Sodium in PDB 2vx9: H. Salinarum Dodecin E45A Mutant

The structure of H. Salinarum Dodecin E45A Mutant, PDB code: 2vx9 was solved by M.Grininger, H.Staudt, P.Johansson, J.Wachtveitl, D.Oesterhelt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.10 / 1.65
Space group	F 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	142.940, 142.940, 142.940, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 20.4

The structure of H. Salinarum Dodecin E45A Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the H. Salinarum Dodecin E45A Mutant (pdb code 2vx9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the H. Salinarum Dodecin E45A Mutant, PDB code: 2vx9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the H. Salinarum Dodecin E45A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of H. Salinarum Dodecin E45A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1065 b:23.7 occ:1.00 O A:HOH2020 2.1 27.7 1.0 O A:HOH2056 2.2 25.3 1.0 OE2 A:GLU14 2.2 22.9 1.0 CD A:GLU14 3.2 20.7 1.0 OE1 A:GLU14 3.4 22.0 1.0 OE1 A:GLU51 4.1 49.7 1.0 OE2 A:GLU51 4.2 43.8 1.0 OE1 A:GLU13 4.4 31.0 1.0 CD A:GLU51 4.4 43.6 1.0 O A:GLU13 4.5 16.7 1.0 CB A:GLU13 4.5 18.4 1.0 CG A:GLU14 4.6 19.1 1.0 C A:GLU13 5.0 16.1 1.0

Sodium binding site 2 out of 4 in the H. Salinarum Dodecin E45A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of H. Salinarum Dodecin E45A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1066 b:27.5 occ:1.00 N A:ALA48 3.3 35.1 1.0 N A:ILE46 3.4 20.3 1.0 N A:GLY47 3.6 28.1 1.0 CB A:ALA45 3.6 16.3 1.0 CA A:ALA45 3.7 16.6 1.0 CB A:ALA48 3.8 36.2 1.0 C A:ALA45 4.0 18.2 1.0 CA A:ALA48 4.1 36.4 1.0 CA A:GLY47 4.2 32.2 1.0 C A:ILE46 4.2 26.8 1.0 C A:GLY47 4.2 34.0 1.0 CA A:ILE46 4.5 23.4 1.0 C A:ALA48 4.8 36.8 1.0 N A:VAL49 4.9 37.1 1.0 O A:ILE46 5.0 28.3 1.0 CG2 A:VAL49 5.0 34.7 1.0

Sodium binding site 3 out of 4 in the H. Salinarum Dodecin E45A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of H. Salinarum Dodecin E45A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1067 b:14.8 occ:0.33 O A:HOH2065 2.4 15.1 1.0 CL A:CL1068 2.7 14.9 0.3 CL A:CL1069 2.7 32.4 0.3 O A:HOH2007 4.3 17.0 1.0 CB A:LEU7 4.4 12.3 1.0 NE2 A:GLN59 4.7 14.3 1.0 OE1 A:GLN59 4.7 13.0 1.0 O A:LYS5 4.8 14.4 1.0 CD2 A:LEU7 4.9 13.0 1.0

Sodium binding site 4 out of 4 in the H. Salinarum Dodecin E45A Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of H. Salinarum Dodecin E45A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1071 b:41.4 occ:1.00 O A:HOH2046 2.4 38.3 1.0 OE2 A:GLU38 4.1 24.6 1.0 OE1 A:GLU38 4.2 27.7 1.0 NZ A:LYS5 4.4 25.9 1.0 O4 A:RBF1064 4.5 25.8 1.0 CD A:GLU38 4.6 25.8 1.0

M.Grininger, H.Staudt, P.Johansson, J.Wachtveitl, D.Oesterhelt. Dodecin Is the Key Player in Flavin Homeostasis of Archaea. J.Biol.Chem. V. 284 13068 2009.
ISSN: ISSN 0021-9258
PubMed: 19224924
DOI: 10.1074/JBC.M808063200