Sodium in PDB 6xnf: GCN4-P1 Peptide Trimer with Tetrafluoroiodophenylalanine Residue at Position 16 (Tfi-F16)

The structure of GCN4-P1 Peptide Trimer with Tetrafluoroiodophenylalanine Residue at Position 16 (Tfi-F16), PDB code: 6xnf 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)	46.21 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.65, 35.19, 47.02, 90, 100.65, 90
R / Rfree (%)	19.7 / 25.4

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

Fluorine	(F)	8 atoms
Iodine	(I)	2 atoms

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

Sodium binding site 1 out of 4 in the GCN4-P1 Peptide Trimer with Tetrafluoroiodophenylalanine Residue at Position 16 (Tfi-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 Tetrafluoroiodophenylalanine Residue at Position 16 (Tfi-F16) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:63.0 occ:1.00 OE2 A:GLU22 3.3 66.4 1.0 CB A:HIS18 3.4 49.8 1.0 CG A:GLU22 3.7 31.5 1.0 CD A:GLU22 3.9 55.1 1.0 O A:HIS18 4.0 26.7 1.0 CG A:HIS18 4.1 62.2 1.0 C A:HIS18 4.1 28.5 1.0 CA A:HIS18 4.3 37.2 1.0 ND1 A:HIS18 4.4 64.3 1.0 O B:HOH214 4.6 43.2 1.0 N A:LEU19 4.8 20.5 1.0 CD2 A:HIS18 5.0 65.5 1.0

Sodium binding site 2 out of 4 in the GCN4-P1 Peptide Trimer with Tetrafluoroiodophenylalanine Residue at Position 16 (Tfi-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 Tetrafluoroiodophenylalanine Residue at Position 16 (Tfi-F16) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:62.9 occ:1.00 CD B:LYS27 2.7 40.6 1.0 O B:HOH218 2.8 34.2 1.0 CG B:LYS27 3.4 38.4 1.0 CA B:ALA24 3.6 26.6 1.0 CG1 B:VAL23 3.8 33.0 1.0 N B:ALA24 3.8 30.5 1.0 OE1 A:GLU22 3.8 55.4 1.0 CB B:ALA24 4.0 26.8 1.0 CE B:LYS27 4.0 49.0 1.0 C B:VAL23 4.1 22.0 1.0 CD A:GLU22 4.1 55.1 1.0 O B:VAL23 4.2 23.1 1.0 CG A:GLU22 4.3 31.5 1.0 NZ B:LYS27 4.3 54.0 1.0 CB B:LYS27 4.4 23.0 1.0 O B:HOH215 4.5 48.9 1.0 CB B:VAL23 4.6 26.3 1.0 CB A:GLU22 4.7 25.6 1.0 OE2 A:GLU22 4.9 66.4 1.0 O B:GLU20 4.9 20.4 1.0 C B:ALA24 4.9 27.9 1.0

Sodium binding site 3 out of 4 in the GCN4-P1 Peptide Trimer with Tetrafluoroiodophenylalanine Residue at Position 16 (Tfi-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 Tetrafluoroiodophenylalanine Residue at Position 16 (Tfi-F16) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:81.5 occ:1.00 CB B:GLU11 3.8 46.6 1.0 CA B:GLU11 4.3 38.2 1.0 OE2 B:GLU10 4.7 71.0 1.0 N B:GLU11 4.7 36.4 1.0 OE2 B:GLU11 4.9 76.0 1.0

Sodium binding site 4 out of 4 in the GCN4-P1 Peptide Trimer with Tetrafluoroiodophenylalanine Residue at Position 16 (Tfi-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 Tetrafluoroiodophenylalanine Residue at Position 16 (Tfi-F16) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:70.6 occ:1.00 OE2 C:GLU22 3.4 56.4 1.0 OE1 C:GLU22 3.5 58.5 1.0 CE A:LYS27 3.5 52.5 1.0 NZ A:LYS27 3.6 49.9 1.0 CD C:GLU22 3.9 46.1 1.0 O C:HOH202 4.1 33.3 1.0 O C:HOH219 4.1 46.0 1.0 CD C:ARG25 4.4 51.9 1.0 NH1 C:ARG25 4.7 77.2 1.0 CD A:LYS27 4.8 41.0 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.