Sodium in PDB 7rpi: Cryo-Em Structure of Murine Dispatched 'T' Conformation

The binding sites of Sodium atom in the Cryo-Em Structure of Murine Dispatched 'T' Conformation (pdb code 7rpi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cryo-Em Structure of Murine Dispatched 'T' Conformation, PDB code: 7rpi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cryo-Em Structure of Murine Dispatched 'T' Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of Murine Dispatched 'T' Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2134 b:72.2 occ:1.00 OD1 A:ASP1049 2.2 70.7 1.0 O A:GLY1045 2.2 67.2 1.0 OG1 A:THR613 2.3 68.4 1.0 OG1 A:THR614 2.3 65.4 1.0 OD2 A:ASP1049 2.4 70.7 1.0 O A:THR610 2.4 69.3 1.0 CG A:ASP1049 2.6 70.7 1.0 C A:GLY1045 3.3 67.2 1.0 CB A:THR613 3.4 68.4 1.0 O A:HOH2202 3.4 30.0 1.0 N A:THR614 3.4 65.4 1.0 C A:THR610 3.5 69.3 1.0 CB A:THR614 3.6 65.4 1.0 CA A:THR610 3.9 69.3 1.0 C A:THR613 3.9 68.4 1.0 CA A:LEU1046 3.9 66.9 1.0 CA A:THR614 4.0 65.4 1.0 N A:LEU1046 4.0 66.9 1.0 CB A:ASP1049 4.1 70.7 1.0 CA A:THR613 4.2 68.4 1.0 O A:LEU1046 4.2 66.9 1.0 C A:LEU1046 4.4 66.9 1.0 CA A:GLY1045 4.4 67.2 1.0 CB A:VAL1048 4.4 70.2 1.0 CB A:THR610 4.5 69.3 1.0 CG2 A:THR613 4.5 68.4 1.0 N A:ASP1049 4.6 70.7 1.0 N A:THR613 4.6 68.4 1.0 O A:VAL609 4.6 70.6 1.0 O A:HOH2213 4.6 30.0 1.0 CG2 A:THR614 4.6 65.4 1.0 O A:THR613 4.7 68.4 1.0 N A:SER611 4.7 68.6 1.0 CA A:ASP1049 4.8 70.7 1.0 CG2 A:VAL1048 4.8 70.2 1.0 N A:VAL1048 5.0 70.2 1.0

Sodium binding site 2 out of 2 in the Cryo-Em Structure of Murine Dispatched 'T' Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of Murine Dispatched 'T' Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na2135 b:76.9 occ:1.00 OD1 A:ASP572 2.2 74.2 1.0 OD2 A:ASP572 2.2 74.2 1.0 O A:HOH2231 2.3 30.0 1.0 O A:MET607 2.3 72.9 1.0 OG A:SER611 2.4 68.6 1.0 OG1 A:THR610 2.5 69.3 1.0 CG A:ASP572 2.6 74.2 1.0 C A:MET607 3.3 72.9 1.0 N A:SER611 3.4 68.6 1.0 CB A:SER611 3.5 68.6 1.0 CA A:MET607 3.6 72.9 1.0 CB A:THR610 3.8 69.3 1.0 O A:HOH2207 3.8 30.0 1.0 CA A:SER611 3.8 68.6 1.0 O A:HOH2205 3.9 30.0 1.0 C A:THR610 4.0 69.3 1.0 O A:HOH2236 4.0 30.0 1.0 CB A:ASP572 4.1 74.2 1.0 CB A:MET607 4.2 72.9 1.0 O A:HOH2214 4.3 30.0 1.0 CA A:THR610 4.3 69.3 1.0 O A:HOH2211 4.4 30.0 1.0 N A:PHE608 4.5 74.8 1.0 O A:SER606 4.6 73.8 1.0 N A:THR610 4.6 69.3 1.0 CD1 A:TYR644 4.7 72.1 1.0 O A:THR610 4.8 69.3 1.0 CA A:ASP572 4.8 74.2 1.0 N A:MET607 4.9 72.9 1.0 CG A:MET607 4.9 72.9 1.0 CG2 A:THR610 4.9 69.3 1.0 O A:PHE608 4.9 74.8 1.0 N A:ASP572 5.0 74.2 1.0 CA A:PHE608 5.0 74.8 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