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

Protein crystallography data

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

Other elements in 5opd:

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

Sodium Binding Sites:

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 5opd

Go back to Sodium Binding Sites List in 5opd
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 5opd

Go back to Sodium Binding Sites List in 5opd
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 5opd

Go back to Sodium Binding Sites List in 5opd
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 5opd

Go back to Sodium Binding Sites List in 5opd
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 5opd

Go back to Sodium Binding Sites List in 5opd
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

Reference:

A.Garcia-Pino, A.Garcia-Pino. N/A N/A.
Page generated: Mon Oct 7 23:14:25 2024

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