Sodium in PDB 4c3v: Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak

All present enzymatic activity of Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak:
3.4.21.62;

The structure of Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak, PDB code: 4c3v was solved by M.Cianci, J.Negroni, J.R.Helliwell, P.J.Halling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.76 / 2.26
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.891, 55.075, 75.311, 90.00, 90.00, 90.00
R / Rfree (%)	15.96 / 22.581

The structure of Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak (pdb code 4c3v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak, PDB code: 4c3v:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1279 b:19.8 occ:0.73 O A:HOH2025 2.3 23.3 1.0 O A:LEU42 2.3 21.6 1.0 O A:HIS39 2.4 26.1 1.0 O A:ALA37 2.5 23.1 1.0 O A:HOH2029 2.8 33.8 1.0 C A:HIS39 3.5 24.8 1.0 C A:LEU42 3.5 22.0 1.0 C A:ALA37 3.6 23.0 1.0 C A:SER38 3.7 21.9 1.0 N A:HIS39 3.8 23.1 1.0 O A:SER38 3.9 22.7 1.0 CA A:SER38 4.0 23.6 1.0 N A:LEU42 4.3 21.3 1.0 CA A:HIS39 4.3 22.4 1.0 N A:SER38 4.3 22.8 1.0 CA A:PRO40 4.4 23.8 1.0 CA A:LEU42 4.4 20.8 1.0 N A:PRO40 4.5 24.3 1.0 N A:ASN43 4.5 21.6 1.0 OD1 A:ASN43 4.5 29.6 1.0 C A:PRO40 4.5 21.7 1.0 CA A:ASN43 4.6 22.2 1.0 CB A:LEU42 4.7 18.3 1.0 O A:PRO40 4.7 21.2 1.0 CA A:ALA37 4.8 24.4 1.0 CB A:HIS39 4.9 20.4 1.0

Sodium binding site 2 out of 3 in the Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1280 b:17.9 occ:1.00 O A:VAL174 2.2 20.7 1.0 O A:TYR171 2.3 19.4 1.0 O A:ALA169 2.3 22.1 1.0 O A:HOH2079 2.4 23.2 1.0 O A:HOH2081 2.4 16.8 1.0 C A:TYR171 3.3 21.6 1.0 C A:VAL174 3.4 21.2 1.0 C A:ALA169 3.5 24.0 1.0 C A:LYS170 3.8 22.7 1.0 N A:VAL174 4.0 21.5 1.0 O A:LYS170 4.0 21.1 1.0 N A:TYR171 4.0 22.2 1.0 CA A:VAL174 4.1 18.4 1.0 N A:ALA176 4.1 20.4 1.0 N A:ASP172 4.1 22.6 1.0 CA A:ASP172 4.2 24.2 1.0 CB A:VAL174 4.2 17.3 1.0 CA A:TYR171 4.3 21.9 1.0 CA A:LYS170 4.3 23.0 1.0 CB A:ALA176 4.3 19.5 1.0 C A:ASP172 4.3 23.5 1.0 N A:LYS170 4.4 23.6 1.0 O A:GLU195 4.4 19.7 1.0 N A:ILE175 4.4 20.3 1.0 OE1 A:GLU197 4.4 18.9 1.0 NH2 A:ARG247 4.5 20.5 1.0 CA A:ALA169 4.5 21.9 1.0 O A:ASP172 4.5 21.9 1.0 C A:ILE175 4.6 21.2 1.0 CA A:ILE175 4.6 20.8 1.0 CB A:GLU195 4.7 24.7 1.0 CA A:ALA176 4.8 20.0 1.0 N A:SER173 4.9 23.3 1.0 O A:PRO168 4.9 19.1 1.0 CG1 A:VAL174 5.0 14.6 1.0

Sodium binding site 3 out of 3 in the Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Extensive Counter-Ion Interactions with Subtilisin in Aqueous Medium, No Cs Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1281 b:28.5 occ:0.41 O A:HOH2105 2.9 32.6 1.0 O A:HOH2120 3.3 39.0 1.0 O A:TYR143 3.7 21.9 1.0 N A:SER244 3.9 24.6 1.0 CB A:ALA243 4.0 21.3 1.0 CB A:SER244 4.1 30.3 1.0 N A:ALA243 4.2 24.6 1.0 CB A:SER242 4.4 25.4 1.0 CA A:ALA243 4.5 24.1 1.0 OG A:SER242 4.6 26.5 1.0 CA A:SER244 4.6 26.2 1.0 C A:ALA243 4.7 25.1 1.0 O A:ALA144 4.7 23.9 1.0 CA A:GLY146 4.7 21.6 1.0 C A:TYR143 4.8 22.3 1.0 N A:GLY146 4.8 23.8 1.0 CE1 A:TYR143 4.9 24.4 1.0 CA A:ALA144 5.0 25.7 1.0

M.Cianci, J.Negroni, J.R.Helliwell, P.J.Halling. Extensive Counter-Ion Interactions Seen at the Surface of Subtilisin in An Aqueous Medium Rsc Adv 2014.
ISSN: ESSN 2046-2069
DOI: 10.1039/C4RA06448H