Sodium in PDB 7rph: Cryo-Em Structure of Murine Dispatched 'R' Conformation

The binding sites of Sodium atom in the Cryo-Em Structure of Murine Dispatched 'R' Conformation (pdb code 7rph). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cryo-Em Structure of Murine Dispatched 'R' Conformation, PDB code: 7rph:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cryo-Em Structure of Murine Dispatched 'R' 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 'R' Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1601 b:61.1 occ:1.00 OD1 A:ASP1049 2.2 63.2 1.0 OG1 A:THR613 2.2 60.7 1.0 O A:GLY1045 2.4 58.4 1.0 O A:THR610 2.7 61.5 1.0 OG1 A:THR614 3.0 58.2 1.0 CG A:ASP1049 3.2 63.2 1.0 CB A:THR613 3.4 60.7 1.0 N A:THR614 3.5 58.2 1.0 C A:GLY1045 3.5 58.4 1.0 C A:THR610 3.6 61.5 1.0 OD2 A:ASP1049 3.6 63.2 1.0 CA A:THR610 3.8 61.5 1.0 C A:THR613 3.8 60.7 1.0 CB A:VAL1048 3.9 61.9 1.0 CA A:THR613 3.9 60.7 1.0 O A:HOH1744 4.1 60.9 1.0 O A:VAL609 4.1 63.5 1.0 CG1 A:VAL1048 4.1 61.9 1.0 CB A:THR614 4.2 58.2 1.0 CA A:THR614 4.3 58.2 1.0 N A:THR613 4.3 60.7 1.0 CA A:GLY1045 4.4 58.4 1.0 N A:LEU1046 4.4 59.2 1.0 O A:LEU1046 4.5 59.2 1.0 N A:ASP1049 4.5 63.2 1.0 CA A:LEU1046 4.5 59.2 1.0 O A:THR613 4.5 60.7 1.0 CG2 A:THR613 4.5 60.7 1.0 CB A:THR610 4.6 61.5 1.0 CB A:ASP1049 4.6 63.2 1.0 CG2 A:VAL1048 4.7 61.9 1.0 C A:LEU1046 4.7 59.2 1.0 N A:SER611 4.7 60.9 1.0 N A:THR610 4.8 61.5 1.0 CA A:ASP1049 4.8 63.2 1.0 CA A:VAL1048 4.8 61.9 1.0 C A:VAL609 4.9 63.5 1.0 N A:VAL1048 4.9 61.9 1.0

Sodium binding site 2 out of 3 in the Cryo-Em Structure of Murine Dispatched 'R' 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 'R' Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1602 b:67.0 occ:1.00 OD1 A:ASP571 2.0 64.5 1.0 O A:GLY567 2.2 62.5 1.0 OG1 A:THR1087 2.6 63.1 1.0 OG1 A:THR1088 2.8 61.6 1.0 O A:ALA1084 3.0 63.3 1.0 CG A:ASP571 3.0 64.5 1.0 OD2 A:ASP571 3.3 64.5 1.0 C A:GLY567 3.4 62.5 1.0 O A:HOH1735 3.4 30.0 1.0 CB A:THR1087 3.6 63.1 1.0 N A:THR1088 3.6 61.6 1.0 C A:ALA1084 3.8 63.3 1.0 CA A:ILE568 3.8 61.4 1.0 CA A:ALA1084 3.9 63.3 1.0 C A:THR1087 3.9 63.1 1.0 N A:ILE568 4.0 61.4 1.0 CB A:THR1088 4.0 61.6 1.0 O A:HOH1741 4.1 63.5 1.0 CA A:THR1087 4.1 63.1 1.0 CA A:THR1088 4.2 61.6 1.0 N A:ASP571 4.3 64.5 1.0 CB A:ASP571 4.3 64.5 1.0 C A:ILE568 4.3 61.4 1.0 CB A:ALA1084 4.4 63.3 1.0 CA A:GLY567 4.5 62.5 1.0 N A:THR1087 4.5 63.1 1.0 O A:THR1087 4.6 63.1 1.0 CA A:ASP571 4.7 64.5 1.0 O A:ILE568 4.7 61.4 1.0 O A:MET1083 4.8 65.7 1.0 N A:ALA570 4.8 65.7 1.0 CG2 A:THR1087 4.8 63.1 1.0 CE2 A:PHE574 4.9 65.0 1.0 CB A:ILE568 4.9 61.4 1.0 N A:GLY569 4.9 62.2 1.0 C A:ALA570 5.0 65.7 1.0

Sodium binding site 3 out of 3 in the Cryo-Em Structure of Murine Dispatched 'R' Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Structure of Murine Dispatched 'R' Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1603 b:64.8 occ:1.00 OD2 A:ASP572 2.3 66.6 1.0 O A:HOH1776 2.3 62.8 1.0 OD1 A:ASP572 2.4 66.6 1.0 OG A:SER611 2.5 60.9 1.0 O A:MET607 2.6 64.9 1.0 CG A:ASP572 2.6 66.6 1.0 OG1 A:THR610 2.8 61.5 1.0 C A:MET607 3.5 64.9 1.0 CB A:SER611 3.6 60.9 1.0 N A:SER611 3.6 60.9 1.0 CA A:MET607 3.8 64.9 1.0 O A:HOH1704 3.8 65.4 1.0 O A:HOH1713 3.9 63.9 1.0 CA A:SER611 4.0 60.9 1.0 CB A:THR610 4.0 61.5 1.0 O A:HOH1708 4.0 64.7 1.0 O A:HOH1739 4.1 62.8 1.0 CB A:ASP572 4.1 66.6 1.0 C A:THR610 4.1 61.5 1.0 CB A:MET607 4.3 64.9 1.0 O A:HOH1712 4.4 62.5 1.0 O A:HOH1780 4.4 61.2 1.0 CA A:THR610 4.5 61.5 1.0 N A:PHE608 4.7 65.3 1.0 CG A:MET607 4.8 64.9 1.0 CD1 A:TYR644 4.8 62.7 1.0 O A:THR610 4.8 61.5 1.0 N A:THR610 4.8 61.5 1.0 CA A:ASP572 4.9 66.6 1.0 O A:SER606 5.0 65.9 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