Sodium in PDB 4nec: Conversion of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis

The structure of Conversion of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis, PDB code: 4nec was solved by K.Hotta, R.M.Keegan, S.Ranganathan, M.Fang, J.Bibby, M.D.Winn, M.Sato, M.Lian, K.Watanabe, D.J.Rigden, C.-Y.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.42 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.187, 146.880, 58.187, 90.00, 102.63, 90.00
R / Rfree (%)	15 / 19

The binding sites of Sodium atom in the Conversion of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis (pdb code 4nec). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Conversion of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis, PDB code: 4nec:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Conversion of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Conversion of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:26.0 occ:1.00 O A:ILE163 2.5 24.3 1.0 O A:ALA157 2.5 21.4 1.0 O A:ILE160 2.8 22.0 1.0 C A:ALA157 3.5 20.4 1.0 O A:ASP161 3.5 24.8 1.0 C A:ILE163 3.7 24.0 1.0 C A:ILE160 3.7 23.4 1.0 CA A:ALA157 3.8 21.4 1.0 C A:ASP161 3.9 23.4 1.0 CA A:ASP161 3.9 25.1 1.0 CB A:ALA157 4.1 21.7 1.0 N A:ASP161 4.3 24.2 1.0 N A:ILE163 4.4 25.7 1.0 CA A:ILE163 4.5 24.6 1.0 N A:PRO164 4.7 22.8 1.0 N A:GLU158 4.7 19.6 1.0 CA A:PRO164 4.7 23.4 1.0 N A:ILE160 4.9 23.2 1.0 N A:GLU162 4.9 25.3 1.0 CA A:ILE160 4.9 23.4 1.0 CB A:ILE163 4.9 23.9 1.0

Sodium binding site 2 out of 3 in the Conversion of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Conversion of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:29.9 occ:1.00 CG A:ARG18 3.9 19.5 0.4 OE2 D:GLU34 3.9 17.0 1.0 OH D:TYR62 3.9 19.0 1.0 NH1 A:ARG18 4.0 14.9 0.4 OG A:SER209 4.3 20.9 1.0 O D:HOH503 4.3 13.3 1.0 O D:GLU34 4.3 16.8 1.0 CG A:ARG18 4.3 19.4 0.6 O A:PRO206 4.4 34.4 1.0 CA D:GLY37 4.5 12.9 1.0 CB A:LYS17 4.7 27.0 1.0 CD A:ARG18 4.8 18.3 0.4 CD D:GLU34 4.9 15.4 1.0 CB A:ARG18 5.0 20.3 0.4

Sodium binding site 3 out of 3 in the Conversion of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Conversion of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:45.1 occ:1.00 O C:ALA157 2.3 27.9 1.0 O C:ILE160 2.6 28.3 1.0 O C:ILE163 2.8 27.5 1.0 O C:ASP161 3.3 29.7 1.0 C C:ALA157 3.4 25.3 1.0 C C:ILE160 3.7 28.8 1.0 C C:ASP161 3.9 28.2 1.0 C C:ILE163 3.9 29.0 1.0 CA C:ASP161 4.0 28.6 1.0 CA C:ALA157 4.0 21.6 1.0 N C:ASP161 4.3 28.7 1.0 CB C:ALA157 4.4 17.9 1.0 N C:ILE163 4.5 29.3 1.0 N C:GLU158 4.6 27.8 1.0 CA C:ILE163 4.7 30.5 1.0 N C:ILE160 4.8 29.2 1.0 CA C:ILE160 4.8 28.2 1.0 N C:GLU162 4.9 27.0 1.0 N C:PRO164 4.9 31.0 1.0 CA C:GLU158 4.9 29.4 1.0 CA C:PRO164 5.0 32.2 1.0

K.Hotta, R.M.Keegan, S.Ranganathan, M.Fang, J.Bibby, M.D.Winn, M.Sato, M.Lian, K.Watanabe, D.J.Rigden, C.-Y.Kim. Conversion of A Disulfide Bond Into A Thioacetal Group During Echinomycin Biosynthesis Angew.Chem.Int.Ed.Engl. 2013.
ISSN: ESSN 1521-3773
PubMed: 24302672
DOI: 10.1002/ANIE.201307404