brother of Cdo (Boc) in A Conserved Manner. J.Biol.Chem. V. 285 24584 2010.
ISSN: ISSN 0021-9258
PubMed: 20519495
DOI: 10.1074/JBC.M110.131680