Sodium in PDB 5opd: Structure of Phosphorylated Ef-Tu in Complex with Gtp

The structure of Structure of Phosphorylated Ef-Tu in Complex with Gtp, PDB code: 5opd was solved by A.Garcia-Pino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.37 / 2.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	59.840, 61.880, 65.480, 70.37, 75.83, 89.41
R / Rfree (%)	18.1 / 25.8

The structure of Structure of Phosphorylated Ef-Tu in Complex with Gtp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iodine	(I)	28 atoms

The binding sites of Sodium atom in the Structure of Phosphorylated Ef-Tu in Complex with Gtp (pdb code 5opd). 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 Phosphorylated Ef-Tu in Complex with Gtp, PDB code: 5opd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na517 b:5.2 occ:1.00 CA A:GLY240 4.1 16.1 1.0 CA A:THR257 4.2 14.6 1.0 O A:CYS256 4.3 17.5 1.0 N A:GLY240 4.4 15.2 1.0 O A:THR257 4.7 16.7 1.0 CG1 A:VAL239 4.7 15.9 1.0 CG2 A:THR257 4.7 15.7 1.0 CB A:THR257 4.8 18.1 1.0 CG2 A:THR255 4.8 15.1 1.0 C A:THR257 4.9 16.8 1.0 C A:CYS256 5.0 17.5 1.0

Sodium binding site 2 out of 5 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na518 b:3.0 occ:1.00 O A:TYR332 3.8 10.5 1.0 O A:HOH728 4.1 12.7 1.0 CD1 A:TYR332 4.2 10.8 1.0 CB A:ALA376 4.2 7.6 1.0 N A:ALA376 4.2 6.1 1.0 C A:PHE375 4.4 7.4 1.0 CA A:PHE375 4.5 4.5 1.0 O A:PHE333 4.7 14.5 1.0 CA A:ALA376 4.8 6.8 1.0 CE1 A:TYR332 4.9 11.1 1.0 C A:TYR332 4.9 11.3 1.0 O A:PHE375 4.9 7.4 1.0 O A:ARG374 4.9 4.9 1.0 N A:PHE375 5.0 4.4 1.0 CB A:TYR332 5.0 9.3 1.0 CG A:TYR332 5.0 10.3 1.0

Sodium binding site 3 out of 5 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na517 b:3.0 occ:1.00 N B:ASP267 3.7 15.6 1.0 CD2 B:LEU266 3.8 26.4 1.0 CB B:LEU266 4.1 15.8 1.0 CG B:LEU266 4.1 21.5 1.0 CA B:LEU266 4.2 16.0 1.0 CG B:GLU268 4.2 21.5 1.0 N B:GLU268 4.3 13.4 1.0 C B:LEU266 4.4 19.7 1.0 O B:GLU268 4.5 15.7 1.0 CA B:ASP267 4.6 15.5 1.0 CB B:ASP267 4.6 18.9 1.0 C B:ASP267 4.9 16.7 1.0

Sodium binding site 4 out of 5 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na518 b:3.0 occ:1.00 O B:HOH707 3.5 23.0 1.0 CG B:GLU118 3.5 23.7 1.0 CD1 B:LEU121 3.8 9.4 1.0 CA B:GLU118 4.4 6.4 1.0 CD B:GLU118 4.4 52.0 1.0 CB B:GLU118 4.5 7.5 1.0 N B:GLU118 4.7 6.9 1.0 OE2 B:GLU118 4.8 37.4 1.0

Sodium binding site 5 out of 5 in the Structure of Phosphorylated Ef-Tu in Complex with Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Phosphorylated Ef-Tu in Complex with Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na519 b:3.0 occ:1.00 OD2 B:ASP337 2.6 34.6 1.0 O B:HOH732 3.3 4.4 1.0 NH2 B:ARG289 3.4 56.9 1.0 CG B:ASP337 3.5 26.6 1.0 N B:ASP337 3.7 11.5 1.0 NH2 B:ARG378 3.9 27.7 1.0 OG1 B:THR336 3.9 18.0 1.0 CB B:ASP337 4.0 12.9 1.0 CA B:THR336 4.1 12.4 1.0 C B:THR336 4.3 15.9 1.0 CE2 B:TYR332 4.4 15.2 1.0 OD1 B:ASP337 4.4 26.9 1.0 CA B:ASP337 4.5 10.8 1.0 CD2 B:TYR332 4.6 13.6 1.0 CZ B:ARG289 4.6 68.6 1.0 CB B:THR336 4.6 16.6 1.0

A.Garcia-Pino, A.Garcia-Pino. N/A N/A.