Calcium in PDB 7rpk: Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog

The structure of Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog (pdb code 7rpk). 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 Murine Dispatched in Complex with Sonic Hedgehog, PDB code: 7rpk:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog


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 Murine Dispatched in Complex with Sonic Hedgehog within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca201 b:103.4 occ:1.00 OE2 H:GLU90 2.3 109.3 1.0 OE2 H:GLU127 2.3 100.1 1.0 OE2 H:GLU91 2.3 108.0 1.0 OD2 H:ASP96 2.3 97.0 1.0 OD1 H:ASP96 2.4 97.0 1.0 OE1 H:GLU91 2.6 108.0 1.0 O H:THR126 2.6 103.7 1.0 CG H:ASP96 2.7 97.0 1.0 CD H:GLU91 2.8 108.0 1.0 CD H:GLU90 2.9 109.3 1.0 OE1 H:GLU90 2.9 109.3 1.0 O H:LYS88 3.3 108.8 1.0 CD H:GLU127 3.4 100.1 1.0 CA H:ASP89 3.5 107.9 1.0 CA H:CA202 3.6 102.1 1.0 N H:GLU90 3.7 109.3 1.0 C H:THR126 3.7 103.7 1.0 C H:ASP89 4.1 107.9 1.0 CA H:GLU127 4.1 100.1 1.0 OE1 H:GLU127 4.1 100.1 1.0 C H:LYS88 4.2 108.8 1.0 OD2 H:ASP89 4.2 107.9 1.0 CB H:ASP96 4.2 97.0 1.0 CG H:GLU91 4.3 108.0 1.0 N H:ASP89 4.3 107.9 1.0 CG H:GLU90 4.3 109.3 1.0 CG H:GLU127 4.3 100.1 1.0 N H:GLU127 4.3 100.1 1.0 CG H:ASP89 4.4 107.9 1.0 CB H:ASP89 4.4 107.9 1.0 N H:GLU91 4.7 108.0 1.0 CA H:GLU90 4.7 109.3 1.0 CA H:THR126 4.8 103.7 1.0 CB H:GLU127 4.8 100.1 1.0 CB H:GLU90 4.8 109.3 1.0

Calcium binding site 2 out of 2 in the Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog


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 Murine Dispatched in Complex with Sonic Hedgehog within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca202 b:102.1 occ:1.00 OD2 H:ASP132 2.3 103.5 1.0 OE1 H:GLU91 2.3 108.0 1.0 OE1 H:GLU127 2.3 100.1 1.0 OE2 H:GLU127 2.4 100.1 1.0 OD1 H:ASP130 2.4 97.8 1.0 OE1 H:GLU90 2.5 109.3 1.0 CD H:GLU127 2.7 100.1 1.0 CD H:GLU91 3.1 108.0 1.0 CG H:ASP132 3.3 103.5 1.0 CD2 H:HIS134 3.3 105.1 1.0 CG H:ASP130 3.3 97.8 1.0 NE2 H:HIS134 3.4 105.1 1.0 CA H:CA201 3.6 103.4 1.0 CG H:GLU91 3.6 108.0 1.0 CD H:GLU90 3.7 109.3 1.0 OD2 H:ASP130 4.0 97.8 1.0 OE2 H:GLU91 4.0 108.0 1.0 OD1 H:ASP132 4.0 103.5 1.0 CB H:ASP132 4.1 103.5 1.0 CG H:GLU127 4.2 100.1 1.0 CB H:ASP130 4.2 97.8 1.0 OE2 H:GLU90 4.3 109.3 1.0 OD1 H:ASP96 4.4 97.0 1.0 CA H:ASP130 4.5 97.8 1.0 CG H:HIS134 4.6 105.1 1.0 CE1 H:HIS134 4.8 105.1 1.0 CG H:GLU90 4.8 109.3 1.0 N H:ASP132 4.8 103.5 1.0 CE1 H:HIS135 5.0 102.6 1.0

Q.Wang, D.E.Asarnow, K.Ding, R.Mann, J.Hatekeyama, Y.Zhang, Y.Ma, Y.Cheng, P.A.Beachy. Dispatched Uses Na+ Flux to Power Release of Lipid-Modified Hedgehog Nature 2021.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-021-03996-0