Sodium in PDB 6jbd: Phosphotransferase-Atp Complex Related to Coa Biosynthesis Pathway

All present enzymatic activity of Phosphotransferase-Atp Complex Related to Coa Biosynthesis Pathway:
2.7.1.169;

The structure of Phosphotransferase-Atp Complex Related to Coa Biosynthesis Pathway, PDB code: 6jbd was solved by A.Kita, A.Kishimoto, T.Shimosaka, H.Tomita, Y.Yokooji, T.Imanaka, H.Atomi, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 2.50
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.323, 95.323, 60.691, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 25.9

The structure of Phosphotransferase-Atp Complex Related to Coa Biosynthesis Pathway also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Calcium	(Ca)	3 atoms

The binding sites of Sodium atom in the Phosphotransferase-Atp Complex Related to Coa Biosynthesis Pathway (pdb code 6jbd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Phosphotransferase-Atp Complex Related to Coa Biosynthesis Pathway, PDB code: 6jbd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Phosphotransferase-Atp Complex Related to Coa Biosynthesis Pathway


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Phosphotransferase-Atp Complex Related to Coa Biosynthesis Pathway within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:24.9 occ:1.00 O A:HOH515 2.6 21.5 1.0 OD1 A:ASN103 2.8 22.2 1.0 O A:PHE101 2.8 23.1 1.0 CA A:ALA9 3.2 18.5 1.0 CB A:ALA9 3.3 15.1 1.0 O A:HOH539 3.3 40.4 1.0 N A:ASN103 3.4 17.7 1.0 C A:GLY102 3.5 18.1 1.0 C A:PHE101 3.6 21.7 1.0 CA A:ASN103 3.6 17.4 1.0 O A:GLY102 3.7 18.7 1.0 CG A:ASN103 3.9 21.4 1.0 OG1 A:THR39 3.9 18.3 1.0 CB A:PHE101 4.0 22.5 1.0 N A:ALA9 4.1 17.9 1.0 N A:GLY102 4.2 19.0 1.0 CA A:GLY102 4.2 16.8 1.0 N A:HIS10 4.3 20.4 1.0 C A:ALA9 4.3 18.9 1.0 CB A:ASN103 4.4 19.8 1.0 O A:PRO8 4.4 19.9 1.0 CA A:PHE101 4.4 23.1 1.0 C A:PRO8 4.6 18.1 1.0 CA A:GLY38 4.7 23.3 1.0 OE1 A:GLN147 4.8 21.7 1.0 N A:THR39 4.8 22.4 1.0 C A:ASN103 4.9 17.9 1.0 CD2 A:PHE95 4.9 26.8 1.0 C A:GLY38 5.0 23.8 1.0

Sodium binding site 2 out of 2 in the Phosphotransferase-Atp Complex Related to Coa Biosynthesis Pathway


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Phosphotransferase-Atp Complex Related to Coa Biosynthesis Pathway within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:26.0 occ:1.00 O2 A:PGE405 2.6 66.8 1.0 O A:LEU169 2.8 18.4 1.0 N A:ILE152 2.9 21.1 1.0 C3 A:PGE405 3.0 68.5 1.0 C4 A:PGE405 3.4 69.4 1.0 O A:ILE152 3.4 23.8 1.0 OD1 A:ASN168 3.5 18.9 1.0 CA A:GLY151 3.5 18.3 1.0 C A:GLY151 3.6 21.4 1.0 CA A:ILE152 3.7 21.8 1.0 C2 A:PGE405 3.9 65.4 1.0 C A:ILE152 3.9 22.8 1.0 N A:LEU169 3.9 20.3 1.0 CB A:ASN168 3.9 21.4 1.0 CE1 A:PHE171 3.9 21.3 1.0 CB A:ILE152 3.9 20.1 1.0 C A:LEU169 4.0 20.3 1.0 CG A:ASN168 4.0 19.2 1.0 CD1 A:PHE171 4.2 20.7 1.0 C1 A:PGE405 4.3 64.4 1.0 O A:GLY150 4.4 14.6 1.0 CG1 A:ILE152 4.5 18.9 1.0 C A:ASN168 4.5 20.6 1.0 CA A:ASN168 4.5 21.4 1.0 CA A:LEU169 4.5 20.1 1.0 N A:GLY151 4.6 16.7 1.0 O3 A:PGE405 4.7 71.1 1.0 O A:GLY151 4.8 22.3 1.0 C A:GLY150 4.9 16.6 1.0

A.Kita, A.Kishimoto, T.Shimosaka, H.Tomita, Y.Yokooji, T.Imanaka, H.Atomi, K.Miki. Crystal Structure of Phosphotransferase Related to Coa Biosynthesis Pathway To Be Published.