Sodium in PDB 4q3a: Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+

The structure of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+, PDB code: 4q3a 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	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.490, 259.850, 48.660, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.4

The structure of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ (pdb code 4q3a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+, PDB code: 4q3a:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine 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-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:39.4 occ:1.00 O A:CYS206 2.6 33.7 1.0 O A:THR204 2.8 26.5 1.0 O A:PRO227 2.8 38.3 1.0 OE1 A:GLU202 2.9 26.6 1.0 OE2 A:GLU202 3.1 26.2 1.0 O A:HOH1113 3.1 36.5 1.0 OG1 A:THR204 3.3 25.4 1.0 CD A:GLU202 3.4 26.0 1.0 C A:CYS206 3.6 35.0 1.0 C A:THR204 3.7 26.5 1.0 N A:CYS206 3.7 32.8 1.0 N A:ALA229 3.9 37.9 1.0 C A:GLY225 3.9 30.0 1.0 CA A:ALA229 3.9 37.6 1.0 CA A:GLY225 3.9 29.2 1.0 C A:PRO227 4.1 38.9 1.0 CB A:ALA229 4.1 36.6 1.0 N A:ILE226 4.1 32.6 1.0 C A:CYS228 4.2 39.6 1.0 CA A:CYS206 4.2 34.5 1.0 O A:GLY225 4.3 29.2 1.0 N A:THR204 4.3 24.8 1.0 CA A:THR204 4.3 25.4 1.0 C A:PRO205 4.4 31.1 1.0 CB A:THR204 4.4 25.7 1.0 N A:PRO205 4.5 28.1 1.0 O A:CYS228 4.6 37.4 1.0 OG1 A:THR209 4.6 31.0 1.0 C A:ILE226 4.6 35.9 1.0 CA A:PRO205 4.6 29.4 1.0 N A:ALA207 4.7 36.0 1.0 OG1 A:THR223 4.7 28.1 1.0 N A:PRO227 4.8 37.4 1.0 CA A:ILE226 4.8 34.8 1.0 CA A:CYS228 4.8 40.4 1.0 CG A:GLU202 4.8 25.5 1.0 O A:ILE226 4.8 37.1 1.0 N A:CYS228 4.9 40.0 1.0 CG2 A:THR209 4.9 33.1 1.0 CA A:ALA207 5.0 37.0 1.0

Sodium binding site 2 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine 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-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:36.3 occ:1.00 O B:PRO227 2.7 38.9 1.0 O B:THR204 2.8 26.7 1.0 O B:CYS206 2.8 35.3 1.0 O B:HOH1058 3.0 35.4 1.0 OE1 B:GLU202 3.0 28.6 1.0 OE2 B:GLU202 3.2 27.4 1.0 CD B:GLU202 3.5 28.0 1.0 OG1 B:THR204 3.6 28.2 1.0 N B:CYS206 3.7 34.1 1.0 C B:GLY225 3.7 30.6 1.0 C B:CYS206 3.7 36.2 1.0 C B:THR204 3.7 27.9 1.0 CA B:GLY225 3.8 29.3 1.0 N B:ILE226 3.8 32.6 1.0 C B:PRO227 4.0 39.0 1.0 N B:ALA229 4.0 39.3 1.0 CB B:ALA229 4.1 38.1 1.0 O B:GLY225 4.1 30.3 1.0 CA B:ALA229 4.1 38.9 1.0 C B:CYS228 4.3 40.3 1.0 CA B:CYS206 4.3 35.9 1.0 C B:PRO205 4.3 32.4 1.0 C B:ILE226 4.4 35.9 1.0 N B:THR204 4.4 27.3 1.0 CA B:ILE226 4.5 34.9 1.0 CA B:THR204 4.5 27.7 1.0 CA B:PRO205 4.5 30.6 1.0 N B:PRO205 4.5 29.6 1.0 N B:PRO227 4.5 37.1 1.0 OG1 B:THR223 4.6 27.7 1.0 CB B:THR204 4.6 28.4 1.0 O B:CYS228 4.7 39.2 1.0 N B:ALA207 4.7 37.1 1.0 O B:ILE226 4.7 35.9 1.0 CA B:CYS228 4.8 42.0 1.0 OG1 B:THR209 4.8 35.8 1.0 N B:CYS228 4.8 40.4 1.0 CA B:PRO227 4.9 38.2 1.0 N B:GLY225 4.9 28.2 1.0 CG B:GLU202 5.0 27.6 1.0

