Calcium in PDB 6n7k: Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II)

The structure of Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) (pdb code 6n7k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II), PDB code: 6n7k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:18.7 occ:1.00 OE2 C:GLU90 2.7 15.6 1.0 CB C:ASP129 2.9 9.0 1.0 CA C:ASP129 3.2 10.8 1.0 CD C:GLU90 3.6 17.6 1.0 OD2 C:ASP129 3.7 16.0 1.0 CG C:ASP129 3.8 11.7 1.0 OE2 C:GLU89 3.9 19.8 1.0 OE1 C:GLU90 4.0 14.5 1.0 CA C:CA204 4.0 12.0 1.0 N C:ASP129 4.1 10.1 1.0 C C:ASP129 4.3 12.8 1.0 NE2 C:HIS134 4.4 15.4 1.0 ND1 C:HIS133 4.4 37.2 1.0 N C:GLU130 4.5 14.0 1.0 OD1 C:ASP95 4.5 10.8 1.0 O C:TRP128 4.7 12.0 1.0 CE1 C:HIS133 4.7 42.2 1.0 C C:TRP128 4.8 11.7 1.0 CG C:GLU90 4.8 16.4 1.0 CD C:GLU89 4.9 20.4 1.0 CG C:GLU126 4.9 20.1 1.0 OD1 C:ASP129 5.0 15.6 1.0 CB C:GLU126 5.0 13.9 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca204 b:12.0 occ:1.00 OE2 C:GLU89 2.4 19.8 1.0 O C:THR125 2.5 11.9 1.0 OD1 C:ASP95 2.5 10.8 1.0 OD2 C:ASP95 2.5 13.6 1.0 OE1 C:GLU89 2.5 19.2 1.0 CG C:ASP95 2.8 12.1 1.0 CD C:GLU89 2.8 20.4 1.0 CG C:GLU126 3.0 20.1 1.0 CA C:GLU126 3.0 9.9 1.0 CB C:GLU126 3.4 13.9 1.0 C C:THR125 3.4 10.1 1.0 N C:GLU126 3.6 8.3 1.0 OE1 C:GLU90 3.9 14.5 1.0 CA C:CA203 4.0 18.7 1.0 C C:GLU126 4.2 12.5 1.0 N C:GLY127 4.2 7.7 1.0 CB C:ASP95 4.2 9.0 1.0 OE2 C:GLU90 4.3 15.6 1.0 CD C:GLU126 4.3 20.4 1.0 CG C:GLU89 4.3 17.4 1.0 CD C:GLU90 4.5 17.6 1.0 OE2 C:GLU126 4.7 18.1 1.0 CA C:THR125 4.7 9.0 1.0 N C:GLU89 4.9 18.5 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca203 b:18.7 occ:1.00 OE2 F:GLU90 2.7 15.6 1.0 CB F:ASP129 2.9 9.0 1.0 CA F:ASP129 3.2 10.8 1.0 CD F:GLU90 3.6 17.6 1.0 OD2 F:ASP129 3.7 16.0 1.0 CG F:ASP129 3.8 11.7 1.0 OE2 F:GLU89 3.9 19.8 1.0 OE1 F:GLU90 4.0 14.5 1.0 CA F:CA204 4.0 12.0 1.0 N F:ASP129 4.1 10.1 1.0 C F:ASP129 4.3 12.8 1.0 NE2 F:HIS134 4.4 15.4 1.0 ND1 F:HIS133 4.4 37.2 1.0 N F:GLU130 4.5 14.0 1.0 OD1 F:ASP95 4.5 10.8 1.0 O F:TRP128 4.7 12.0 1.0 CE1 F:HIS133 4.7 42.2 1.0 C F:TRP128 4.8 11.7 1.0 CG F:GLU90 4.8 16.4 1.0 CD F:GLU89 4.9 20.4 1.0 CG F:GLU126 4.9 20.1 1.0 OD1 F:ASP129 5.0 15.6 1.0 CB F:GLU126 5.0 13.9 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Tetrameric PTCH1 in Complex with Shhnp (Form II) within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca204 b:12.0 occ:1.00 OE2 F:GLU89 2.4 19.8 1.0 O F:THR125 2.5 11.9 1.0 OD1 F:ASP95 2.5 10.8 1.0 OD2 F:ASP95 2.5 13.6 1.0 OE1 F:GLU89 2.5 19.2 1.0 CG F:ASP95 2.8 12.1 1.0 CD F:GLU89 2.8 20.4 1.0 CG F:GLU126 3.0 20.1 1.0 CA F:GLU126 3.0 9.9 1.0 CB F:GLU126 3.4 13.9 1.0 C F:THR125 3.4 10.1 1.0 N F:GLU126 3.6 8.3 1.0 OE1 F:GLU90 3.9 14.5 1.0 CA F:CA203 4.0 18.7 1.0 C F:GLU126 4.2 12.5 1.0 N F:GLY127 4.2 7.7 1.0 CB F:ASP95 4.2 9.0 1.0 OE2 F:GLU90 4.3 15.6 1.0 CD F:GLU126 4.3 20.4 1.0 CG F:GLU89 4.3 17.4 1.0 CD F:GLU90 4.5 17.6 1.0 OE2 F:GLU126 4.7 18.1 1.0 CA F:THR125 4.7 9.0 1.0 N F:GLU89 4.9 18.5 1.0

N.Yan, X.Gong, H.W.Qian. Cryo-Em Structure of the 2:1 HPTCH1-Shhp Complex To Be Published.