Sodium in PDB 7d3e: Cryo-Em Structure of Human DUOX1-DUOXA1 in Low-Calcium State

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

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

Iron

(Fe)

4 atoms

The binding sites of Sodium atom in the Cryo-Em Structure of Human DUOX1-DUOXA1 in Low-Calcium State (pdb code 7d3e). 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 Low-Calcium State, PDB code: 7d3e:
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 Low-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 Low-Calcium State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1608 b:65.4 occ:1.00 O A:VAL399 2.4 97.5 1.0 O A:THR332 2.5 89.3 1.0 OD1 A:ASP397 2.5 95.8 1.0 O A:ARG395 2.5 96.0 1.0 OG1 A:THR332 3.3 87.1 1.0 C A:VAL399 3.6 85.8 1.0 C A:ARG395 3.6 91.4 1.0 C A:THR332 3.6 84.0 1.0 CG A:ASP397 3.6 99.2 1.0 N A:ARG395 4.0 89.5 1.0 CB A:GLU394 4.0 85.8 1.0 N A:ASP397 4.2 0.4 1.0 OD2 A:ASP397 4.2 0.5 1.0 CA A:THR332 4.2 75.5 1.0 CB A:VAL399 4.2 79.7 1.0 CA A:VAL399 4.2 77.6 1.0 CA A:ARG395 4.2 82.2 1.0 N A:VAL399 4.3 83.5 1.0 CB A:THR332 4.4 83.5 1.0 O A:ASP397 4.4 1.0 1.0 C A:GLU394 4.5 90.6 1.0 CB A:ARG395 4.5 80.4 1.0 N A:LEU400 4.6 75.6 1.0 C A:ASP397 4.7 93.4 1.0 N A:MET333 4.7 79.9 1.0 N A:GLU396 4.7 94.6 1.0 CG1 A:VAL399 4.7 85.2 1.0 CA A:ASP397 4.8 89.5 1.0 CB A:ASP397 4.8 86.0 1.0 CA A:LEU400 4.8 72.5 1.0 CA A:GLU394 4.9 81.1 1.0 CG A:GLU394 5.0 96.1 1.0 CA A:MET333 5.0 75.4 1.0

Sodium binding site 2 out of 4 in the Cryo-Em Structure of Human DUOX1-DUOXA1 in Low-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 Low-Calcium State within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1609 b:49.0 occ:1.00 O A:TRP172 2.4 70.6 1.0 OG A:SER176 2.4 75.0 1.0 OD1 A:ASP174 2.5 72.2 1.0 O A:ASP109 2.5 76.8 1.0 OG1 A:THR170 2.5 75.2 1.0 O A:THR170 2.5 72.5 1.0 OD1 A:ASP109 2.7 84.0 1.0 CB A:SER176 3.2 68.8 1.0 C A:THR170 3.5 65.0 1.0 C A:ASP109 3.5 68.6 1.0 C A:TRP172 3.6 69.6 1.0 CG A:ASP109 3.6 84.6 1.0 CG A:ASP174 3.7 80.4 1.0 CB A:THR170 3.8 64.5 1.0 N A:SER176 4.0 67.1 1.0 N A:ASP174 4.0 73.9 1.0 CA A:THR170 4.0 62.0 1.0 CA A:SER176 4.2 57.2 1.0 N A:THR170 4.2 63.0 1.0 N A:TRP172 4.2 69.0 1.0 OD2 A:ASP109 4.2 92.7 1.0 OD2 A:ASP174 4.3 85.1 1.0 CA A:ASP109 4.3 63.3 1.0 CA A:TRP172 4.4 57.4 1.0 N A:LEU110 4.5 72.0 1.0 CB A:ASP109 4.5 64.6 1.0 C A:GLY171 4.6 65.5 1.0 N A:LEU173 4.6 64.7 1.0 N A:GLY171 4.6 60.4 1.0 CA A:LEU110 4.6 54.0 1.0 CA A:LEU173 4.7 60.1 1.0 CB A:ASP174 4.8 68.1 1.0 CA A:ASP174 4.8 64.0 1.0 CG2 A:THR170 4.8 67.0 1.0 N A:GLY175 4.9 64.6 1.0 CB A:TRP172 4.9 59.8 1.0 C A:LEU173 4.9 72.2 1.0 C A:ASP174 4.9 70.1 1.0 O A:LEU110 5.0 73.2 1.0 C A:SER176 5.0 66.0 1.0 CA A:GLY171 5.0 55.6 1.0

