Sodium in PDB 6xnm: GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16

The structure of GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16, PDB code: 6xnm was solved by R.K.Rowe Hartje, R.S.Czarny, A.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.77 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.553, 34.482, 46.936, 90, 100.65, 90
R / Rfree (%)	22.5 / 35.8

The binding sites of Sodium atom in the GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16 (pdb code 6xnm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16, PDB code: 6xnm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:44.5 occ:1.00 NZ A:LYS15 2.9 15.1 1.0 CE A:LYS15 4.0 41.9 1.0 OE1 C:GLU20 4.4 25.1 1.0 OE2 C:GLU20 4.6 27.7 1.0 CD A:LYS15 4.9 33.6 1.0 CD C:GLU20 4.9 27.2 1.0

Sodium binding site 2 out of 7 in the GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:46.3 occ:1.00 O A:HOH203 2.4 51.9 1.0 NZ A:LYS8 3.5 16.3 0.5 OE1 A:GLU11 4.1 46.0 1.0 CE A:LYS8 4.5 32.3 0.5

Sodium binding site 3 out of 7 in the GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:57.2 occ:1.00 O B:HOH204 3.3 28.9 1.0 OE2 B:GLU20 3.6 36.3 1.0 CD B:GLU20 3.8 36.2 1.0 CG B:GLU20 4.0 35.6 1.0 O B:HOH211 4.0 17.0 1.0 CB B:GLU20 4.3 22.9 1.0 OE1 B:GLU20 4.4 32.0 1.0 O B:HOH202 5.0 22.7 1.0

Sodium binding site 4 out of 7 in the GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:41.2 occ:1.00 OE2 B:GLU11 2.5 47.1 1.0 OE1 B:GLU11 2.5 42.0 1.0 CD B:GLU11 2.7 41.5 1.0 NZ B:LYS8 3.2 32.4 0.1 NZ B:LYS8 3.9 28.0 0.9 CG B:GLU11 4.0 40.9 1.0 CE B:LYS8 4.5 38.2 0.1 CD B:LYS8 4.7 41.9 0.1

Sodium binding site 5 out of 7 in the GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:28.8 occ:1.00 NH2 C:ARG1 3.3 31.1 0.2 NH1 C:ARG1 3.8 33.1 0.2 CZ C:ARG1 4.0 34.5 0.2 NH2 C:ARG1 4.3 34.3 0.8 OE2 B:GLU6 4.9 56.0 1.0

Sodium binding site 6 out of 7 in the GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:32.5 occ:1.00 CB C:LEU13 3.9 23.8 1.0 OE2 A:GLU11 3.9 31.7 1.0 CD2 C:LEU13 4.0 45.1 1.0 O C:LEU13 4.2 28.0 1.0 CG C:LEU13 4.4 45.2 1.0 C C:LEU13 4.6 24.0 1.0 CA C:LEU13 4.7 23.0 1.0 CD1 C:LEU13 4.7 34.8 1.0 CE A:LYS15 4.8 41.9 1.0

Sodium binding site 7 out of 7 in the GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of GCN4-P1 Peptide Trimer with Tyrosine Residue at Position 16 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na103 b:28.7 occ:1.00 CE C:LYS27 2.7 52.1 1.0 O A:HOH215 3.1 60.8 1.0 NZ C:LYS27 3.6 35.8 1.0 CD C:LYS27 3.7 42.9 1.0 CG C:LYS27 3.8 46.2 1.0 O C:HOH205 4.8 29.3 1.0 CB C:LYS27 5.0 44.4 1.0

R.K.Rowe Hartje, M.Ferrero, G.Cavallo, P.Metrangolo, A.Ho, R.Czarny, P.S.Ho. Engineering Specific Protein-Protein Interactions Through Halogen and Hydrogen Bonds To Be Published.