Sodium in PDB 7djk: Structure of Four Truncated and Mutated Forms of Quenching Protein

The structure of Structure of Four Truncated and Mutated Forms of Quenching Protein, PDB code: 7djk was solved by G.M.Yu, X.W.Pan, M.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.84 / 2.80
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	183.191, 183.191, 120.894, 90, 90, 90
R / Rfree (%)	17.8 / 21.8

The structure of Structure of Four Truncated and Mutated Forms of Quenching Protein also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Structure of Four Truncated and Mutated Forms of Quenching Protein (pdb code 7djk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Four Truncated and Mutated Forms of Quenching Protein, PDB code: 7djk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of Four Truncated and Mutated Forms of Quenching Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Four Truncated and Mutated Forms of Quenching Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:60.5 occ:1.00 CB A:THR677 4.0 20.6 1.0 CB A:ASN663 4.1 28.0 1.0 CG2 A:THR677 4.2 20.6 1.0 CA A:ASN663 4.2 19.3 1.0 OG1 A:THR677 4.2 29.1 1.0 CE2 A:PHE612 4.3 25.8 1.0 O A:GLY662 4.3 31.3 1.0 CZ A:PHE612 4.5 25.5 1.0 O A:HOH1278 4.7 23.5 1.0 O A:ASN663 4.8 40.4 1.0 C A:ASN663 4.8 19.6 1.0

Sodium binding site 2 out of 5 in the Structure of Four Truncated and Mutated Forms of Quenching Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Four Truncated and Mutated Forms of Quenching Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1104 b:73.1 occ:1.00 N A:LEU628 2.4 29.4 1.0 O A:HOH1235 2.5 33.4 1.0 O A:LEU628 2.6 31.0 1.0 OD1 A:ASP686 2.7 28.1 1.0 CA A:GLY627 3.3 31.1 1.0 C A:GLY627 3.3 36.7 1.0 CA A:LEU628 3.3 29.1 1.0 C A:LEU628 3.3 29.2 1.0 O A:HOH1252 3.4 24.0 1.0 CG A:ASP686 3.8 34.0 1.0 O A:VAL687 3.8 50.1 1.0 O A:LEU572 3.8 39.4 1.0 CB A:LEU628 3.9 37.0 1.0 CB A:LYS571 4.0 34.4 1.0 OD2 A:ASP686 4.2 45.1 1.0 O A:HOH1219 4.3 36.1 1.0 CD A:LYS571 4.3 21.5 1.0 CG A:LYS571 4.4 31.7 1.0 N A:VAL687 4.4 20.8 1.0 O A:GLY627 4.5 40.7 1.0 N A:ALA629 4.6 27.3 1.0 CG1 A:VAL687 4.7 48.1 1.0 N A:LEU572 4.7 38.9 1.0 N A:GLY627 4.7 32.1 1.0 C A:LEU572 4.8 32.5 1.0 CG A:LEU628 4.8 38.9 1.0 C A:VAL687 4.8 36.1 1.0 CB A:ASP686 5.0 23.0 1.0

Sodium binding site 3 out of 5 in the Structure of Four Truncated and Mutated Forms of Quenching Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Four Truncated and Mutated Forms of Quenching Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1105 b:50.8 occ:1.00 O A:HOH1283 2.9 26.2 1.0 O A:HOH1290 4.2 48.8 1.0 CE1 A:TYR724 4.2 54.7 1.0 O A:GLY723 4.4 19.4 1.0 CD1 A:TYR724 4.4 47.0 1.0 OH A:TYR670 4.5 39.1 1.0 CZ A:TYR670 4.5 37.5 1.0 C A:GLY723 4.5 19.8 1.0 CZ A:TYR724 4.6 51.9 1.0 CE2 A:TYR670 4.7 37.7 1.0 N A:TYR724 4.9 30.4 1.0 CA A:GLY723 5.0 19.6 1.0 CG A:TYR724 5.0 30.5 1.0

Sodium binding site 4 out of 5 in the Structure of Four Truncated and Mutated Forms of Quenching Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Four Truncated and Mutated Forms of Quenching Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1106 b:52.4 occ:1.00 O A:HOH1251 2.4 51.7 1.0 O A:HOH1282 2.4 45.7 1.0 CE2 A:PHE719 4.0 43.4 1.0 O A:GLN769 4.2 68.9 1.0 CZ A:PHE719 4.3 43.4 1.0 O A:HOH1270 4.5 35.9 1.0 CD2 A:PHE719 4.6 47.5 1.0 N A:GLY771 4.6 36.1 1.0 C A:THR770 4.9 32.6 1.0 CG A:PRO733 4.9 23.1 1.0 CA A:GLY771 5.0 34.2 1.0

Sodium binding site 5 out of 5 in the Structure of Four Truncated and Mutated Forms of Quenching Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Four Truncated and Mutated Forms of Quenching Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1107 b:57.7 occ:1.00 O A:HOH1255 2.6 42.0 1.0 NE2 A:GLN671 3.3 85.1 1.0 CG A:GLN734 3.8 54.6 1.0 CB A:GLN734 4.0 37.5 1.0 CA A:GLN734 4.1 39.1 1.0 N A:GLN734 4.5 40.3 1.0 O A:GLY721 4.5 37.5 1.0 CA A:ASN722 4.6 32.6 1.0 CD A:GLN671 4.6 87.6 1.0 CG1 A:VAL718 4.7 21.9 1.0 C A:PRO733 4.9 39.6 1.0

G.Yu, J.Hao, X.Pan, L.Shi, Y.Zhang, J.Wang, H.Fan, Y.Xiao, F.Yang, J.Lou, W.Chang, A.Malnoe, M.Li. Structure of Arabidopsis SOQ1 Lumenal Region Unveils C-Terminal Domain Essential For Negative Regulation of Photoprotective Qh. Nat.Plants V. 8 840 2022.
ISSN: ESSN 2055-0278
PubMed: 35798975
DOI: 10.1038/S41477-022-01177-Z