Sodium in PDB 6iam: Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches

The structure of Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches, PDB code: 6iam was solved by L.Werel, L.-O.Essen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.49 / 1.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.526, 46.560, 66.168, 90.00, 107.22, 90.00
R / Rfree (%)	14.8 / 17

The structure of Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches also contains other interesting chemical elements:

Potassium

(K)

3 atoms

The binding sites of Sodium atom in the Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches (pdb code 6iam). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches, PDB code: 6iam:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:30.8 occ:0.86 O A:HOH832 2.4 23.8 1.0 O A:VAL268 2.7 12.2 1.0 O A:HOH825 2.8 33.8 1.0 HZ3 A:LYS272 3.3 24.6 1.0 HA A:THR269 3.4 13.8 1.0 HZ1 A:LYS272 3.5 24.6 1.0 HG23 A:VAL268 3.6 17.4 1.0 HB A:VAL268 3.7 16.7 1.0 C A:VAL268 3.7 11.9 1.0 NZ A:LYS272 3.8 20.5 1.0 O A:HOH638 3.9 27.8 1.0 HZ2 A:LYS272 4.1 24.6 1.0 CA A:THR269 4.2 11.5 1.0 O A:HOH523 4.2 26.2 1.0 CG2 A:VAL268 4.3 14.5 1.0 CB A:VAL268 4.3 13.9 1.0 N A:THR269 4.4 11.7 1.0 HG21 A:VAL268 4.5 17.4 1.0 O A:HOH710 4.5 26.3 1.0 CA A:VAL268 4.7 12.8 1.0 C A:THR269 4.7 13.2 1.0 O A:THR269 4.8 13.4 1.0 HG22 A:THR269 4.9 13.6 1.0

Sodium binding site 2 out of 2 in the Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:36.8 occ:1.00 O A:HOH853 2.3 28.8 1.0 OE1 A:GLU322 2.7 27.9 1.0 O A:HOH796 2.8 38.4 1.0 O B:HOH112 2.9 16.8 1.0 HB2 A:GLU322 2.9 22.7 1.0 CD A:GLU322 3.2 28.6 1.0 HA41 B:XY55 3.3 23.6 1.0 HA31 B:XY55 3.4 26.4 1.0 HB3 A:GLU322 3.5 22.7 1.0 CB A:GLU322 3.6 18.9 1.0 OE2 A:GLU322 3.8 31.4 1.0 CA4 B:XY55 3.8 19.7 1.0 CA3 B:XY55 3.9 22.0 1.0 CG A:GLU322 4.0 24.3 1.0 O B:HOH102 4.0 24.2 1.0 O B:HOH117 4.1 30.2 1.0 HG3 A:GLU322 4.3 29.2 1.0 O B:ALA4 4.4 19.6 1.0 H A:GLU322 4.4 14.9 1.0 O A:HOH683 4.6 23.1 1.0 O A:HOH594 4.6 26.2 1.0 HG2 A:GLU322 4.8 29.2 1.0 O A:HOH501 4.9 30.1 1.0 CA A:GLU322 4.9 15.0 1.0 HB2 A:ALA47 5.0 11.0 1.0 CA5 B:XY55 5.0 19.6 1.0

L.Albert, A.Penalver, N.Djokovic, L.Werel, M.Hoffarth, D.Ruzic, J.Xu, L.O.Essen, K.Nikolic, Y.Dou, O.Vazquez. Modulating Protein-Protein Interactions with Visible-Light-Responsive Peptide Backbone Photoswitches. Chembiochem V. 20 1417 2019.
ISSN: ESSN 1439-7633
PubMed: 30675988
DOI: 10.1002/CBIC.201800737