Sodium in PDB 4q3e: Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+

The structure of Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+, PDB code: 4q3e 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 (°)	79.080, 210.460, 77.640, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.5

The structure of Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+ also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+ (pdb code 4q3e). 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 Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+, PDB code: 4q3e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:49.4 occ:1.00 O A:PRO227 2.8 45.1 1.0 O A:CYS206 2.8 38.6 1.0 O A:THR204 2.8 30.9 1.0 OE1 A:GLU202 3.0 35.2 1.0 O A:HOH1004 3.1 38.5 1.0 OE2 A:GLU202 3.3 35.9 1.0 OG1 A:THR204 3.3 33.6 1.0 CD A:GLU202 3.5 35.0 1.0 N A:CYS206 3.7 36.5 1.0 C A:THR204 3.7 32.4 1.0 C A:CYS206 3.7 39.9 1.0 C A:GLY225 3.8 37.5 1.0 N A:ILE226 3.8 38.9 1.0 CA A:GLY225 3.9 35.3 1.0 N A:ALA229 3.9 41.9 1.0 C A:PRO227 4.0 43.9 1.0 CA A:ALA229 4.0 41.8 1.0 CB A:ALA229 4.2 39.7 1.0 C A:CYS228 4.2 45.0 1.0 O A:GLY225 4.3 36.1 1.0 CA A:CYS206 4.3 38.9 1.0 N A:THR204 4.3 31.8 1.0 C A:ILE226 4.3 43.0 1.0 CA A:THR204 4.4 31.7 1.0 C A:PRO205 4.4 34.7 1.0 CB A:THR204 4.5 32.9 1.0 CA A:ILE226 4.5 42.4 1.0 N A:PRO205 4.5 32.8 1.0 N A:PRO227 4.5 44.3 1.0 O A:CYS228 4.6 44.5 1.0 O A:ILE226 4.6 42.6 1.0 CA A:PRO205 4.6 33.5 1.0 OG1 A:THR223 4.7 35.7 1.0 CA A:CYS228 4.7 46.2 1.0 N A:ALA207 4.7 41.4 1.0 OG1 A:THR209 4.8 38.8 1.0 N A:CYS228 4.8 44.5 1.0 CA A:PRO227 4.9 43.5 1.0 N A:GLY225 4.9 34.2 1.0 CG A:GLU202 4.9 34.5 1.0

Sodium binding site 2 out of 2 in the Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pyld Cocrystallized with L-Ornithine-Nd-D-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:59.9 occ:1.00 O B:THR204 2.7 36.6 1.0 OE1 B:GLU202 2.8 40.3 1.0 O B:HOH1005 2.9 37.8 1.0 O B:PRO227 2.9 47.9 1.0 O B:CYS206 2.9 45.8 1.0 OE2 B:GLU202 3.2 35.8 1.0 CD B:GLU202 3.3 38.6 1.0 OG1 B:THR204 3.4 39.5 1.0 C B:THR204 3.6 38.5 1.0 C B:GLY225 3.8 44.4 1.0 N B:CYS206 3.8 42.9 1.0 N B:ALA229 3.8 50.9 1.0 CA B:GLY225 3.9 42.9 1.0 C B:CYS206 3.9 45.8 1.0 N B:ILE226 3.9 46.6 1.0 CA B:ALA229 4.0 49.9 1.0 CB B:ALA229 4.1 48.6 1.0 C B:PRO227 4.1 49.4 1.0 O B:GLY225 4.1 44.5 1.0 N B:THR204 4.2 37.7 1.0 C B:CYS228 4.3 51.7 1.0 CA B:THR204 4.3 38.2 1.0 CB B:THR204 4.4 39.7 1.0 CA B:CYS206 4.5 43.9 1.0 C B:ILE226 4.5 49.5 1.0 C B:PRO205 4.5 40.9 1.0 OG1 B:THR223 4.5 43.7 1.0 N B:PRO205 4.5 38.6 1.0 CA B:ILE226 4.6 50.5 1.0 CA B:PRO205 4.7 39.9 1.0 O B:ILE226 4.7 48.5 1.0 N B:PRO227 4.7 50.0 1.0 O B:CYS228 4.7 51.3 1.0 CA B:CYS228 4.8 52.9 1.0 CG B:GLU202 4.8 37.7 1.0 OG1 B:THR209 4.8 44.8 1.0 N B:GLY225 4.9 41.0 1.0 N B:ALA207 4.9 45.7 1.0 N B:CYS228 4.9 50.5 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