Zinc 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:

Calcium	(Ca)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was determined in the Cryo-Em Structure of Murine Dispatched in Complex with Sonic Hedgehog, PDB code: 7rpk:

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn203 b:116.8 occ:1.00 OD1 H:ASP148 1.7 99.0 1.0 NE2 H:HIS141 1.9 93.9 1.0 ND1 H:HIS183 2.0 92.9 1.0 CG H:ASP148 2.7 99.0 1.0 CE1 H:HIS141 2.9 93.9 1.0 CE1 H:HIS183 2.9 92.9 1.0 OD2 H:ASP148 3.0 99.0 1.0 CD2 H:HIS141 3.0 93.9 1.0 CG H:HIS183 3.1 92.9 1.0 OE1 H:GLU177 3.7 101.2 1.0 CB H:HIS183 3.7 92.9 1.0 CD2 H:HIS135 3.9 102.6 1.0 NE2 H:HIS135 4.0 102.6 1.0 ND1 H:HIS141 4.0 93.9 1.0 NE2 H:HIS183 4.1 92.9 1.0 CB H:ASP148 4.1 99.0 1.0 CG H:HIS141 4.1 93.9 1.0 CD2 H:HIS183 4.2 92.9 1.0 CD H:GLU177 4.5 101.2 1.0 CA H:HIS183 4.6 92.9 1.0 CA H:ASP148 4.6 99.0 1.0 N H:ASP148 4.6 99.0 1.0 OE2 H:GLU177 4.6 101.2 1.0 O H:VAL147 4.6 94.2 1.0 NE2 H:HIS181 4.7 104.7 1.0 C H:VAL147 4.7 94.2 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