Sodium in PDB 7d3f: Cryo-Em Structure of Human DUOX1-DUOXA1 in High-Calcium State

All present enzymatic activity of Cryo-Em Structure of Human DUOX1-DUOXA1 in High-Calcium State:
1.6.3.1;

The structure of Cryo-Em Structure of Human DUOX1-DUOXA1 in High-Calcium State also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Calcium	(Ca)	4 atoms

The binding sites of Sodium atom in the Cryo-Em Structure of Human DUOX1-DUOXA1 in High-Calcium State (pdb code 7d3f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Cryo-Em Structure of Human DUOX1-DUOXA1 in High-Calcium State, PDB code: 7d3f:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Cryo-Em Structure of Human DUOX1-DUOXA1 in High-Calcium State


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 DUOX1-DUOXA1 in High-Calcium State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1610 b:44.6 occ:1.00 O A:THR332 2.5 54.4 1.0 O A:VAL399 2.5 62.8 1.0 OD1 A:ASP397 2.5 64.0 1.0 O A:ARG395 2.5 62.5 1.0 OG1 A:THR332 3.4 56.0 1.0 C A:VAL399 3.6 54.8 1.0 C A:THR332 3.6 48.2 1.0 C A:ARG395 3.7 57.5 1.0 CG A:ASP397 3.7 66.3 1.0 N A:ARG395 4.0 54.5 1.0 CB A:GLU394 4.0 53.5 1.0 N A:ASP397 4.2 65.9 1.0 OD2 A:ASP397 4.3 71.2 1.0 CA A:ARG395 4.3 52.9 1.0 CA A:VAL399 4.3 50.5 1.0 CA A:THR332 4.3 40.9 1.0 CB A:VAL399 4.3 51.2 1.0 N A:VAL399 4.3 53.4 1.0 O A:ASP397 4.3 71.8 1.0 CB A:THR332 4.4 47.8 1.0 C A:GLU394 4.5 52.0 1.0 CB A:ARG395 4.6 50.2 1.0 C A:ASP397 4.6 61.6 1.0 N A:LEU400 4.6 51.0 1.0 N A:MET333 4.7 47.7 1.0 N A:GLU396 4.7 59.1 1.0 CA A:ASP397 4.8 56.6 1.0 CB A:ASP397 4.8 53.8 1.0 CG1 A:VAL399 4.8 54.7 1.0 CA A:LEU400 4.9 49.9 1.0 CG A:GLU394 4.9 59.1 1.0 CA A:GLU394 4.9 44.2 1.0 CA A:MET333 5.0 42.5 1.0

Sodium binding site 2 out of 4 in the Cryo-Em Structure of Human DUOX1-DUOXA1 in High-Calcium State


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 DUOX1-DUOXA1 in High-Calcium State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1611 b:26.8 occ:1.00 O A:TRP172 2.4 49.9 1.0 OG A:SER176 2.4 53.5 1.0 OG1 A:THR170 2.5 50.3 1.0 O A:ASP109 2.6 49.0 1.0 O A:THR170 2.6 48.1 1.0 OD1 A:ASP174 2.6 47.9 1.0 OD1 A:ASP109 2.7 52.9 1.0 CB A:SER176 3.0 39.0 1.0 C A:THR170 3.5 37.8 1.0 C A:TRP172 3.6 37.9 1.0 C A:ASP109 3.6 36.5 1.0 CG A:ASP109 3.7 52.1 1.0 CB A:THR170 3.8 36.9 1.0 CG A:ASP174 3.8 43.1 1.0 N A:SER176 3.9 43.7 1.0 CA A:SER176 4.0 32.4 1.0 CA A:THR170 4.1 33.4 1.0 N A:ASP174 4.1 45.9 1.0 N A:TRP172 4.2 41.1 1.0 N A:THR170 4.3 35.1 1.0 OD2 A:ASP109 4.3 63.4 1.0 CA A:ASP109 4.4 35.2 1.0 CA A:TRP172 4.4 33.0 1.0 OD2 A:ASP174 4.5 50.5 1.0 C A:GLY171 4.5 36.8 1.0 N A:LEU173 4.6 36.8 1.0 N A:LEU110 4.6 40.6 1.0 CB A:ASP109 4.6 38.3 1.0 N A:GLY171 4.6 38.1 1.0 CA A:LEU173 4.7 35.2 1.0 CA A:LEU110 4.7 34.0 1.0 CG2 A:THR170 4.8 40.1 1.0 CA A:ASP174 4.8 35.3 1.0 N A:GLY175 4.9 40.3 1.0 CB A:TRP172 4.9 34.3 1.0 CB A:ASP174 4.9 42.5 1.0 C A:LEU173 4.9 42.0 1.0 C A:ASP174 4.9 39.8 1.0 O A:LEU110 5.0 48.0 1.0 CA A:GLY171 5.0 34.1 1.0 C A:SER176 5.0 36.5 1.0