Sodium binding site 3 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Na902 b:50.4 occ:1.00 O C:CYS206 2.7 41.3 1.0 O C:PRO227 2.7 50.8 1.0 O C:THR204 2.9 38.5 1.0 O C:HOH1039 3.1 40.4 1.0 OE1 C:GLU202 3.1 43.9 1.0 OE2 C:GLU202 3.1 43.1 1.0 CD C:GLU202 3.5 43.3 1.0 OG1 C:THR204 3.5 40.3 1.0 N C:CYS206 3.5 41.8 1.0 C C:CYS206 3.6 43.3 1.0 C C:THR204 3.7 39.0 1.0 C C:GLY225 3.8 43.1 1.0 N C:ALA229 3.9 54.2 1.0 C C:PRO227 3.9 51.6 1.0 CA C:ALA229 3.9 53.8 1.0 CA C:GLY225 4.0 41.4 1.0 CB C:ALA229 4.0 53.3 1.0 N C:ILE226 4.0 45.1 1.0 CA C:CYS206 4.2 42.6 1.0 O C:GLY225 4.2 42.9 1.0 C C:CYS228 4.2 55.2 1.0 C C:PRO205 4.2 41.3 1.0 C C:ILE226 4.4 47.3 1.0 N C:THR204 4.5 39.4 1.0 CA C:THR204 4.5 39.1 1.0 N C:PRO205 4.5 39.9 1.0 CA C:PRO205 4.5 40.1 1.0 CB C:THR204 4.6 40.4 1.0 N C:PRO227 4.6 49.0 1.0 O C:CYS228 4.6 56.6 1.0 OG1 C:THR223 4.6 39.7 1.0 O C:ILE226 4.6 46.8 1.0 CA C:ILE226 4.6 46.7 1.0 N C:ALA207 4.6 44.4 1.0 CA C:CYS228 4.7 54.8 1.0 N C:CYS228 4.8 53.9 1.0 OG1 C:THR209 4.8 50.9 1.0 CG C:GLU202 4.9 43.1 1.0 CA C:PRO227 4.9 50.4 1.0

Sodium binding site 4 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pyld Cocrystallized with L-Lysine-Ne-3S-Methyl-L-Ornithine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Na902 b:53.1 occ:1.00 O D:CYS206 2.6 39.0 1.0 O D:PRO227 2.8 56.5 1.0 O D:THR204 3.0 37.8 1.0 O D:HOH1007 3.0 43.2 1.0 OE1 D:GLU202 3.0 41.2 1.0 OE2 D:GLU202 3.2 42.6 1.0 CD D:GLU202 3.4 43.7 1.0 C D:CYS206 3.7 40.0 1.0 N D:ALA229 3.7 57.5 1.0 N D:CYS206 3.7 39.0 1.0 C D:GLY225 3.8 49.9 1.0 C D:THR204 3.8 39.5 1.0 CA D:ALA229 3.9 56.8 1.0 CA D:GLY225 3.9 48.6 1.0 CB D:ALA229 3.9 57.9 1.0 C D:PRO227 3.9 57.5 1.0 N D:ILE226 4.0 52.9 1.0 C D:CYS228 4.2 58.0 1.0 O D:GLY225 4.2 49.5 1.0 CB D:THR204 4.3 43.3 1.0 CA D:CYS206 4.3 38.7 1.0 CA D:THR204 4.4 41.1 1.0 C D:ILE226 4.4 54.1 1.0 N D:THR204 4.5 40.3 1.0 C D:PRO205 4.5 38.9 1.0 N D:PRO227 4.6 55.2 1.0 OG1 D:THR223 4.6 51.2 1.0 O D:CYS228 4.6 56.4 1.0 N D:PRO205 4.6 39.6 1.0 CA D:ILE226 4.7 54.7 1.0 O D:ILE226 4.7 53.5 1.0 CA D:CYS228 4.7 59.8 1.0 CA D:PRO205 4.7 39.1 1.0 N D:ALA207 4.7 40.3 1.0 N D:CYS228 4.8 60.0 1.0 OG1 D:THR209 4.8 45.6 1.0 CG D:GLU202 4.9 44.7 1.0 CA D:PRO227 4.9 56.6 1.0 N D:GLY225 5.0 46.8 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