Sodium in PDB 7lfy: Cryo-Em Structure of Human Cgmp-Bound Open CNGA1 Channel in Na+

The binding sites of Sodium atom in the Cryo-Em Structure of Human Cgmp-Bound Open CNGA1 Channel in Na+ (pdb code 7lfy). 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 Human Cgmp-Bound Open CNGA1 Channel in Na+, PDB code: 7lfy:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cryo-Em Structure of Human Cgmp-Bound Open CNGA1 Channel in Na+


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 Human Cgmp-Bound Open CNGA1 Channel in Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:30.0 occ:1.00 NA A:NA703 2.5 30.0 1.0 O B:HOH801 3.1 30.0 1.0 O A:HOH801 3.1 30.0 1.0 O D:HOH801 3.1 30.0 1.0 O C:HOH801 3.1 30.0 1.0 O D:THR362 3.4 17.5 1.0 O A:THR362 3.4 17.5 1.0 O C:THR362 3.4 17.5 1.0 O B:THR362 3.4 17.5 1.0 C D:THR362 4.5 17.5 1.0 C A:THR362 4.5 17.5 1.0 C C:THR362 4.5 17.5 1.0 C B:THR362 4.5 17.5 1.0 CA D:ILE363 4.7 17.6 1.0 CA C:ILE363 4.7 17.6 1.0 CA A:ILE363 4.7 17.6 1.0 CA B:ILE363 4.7 17.6 1.0 OG1 D:THR362 4.9 17.5 1.0 OG1 A:THR362 5.0 17.5 1.0 OG1 C:THR362 5.0 17.5 1.0 OG1 B:THR362 5.0 17.5 1.0

Sodium binding site 2 out of 3 in the Cryo-Em Structure of Human Cgmp-Bound Open CNGA1 Channel in Na+


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 Human Cgmp-Bound Open CNGA1 Channel in Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:30.0 occ:1.00 NA A:NA702 2.5 30.0 1.0 NA A:NA704 3.3 30.0 1.0 O D:ILE363 3.3 17.6 1.0 O C:ILE363 3.4 17.6 1.0 O A:ILE363 3.4 17.6 1.0 O B:ILE363 3.4 17.6 1.0 O D:THR362 4.1 17.5 1.0 O A:THR362 4.1 17.5 1.0 O C:THR362 4.1 17.5 1.0 O B:THR362 4.1 17.5 1.0 CA D:ILE363 4.1 17.6 1.0 C D:ILE363 4.1 17.6 1.0 CA C:ILE363 4.1 17.6 1.0 C C:ILE363 4.1 17.6 1.0 C A:ILE363 4.1 17.6 1.0 CA A:ILE363 4.1 17.6 1.0 CA B:ILE363 4.2 17.6 1.0 C B:ILE363 4.2 17.6 1.0 CG2 C:ILE363 4.6 17.6 1.0 CG2 D:ILE363 4.6 17.6 1.0 CG2 A:ILE363 4.6 17.6 1.0 CG2 B:ILE363 4.6 17.6 1.0 OE2 C:GLU365 4.8 19.7 1.0 OE2 D:GLU365 4.8 19.7 1.0 OE2 B:GLU365 4.8 19.7 1.0 OE2 A:GLU365 4.8 19.7 1.0

Sodium binding site 3 out of 3 in the Cryo-Em Structure of Human Cgmp-Bound Open CNGA1 Channel in Na+


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 Human Cgmp-Bound Open CNGA1 Channel in Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na704 b:30.0 occ:1.00 OE2 C:GLU365 2.3 19.7 1.0 OE2 D:GLU365 2.3 19.7 1.0 OE2 A:GLU365 2.3 19.7 1.0 OE2 B:GLU365 2.3 19.7 1.0 NA A:NA703 3.3 30.0 1.0 CD C:GLU365 3.4 19.7 1.0 CD D:GLU365 3.4 19.7 1.0 CD A:GLU365 3.4 19.7 1.0 CD B:GLU365 3.4 19.7 1.0 O D:ILE363 3.5 17.6 1.0 O A:ILE363 3.5 17.6 1.0 O C:ILE363 3.5 17.6 1.0 O B:ILE363 3.5 17.6 1.0 OE1 C:GLU365 4.1 19.7 1.0 OE1 D:GLU365 4.1 19.7 1.0 OE1 A:GLU365 4.1 19.7 1.0 OE1 B:GLU365 4.1 19.7 1.0 CG D:GLU365 4.3 19.7 1.0 CG C:GLU365 4.3 19.7 1.0 CG A:GLU365 4.3 19.7 1.0 CG B:GLU365 4.4 19.7 1.0 C D:ILE363 4.7 17.6 1.0 C A:ILE363 4.7 17.6 1.0 C C:ILE363 4.7 17.6 1.0 C B:ILE363 4.7 17.6 1.0

J.Xue, Y.Han, W.Zeng, Y.Wang, Y.Jiang. Structural Mechanisms of Gating and Selectivity of Human Rod CNGA1 Channel. Neuron 2021.
ISSN: ISSN 0896-6273
PubMed: 33651975
DOI: 10.1016/J.NEURON.2021.02.007