Sodium in PDB 4q39: Pyld in Complex with Pyrrolysine and Nadh

The structure of Pyld in Complex with Pyrrolysine and Nadh, PDB code: 4q39 was solved by F.Quitterer, P.Beck, A.Bacher, M.Groll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	48.500, 142.720, 167.310, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 19.8

The structure of Pyld in Complex with Pyrrolysine and Nadh also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Pyld in Complex with Pyrrolysine and Nadh (pdb code 4q39). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pyld in Complex with Pyrrolysine and Nadh, PDB code: 4q39:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pyld in Complex with Pyrrolysine and Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pyld in Complex with Pyrrolysine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:39.9 occ:1.00 O A:CYS206 2.6 30.4 1.0 O A:PRO227 2.8 32.4 1.0 O A:THR204 2.8 25.5 1.0 OE1 A:GLU202 3.1 24.5 1.0 O A:HOH1013 3.1 24.4 1.0 OE2 A:GLU202 3.3 23.6 1.0 OG1 A:THR204 3.5 26.1 1.0 CD A:GLU202 3.5 24.0 1.0 C A:THR204 3.7 25.8 1.0 C A:CYS206 3.7 31.9 1.0 N A:CYS206 3.7 30.4 1.0 C A:GLY225 3.7 24.7 1.0 N A:ALA229 3.8 31.3 1.0 N A:ILE226 3.8 26.8 1.0 CA A:GLY225 3.9 23.7 1.0 CA A:ALA229 3.9 31.9 1.0 C A:PRO227 4.0 32.7 1.0 CB A:ALA229 4.0 32.4 1.0 O A:GLY225 4.2 25.8 1.0 C A:CYS228 4.2 31.7 1.0 CA A:CYS206 4.3 32.5 1.0 N A:THR204 4.3 23.5 1.0 CA A:THR204 4.4 25.2 1.0 C A:ILE226 4.4 30.1 1.0 C A:PRO205 4.4 30.2 1.0 CA A:ILE226 4.5 28.8 1.0 CB A:THR204 4.5 25.9 1.0 N A:PRO205 4.5 27.3 1.0 N A:PRO227 4.6 31.7 1.0 CA A:PRO205 4.6 28.5 1.0 O A:CYS228 4.6 31.0 1.0 O A:ILE226 4.7 31.4 1.0 OG1 A:THR223 4.7 22.6 1.0 N A:ALA207 4.7 32.1 1.0 CA A:CYS228 4.8 32.9 1.0 OG1 A:THR209 4.8 31.2 1.0 N A:CYS228 4.8 31.8 1.0 CA A:PRO227 4.9 32.6 1.0 CG A:GLU202 4.9 23.5 1.0 N A:GLY225 5.0 23.0 1.0 CA A:ALA207 5.0 33.4 1.0

Sodium binding site 2 out of 2 in the Pyld in Complex with Pyrrolysine and Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pyld in Complex with Pyrrolysine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:46.8 occ:1.00 O B:PRO227 2.6 47.4 1.0 O B:CYS206 2.7 38.8 1.0 O B:THR204 2.8 34.6 1.0 OE1 B:GLU202 3.0 40.4 1.0 O B:HOH1001 3.1 35.1 1.0 OE2 B:GLU202 3.3 37.0 1.0 OG1 B:THR204 3.5 36.5 1.0 CD B:GLU202 3.5 38.2 1.0 N B:ALA229 3.6 46.5 1.0 C B:CYS206 3.6 39.9 1.0 N B:CYS206 3.7 37.6 1.0 CA B:ALA229 3.7 45.6 1.0 C B:THR204 3.8 35.5 1.0 C B:GLY225 3.8 39.4 1.0 C B:PRO227 3.8 46.5 1.0 CB B:ALA229 3.8 46.8 1.0 CA B:GLY225 3.9 38.0 1.0 N B:ILE226 4.0 41.8 1.0 C B:CYS228 4.0 47.2 1.0 O B:GLY225 4.2 37.7 1.0 CA B:CYS206 4.2 39.3 1.0 C B:PRO205 4.4 37.7 1.0 C B:ILE226 4.4 44.2 1.0 O B:CYS228 4.4 47.8 1.0 N B:THR204 4.5 35.5 1.0 CA B:THR204 4.5 35.1 1.0 N B:PRO227 4.5 45.7 1.0 CA B:CYS228 4.6 48.3 1.0 OG1 B:THR223 4.6 40.0 1.0 CB B:THR204 4.6 36.2 1.0 CA B:ILE226 4.6 44.4 1.0 N B:PRO205 4.6 36.4 1.0 CA B:PRO205 4.6 36.4 1.0 N B:ALA207 4.6 41.2 1.0 N B:CYS228 4.7 47.5 1.0 O B:ILE226 4.8 44.9 1.0 CA B:PRO227 4.8 46.4 1.0 OG1 B:THR209 4.9 40.2 1.0 CG B:GLU202 5.0 38.5 1.0 CA B:ALA207 5.0 42.7 1.0

F.Quitterer, P.Beck, A.Bacher, M.Groll. The Formation of Pyrroline and Tetrahydropyridine Rings in Amino Acids Catalyzed By Pyrrolysine Synthase (Pyld). Angew.Chem.Int.Ed.Engl. V. 53 8150 2014.
ISSN: ISSN 1433-7851
PubMed: 24916332
DOI: 10.1002/ANIE.201402595