Sodium in PDB 6xne: GCN4-P1 Peptide Trimer with P-Methylphenylalanine Residue at Position 16 (Me-F16)

The structure of GCN4-P1 Peptide Trimer with P-Methylphenylalanine Residue at Position 16 (Me-F16), PDB code: 6xne 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)	20.10 / 1.96
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.138, 34.891, 47.041, 90, 100.63, 90
R / Rfree (%)	21 / 30.9

The structure of GCN4-P1 Peptide Trimer with P-Methylphenylalanine Residue at Position 16 (Me-F16) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the GCN4-P1 Peptide Trimer with P-Methylphenylalanine Residue at Position 16 (Me-F16) (pdb code 6xne). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the GCN4-P1 Peptide Trimer with P-Methylphenylalanine Residue at Position 16 (Me-F16), PDB code: 6xne:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the GCN4-P1 Peptide Trimer with P-Methylphenylalanine Residue at Position 16 (Me-F16)


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 P-Methylphenylalanine Residue at Position 16 (Me-F16) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:45.7 occ:1.00 N A:MET2 2.9 22.4 1.0 N A:ARG1 3.2 36.4 1.0 CB A:MET2 3.5 45.3 1.0 CA A:ARG1 3.7 37.6 1.0 CB A:ARG1 3.7 21.3 1.0 CA A:MET2 3.8 23.4 1.0 C A:ARG1 3.8 37.3 1.0 NH2 C:ARG1 4.3 42.5 0.5 N A:LYS3 4.5 31.0 1.0 C A:MET2 4.7 22.3 1.0 CG A:MET2 4.9 56.1 1.0

Sodium binding site 2 out of 6 in the GCN4-P1 Peptide Trimer with P-Methylphenylalanine Residue at Position 16 (Me-F16)


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 P-Methylphenylalanine Residue at Position 16 (Me-F16) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na102 b:36.5 occ:0.50 CD2 A:LEU13 2.8 23.5 0.3 O A:HOH221 3.4 20.6 1.0 O C:HOH202 3.6 27.7 1.0 CG A:LEU13 4.0 24.9 0.3 CD2 A:LEU13 4.2 22.6 0.7 CD1 A:LEU13 4.3 23.7 0.3 CD1 A:LEU13 4.5 23.5 0.7 CB A:LEU13 4.5 20.2 0.7 CB A:LEU13 4.6 21.5 0.3 CG A:LEU13 4.6 23.8 0.7 O A:HOH227 4.6 13.4 1.0 NZ C:LYS15 5.0 28.2 1.0

Sodium binding site 3 out of 6 in the GCN4-P1 Peptide Trimer with P-Methylphenylalanine Residue at Position 16 (Me-F16)


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 P-Methylphenylalanine Residue at Position 16 (Me-F16) within 5.0Å range:

Sodium binding site 4 out of 6 in the GCN4-P1 Peptide Trimer with P-Methylphenylalanine Residue at Position 16 (Me-F16)


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 P-Methylphenylalanine Residue at Position 16 (Me-F16) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:31.9 occ:1.00 O B:HOH212 2.7 72.0 1.0 NE2 B:GLN4 3.2 20.9 1.0 CD B:GLN4 3.8 27.0 1.0 CG B:GLN4 4.0 27.4 1.0 NZ B:LYS3 4.2 40.4 1.0 CG B:LYS3 4.3 28.5 1.0 CD B:LYS3 4.4 34.7 1.0 OD2 B:ASP7 4.4 28.1 1.0 CB B:LYS3 4.4 28.2 1.0 OE1 B:GLN4 4.6 31.7 1.0 N B:GLN4 4.7 29.3 1.0 C B:LYS3 4.9 18.8 1.0 CE B:LYS3 4.9 34.8 1.0 CA B:GLN4 4.9 28.4 1.0

Sodium binding site 5 out of 6 in the GCN4-P1 Peptide Trimer with P-Methylphenylalanine Residue at Position 16 (Me-F16)


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 P-Methylphenylalanine Residue at Position 16 (Me-F16) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:42.7 occ:1.00 NA C:NA102 2.6 45.0 1.0 CB C:ARG25 3.9 24.6 1.0 CG C:ARG25 3.9 24.0 1.0 CD1 C:LEU29 4.0 35.8 1.0 CD C:ARG25 4.0 38.3 1.0 O C:HOH213 4.5 19.1 1.0 CG C:LEU29 4.6 39.7 1.0 CA C:ARG25 4.7 28.4 1.0 CD2 C:LEU29 4.9 45.5 1.0

Sodium binding site 6 out of 6 in the GCN4-P1 Peptide Trimer with P-Methylphenylalanine Residue at Position 16 (Me-F16)


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 P-Methylphenylalanine Residue at Position 16 (Me-F16) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na102 b:45.0 occ:1.00 NA C:NA101 2.6 42.7 1.0 CG C:LEU29 3.3 39.7 1.0 O C:ARG25 3.3 26.9 1.0 CD1 C:LEU29 3.5 35.8 1.0 CD2 C:LEU29 3.7 45.5 1.0 C C:ARG25 3.9 32.5 1.0 CA C:ARG25 3.9 28.4 1.0 CB C:ARG25 4.0 24.6 1.0 CB C:LYS28 4.4 40.0 0.5 CB C:LYS28 4.4 39.9 0.5 CG C:ARG25 4.4 24.0 1.0 CB C:LEU29 4.6 38.6 1.0 N C:LEU29 4.7 37.8 1.0 C C:LYS28 4.9 40.1 0.5 C C:LYS28 4.9 40.1 0.5 N C:LEU26 5.0 25.8 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.