Sodium binding site 3 out of 4 in the Cryo-Em Structure of Human DUOX1-DUOXA1 in High-Calcium State


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 DUOX1-DUOXA1 in High-Calcium State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1610 b:46.6 occ:1.00 O C:THR332 2.5 55.7 1.0 O C:VAL399 2.5 64.4 1.0 OD1 C:ASP397 2.5 65.1 1.0 O C:ARG395 2.5 64.0 1.0 OG1 C:THR332 3.4 56.5 1.0 C C:VAL399 3.6 56.1 1.0 C C:THR332 3.6 49.6 1.0 C C:ARG395 3.7 59.0 1.0 CG C:ASP397 3.7 68.0 1.0 N C:ARG395 4.0 56.9 1.0 CB C:GLU394 4.0 53.9 1.0 N C:ASP397 4.2 67.9 1.0 OD2 C:ASP397 4.3 73.0 1.0 CA C:ARG395 4.3 55.3 1.0 CA C:VAL399 4.3 51.3 1.0 CA C:THR332 4.3 42.3 1.0 CB C:VAL399 4.3 52.8 1.0 N C:VAL399 4.3 54.0 1.0 O C:ASP397 4.3 73.5 1.0 CB C:THR332 4.4 48.5 1.0 C C:GLU394 4.5 53.4 1.0 CB C:ARG395 4.6 52.4 1.0 C C:ASP397 4.6 63.3 1.0 N C:LEU400 4.6 51.4 1.0 N C:MET333 4.7 48.3 1.0 N C:GLU396 4.7 60.4 1.0 CA C:ASP397 4.8 58.4 1.0 CB C:ASP397 4.8 56.1 1.0 CG1 C:VAL399 4.8 56.7 1.0 CA C:LEU400 4.9 50.6 1.0 CG C:GLU394 4.9 60.0 1.0 CA C:GLU394 4.9 46.0 1.0 CA C:MET333 5.0 44.4 1.0

Sodium binding site 4 out of 4 in the Cryo-Em Structure of Human DUOX1-DUOXA1 in High-Calcium State


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryo-Em Structure of Human DUOX1-DUOXA1 in High-Calcium State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1611 b:27.8 occ:1.00 O C:TRP172 2.4 49.9 1.0 OG C:SER176 2.4 53.7 1.0 OG1 C:THR170 2.5 50.9 1.0 O C:THR170 2.6 49.3 1.0 O C:ASP109 2.6 48.4 1.0 OD1 C:ASP174 2.6 49.0 1.0 OD1 C:ASP109 2.7 52.9 1.0 CB C:SER176 3.0 39.2 1.0 C C:THR170 3.5 38.8 1.0 C C:TRP172 3.6 38.7 1.0 C C:ASP109 3.6 36.9 1.0 CG C:ASP109 3.7 52.4 1.0 CB C:THR170 3.7 37.8 1.0 CG C:ASP174 3.8 44.1 1.0 N C:SER176 3.9 45.0 1.0 CA C:SER176 4.0 33.2 1.0 CA C:THR170 4.0 33.7 1.0 N C:ASP174 4.1 46.4 1.0 N C:TRP172 4.2 41.8 1.0 N C:THR170 4.3 35.4 1.0 OD2 C:ASP109 4.3 63.0 1.0 CA C:ASP109 4.4 35.7 1.0 CA C:TRP172 4.4 34.2 1.0 OD2 C:ASP174 4.5 50.8 1.0 C C:GLY171 4.5 38.2 1.0 N C:LEU173 4.6 37.6 1.0 CB C:ASP109 4.6 39.5 1.0 N C:LEU110 4.6 42.4 1.0 N C:GLY171 4.6 38.4 1.0 CA C:LEU173 4.7 36.2 1.0 CA C:LEU110 4.7 35.6 1.0 CG2 C:THR170 4.8 40.4 1.0 CA C:ASP174 4.8 36.5 1.0 N C:GLY175 4.9 41.4 1.0 CB C:TRP172 4.9 35.6 1.0 CB C:ASP174 4.9 43.1 1.0 C C:LEU173 4.9 42.9 1.0 C C:ASP174 4.9 40.6 1.0 O C:LEU110 4.9 47.9 1.0 CA C:GLY171 5.0 35.1 1.0 C C:SER176 5.0 37.4 1.0

L.Chen, J.X.Wu. Cryo-Em Structure of Human DUOX1-DUOXA1 in High-Calcium State To Be Published.