Calcium in PDB 6dmy: Cryo-Em Structure of Human PTCH1 and Shhn Complex

The structure of Cryo-Em Structure of Human PTCH1 and Shhn Complex also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Cryo-Em Structure of Human PTCH1 and Shhn Complex (pdb code 6dmy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cryo-Em Structure of Human PTCH1 and Shhn Complex, PDB code: 6dmy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Human PTCH1 and Shhn Complex


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 Human PTCH1 and Shhn Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:18.7 occ:1.00 OE2 B:GLU90 2.7 15.6 1.0 CB B:ASP129 2.9 9.0 1.0 CA B:ASP129 3.2 10.8 1.0 CD B:GLU90 3.6 17.6 1.0 OD1 B:ASP129 3.7 16.0 1.0 CG B:ASP129 3.8 11.7 1.0 OE2 B:GLU89 3.9 19.8 1.0 OE1 B:GLU90 4.0 14.5 1.0 CA B:CA204 4.0 12.0 1.0 N B:ASP129 4.1 10.1 1.0 C B:ASP129 4.3 12.8 1.0 NE2 B:HIS134 4.4 15.4 1.0 ND1 B:HIS133 4.4 37.2 1.0 N B:GLU130 4.5 14.0 1.0 OD1 B:ASP95 4.5 10.8 1.0 O B:TRP128 4.7 12.0 1.0 CE1 B:HIS133 4.7 42.2 1.0 C B:TRP128 4.8 11.7 1.0 CG B:GLU90 4.8 16.4 1.0 CD B:GLU89 4.9 20.4 1.0 CG B:GLU126 4.9 20.1 1.0 OD2 B:ASP129 5.0 15.6 1.0 CB B:GLU126 5.0 13.9 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Human PTCH1 and Shhn Complex


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 Human PTCH1 and Shhn Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:12.0 occ:1.00 OE2 B:GLU89 2.4 19.8 1.0 O B:THR125 2.5 11.9 1.0 OD1 B:ASP95 2.5 10.8 1.0 OD2 B:ASP95 2.5 13.6 1.0 OE1 B:GLU89 2.5 19.2 1.0 CG B:ASP95 2.8 12.1 1.0 CD B:GLU89 2.8 20.4 1.0 CG B:GLU126 3.0 20.1 1.0 CA B:GLU126 3.0 9.9 1.0 CB B:GLU126 3.4 13.9 1.0 C B:THR125 3.4 10.1 1.0 N B:GLU126 3.6 8.3 1.0 OE1 B:GLU90 3.9 14.5 1.0 CA B:CA203 4.0 18.7 1.0 C B:GLU126 4.2 12.5 1.0 N B:GLY127 4.2 7.7 1.0 CB B:ASP95 4.2 9.0 1.0 OE2 B:GLU90 4.3 15.6 1.0 CD B:GLU126 4.3 20.4 1.0 CG B:GLU89 4.3 17.4 1.0 CD B:GLU90 4.5 17.6 1.0 OE2 B:GLU126 4.7 18.1 1.0 CA B:THR125 4.7 9.0 1.0 N B:GLU89 4.9 18.5 1.0

X.Gong, H.Qian, P.Cao, X.Zhao, Q.Zhou, J.Lei, N.Yan. Structural Basis For the Recognition of Sonic Hedgehog By Human PATCHED1. Science V. 361 2018.
ISSN: ESSN 1095-9203
PubMed: 29954986
DOI: 10.1126/SCIENCE.AAS8935