Sodium in PDB 6xnl: GCN4-P1 Peptide Trimer with Iodo-Phenylalanine Residue at Position 16 (Ipf-F16)

The structure of GCN4-P1 Peptide Trimer with Iodo-Phenylalanine Residue at Position 16 (Ipf-F16), PDB code: 6xnl 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)	19.85 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.069, 34.848, 46.712, 90, 100.44, 90
R / Rfree (%)	22.2 / 32.1

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

Iodine

(I)

1 atom

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

Sodium binding site 1 out of 2 in the GCN4-P1 Peptide Trimer with Iodo-Phenylalanine Residue at Position 16 (Ipf-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 Iodo-Phenylalanine Residue at Position 16 (Ipf-F16) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:66.9 occ:1.00 OE2 B:GLU22 3.2 44.0 1.0 CB B:ASN21 3.4 39.0 1.0 CD B:ARG25 3.6 64.6 1.0 C B:ASN21 3.6 40.5 1.0 CG B:ARG25 3.6 52.5 1.0 O B:ASN21 3.7 43.4 1.0 N B:GLU22 3.8 33.8 1.0 CA B:ASN21 4.1 35.6 1.0 CD B:GLU22 4.1 51.2 1.0 CA B:GLU22 4.2 39.9 1.0 CG B:ASN21 4.5 40.6 1.0 CB B:ARG25 4.6 42.8 1.0 CG B:GLU22 4.6 48.9 1.0 NE B:ARG25 4.8 74.4 1.0 ND2 B:ASN21 4.9 47.1 1.0 O B:HIS18 5.0 31.6 1.0

Sodium binding site 2 out of 2 in the GCN4-P1 Peptide Trimer with Iodo-Phenylalanine Residue at Position 16 (Ipf-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 Iodo-Phenylalanine Residue at Position 16 (Ipf-F16) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na102 b:52.5 occ:1.00 CD1 B:LEU26 2.2 59.9 1.0 O B:GLU22 2.6 41.2 1.0 NZ C:LYS27 2.7 64.3 1.0 CB B:ARG25 3.1 42.8 1.0 C B:GLU22 3.4 35.5 1.0 CA B:GLU22 3.4 39.9 1.0 OE2 B:GLU22 3.5 44.0 1.0 NE B:ARG25 3.5 74.4 1.0 CG B:LEU26 3.6 44.8 1.0 N B:LEU26 3.7 44.8 1.0 CB B:GLU22 3.9 45.7 1.0 CD B:ARG25 3.9 64.6 1.0 CE C:LYS27 4.0 59.8 1.0 CG B:ARG25 4.0 52.5 1.0 CD2 B:LEU26 4.0 49.4 1.0 CD B:GLU22 4.0 51.2 1.0 CA B:ARG25 4.1 41.2 1.0 C B:ARG25 4.2 43.3 1.0 CB B:LEU26 4.4 47.0 1.0 CA B:LEU26 4.4 45.0 1.0 CZ B:ARG25 4.5 68.1 1.0 CG C:LYS27 4.5 56.4 1.0 CG B:GLU22 4.6 48.9 1.0 N B:ARG25 4.6 41.7 1.0 N B:VAL23 4.6 28.4 1.0 NH1 B:ARG25 4.6 60.7 1.0 O B:ASN21 4.7 43.4 1.0 OE1 B:GLU22 4.7 56.6 1.0 N B:GLU22 4.7 33.8 1.0 CD C:LYS27 4.9 58.5 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.