Sodium binding site 3 out of 4 in the Cryo-Em Structure of Human DUOX1-DUOXA1 in Low-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 Low-Calcium State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1608 b:66.1 occ:1.00 O C:VAL399 2.4 98.4 1.0 O C:THR332 2.5 89.6 1.0 OD1 C:ASP397 2.5 96.1 1.0 O C:ARG395 2.5 96.5 1.0 OG1 C:THR332 3.3 87.3 1.0 C C:VAL399 3.6 87.3 1.0 C C:ARG395 3.6 92.4 1.0 C C:THR332 3.6 84.8 1.0 CG C:ASP397 3.6 0.1 1.0 N C:ARG395 4.0 90.6 1.0 CB C:GLU394 4.0 86.2 1.0 N C:ASP397 4.2 0.4 1.0 OD2 C:ASP397 4.2 0.1 1.0 CA C:THR332 4.2 76.4 1.0 CB C:VAL399 4.2 81.3 1.0 CA C:VAL399 4.2 79.3 1.0 CA C:ARG395 4.2 83.5 1.0 N C:VAL399 4.3 84.3 1.0 CB C:THR332 4.4 84.8 1.0 O C:ASP397 4.4 0.4 1.0 C C:GLU394 4.5 91.7 1.0 CB C:ARG395 4.5 81.6 1.0 N C:LEU400 4.6 76.5 1.0 C C:ASP397 4.7 94.8 1.0 N C:MET333 4.7 80.4 1.0 N C:GLU396 4.7 96.1 1.0 CG1 C:VAL399 4.7 86.3 1.0 CA C:ASP397 4.8 91.2 1.0 CB C:ASP397 4.8 87.9 1.0 CA C:LEU400 4.8 74.1 1.0 CA C:GLU394 4.9 82.4 1.0 CG C:GLU394 5.0 96.7 1.0 CA C:MET333 5.0 76.2 1.0

Sodium binding site 4 out of 4 in the Cryo-Em Structure of Human DUOX1-DUOXA1 in Low-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 Low-Calcium State within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1609 b:54.8 occ:1.00 OG C:SER176 2.4 75.6 1.0 O C:TRP172 2.4 71.4 1.0 OD1 C:ASP174 2.5 73.5 1.0 O C:ASP109 2.5 77.8 1.0 OG1 C:THR170 2.5 76.2 1.0 O C:THR170 2.5 73.6 1.0 OD1 C:ASP109 2.7 84.6 1.0 CB C:SER176 3.2 69.2 1.0 C C:THR170 3.5 65.7 1.0 C C:ASP109 3.5 69.3 1.0 C C:TRP172 3.6 70.1 1.0 CG C:ASP109 3.6 85.6 1.0 CG C:ASP174 3.7 81.0 1.0 CB C:THR170 3.7 65.1 1.0 N C:SER176 4.0 68.1 1.0 N C:ASP174 4.0 75.0 1.0 CA C:THR170 4.0 62.2 1.0 CA C:SER176 4.2 57.7 1.0 N C:THR170 4.2 63.5 1.0 N C:TRP172 4.2 69.1 1.0 OD2 C:ASP109 4.2 93.4 1.0 OD2 C:ASP174 4.3 85.0 1.0 CA C:ASP109 4.3 64.1 1.0 CA C:TRP172 4.4 57.7 1.0 N C:LEU110 4.5 72.8 1.0 CB C:ASP109 4.5 65.6 1.0 C C:GLY171 4.6 65.9 1.0 N C:LEU173 4.6 65.5 1.0 N C:GLY171 4.6 60.8 1.0 CA C:LEU110 4.6 55.0 1.0 CA C:LEU173 4.7 61.3 1.0 CB C:ASP174 4.8 69.1 1.0 CA C:ASP174 4.8 65.3 1.0 CG2 C:THR170 4.8 67.5 1.0 N C:GLY175 4.9 65.9 1.0 CB C:TRP172 4.9 60.1 1.0 C C:LEU173 4.9 73.6 1.0 C C:ASP174 4.9 71.4 1.0 O C:LEU110 5.0 73.6 1.0 C C:SER176 5.0 66.5 1.0 CA C:GLY171 5.0 56.0 1.0

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