Sodium in PDB 4q3c: Pyld Cocrystallized with L-Lysine-Ne-L-Lysine and Nad+

The structure of Pyld Cocrystallized with L-Lysine-Ne-L-Lysine and Nad+, PDB code: 4q3c 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 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.250, 259.770, 48.930, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 19.8

The structure of Pyld Cocrystallized with L-Lysine-Ne-L-Lysine 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-L-Lysine and Nad+ (pdb code 4q3c). 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-L-Lysine and Nad+, PDB code: 4q3c:
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-L-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-Lysine-Ne-L-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:39.5 occ:1.00 O A:CYS206 2.7 28.9 1.0 O A:THR204 2.8 25.5 1.0 O A:PRO227 2.8 42.5 1.0 OE1 A:GLU202 3.1 29.8 1.0 O A:HOH1067 3.1 32.4 1.0 OE2 A:GLU202 3.2 25.7 1.0 CD A:GLU202 3.5 26.0 1.0 C A:THR204 3.6 24.6 1.0 N A:CYS206 3.7 28.1 1.0 C A:CYS206 3.7 29.2 1.0 CG2 A:THR204 3.8 25.8 1.0 C A:GLY225 3.8 29.4 1.0 CA A:GLY225 3.9 25.8 1.0 N A:ALA229 3.9 34.5 1.0 CA A:ALA229 4.0 34.3 1.0 C A:PRO227 4.0 39.5 1.0 CB A:ALA229 4.1 36.1 1.0 CB A:THR204 4.1 28.9 1.0 N A:ILE226 4.1 35.2 1.0 O A:GLY225 4.2 33.0 1.0 CA A:THR204 4.3 25.9 1.0 C A:CYS228 4.3 36.6 1.0 CA A:CYS206 4.3 28.2 1.0 C A:PRO205 4.4 28.6 1.0 N A:THR204 4.4 24.1 1.0 N A:PRO205 4.4 27.4 1.0 C A:ILE226 4.5 36.3 1.0 CA A:PRO205 4.5 26.3 1.0 OG1 A:THR223 4.6 26.5 1.0 O A:ILE226 4.7 36.4 1.0 N A:PRO227 4.7 38.1 1.0 N A:ALA207 4.7 33.4 1.0 CA A:ILE226 4.8 39.1 1.0 CA A:CYS228 4.8 36.0 1.0 OG1 A:THR209 4.8 32.4 1.0 O A:CYS228 4.8 41.3 1.0 N A:CYS228 4.8 37.6 1.0 CG A:GLU202 5.0 23.9 1.0 N A:GLY225 5.0 23.6 1.0

Sodium binding site 2 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-L-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-Lysine-Ne-L-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:43.9 occ:1.00 O B:CYS206 2.7 34.2 1.0 O B:PRO227 2.8 39.4 1.0 OE1 B:GLU202 2.9 35.2 1.0 O B:THR204 2.9 30.8 1.0 O B:HOH1091 3.0 36.4 1.0 OE2 B:GLU202 3.1 25.1 1.0 CD B:GLU202 3.3 28.7 1.0 OG1 B:THR204 3.4 30.9 1.0 C B:CYS206 3.7 33.8 1.0 N B:CYS206 3.7 29.8 1.0 C B:THR204 3.8 27.7 1.0 N B:ALA229 3.8 41.9 1.0 CA B:ALA229 3.9 37.6 1.0 CB B:ALA229 3.9 35.0 1.0 CA B:GLY225 3.9 25.5 1.0 C B:GLY225 3.9 27.2 1.0 C B:PRO227 4.0 38.6 1.0 N B:ILE226 4.1 34.3 1.0 C B:CYS228 4.2 36.5 1.0 CA B:CYS206 4.3 32.6 1.0 O B:GLY225 4.4 31.8 1.0 N B:THR204 4.4 26.0 1.0 CB B:THR204 4.5 26.8 1.0 CA B:THR204 4.5 27.5 1.0 C B:PRO205 4.5 29.1 1.0 O B:CYS228 4.5 39.2 1.0 OG1 B:THR223 4.6 27.6 1.0 N B:PRO205 4.7 28.7 1.0 C B:ILE226 4.7 36.1 1.0 CA B:CYS228 4.7 35.4 1.0 OG1 B:THR209 4.7 40.1 1.0 CA B:PRO205 4.7 27.5 1.0 N B:PRO227 4.8 36.4 1.0 N B:ALA207 4.8 34.2 1.0 CG B:GLU202 4.8 26.4 1.0 CA B:ILE226 4.8 37.8 1.0 N B:CYS228 4.8 36.4 1.0 N B:GLY225 4.9 25.6 1.0 O B:ILE226 5.0 42.7 1.0

Sodium binding site 3 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-L-Lysine 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-L-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Na902 b:60.4 occ:1.00 O C:PRO227 2.6 62.1 1.0 O C:THR204 2.6 47.5 1.0 O C:CYS206 2.8 45.9 1.0 OE1 C:GLU202 3.2 52.4 1.0 OE2 C:GLU202 3.3 53.0 1.0 C C:GLY225 3.6 48.5 1.0 CD C:GLU202 3.6 48.3 1.0 C C:THR204 3.7 44.7 1.0 N C:ALA229 3.7 51.7 1.0 N C:CYS206 3.7 42.8 1.0 CA C:GLY225 3.8 47.7 1.0 C C:CYS206 3.8 42.2 1.0 C C:PRO227 3.8 57.2 1.0 N C:ILE226 3.8 50.0 1.0 O C:GLY225 3.9 46.5 1.0 CA C:ALA229 3.9 51.8 1.0 CB C:ALA229 4.0 50.8 1.0 C C:CYS228 4.1 55.2 1.0 C C:ILE226 4.3 56.1 1.0 CG2 C:THR204 4.3 43.6 1.0 C C:PRO205 4.4 44.5 1.0 CA C:CYS206 4.4 44.4 1.0 N C:PRO227 4.4 60.7 1.0 CA C:THR204 4.5 42.3 1.0 CA C:ILE226 4.5 55.0 1.0 O C:CYS228 4.5 54.0 1.0 CB C:THR204 4.5 44.9 1.0 N C:PRO205 4.5 44.1 1.0 O C:ILE226 4.6 61.9 1.0 OG1 C:THR223 4.6 49.6 1.0 CA C:CYS228 4.6 55.8 1.0 N C:THR204 4.6 41.3 1.0 CA C:PRO205 4.6 45.7 1.0 N C:CYS228 4.6 51.5 1.0 CA C:PRO227 4.8 58.4 1.0 CD C:PRO227 4.8 60.0 1.0 N C:ALA207 4.8 44.2 1.0 N C:GLY225 4.9 50.0 1.0

Sodium binding site 4 out of 4 in the Pyld Cocrystallized with L-Lysine-Ne-L-Lysine 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-L-Lysine and Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Na902 b:51.9 occ:1.00 O D:PRO227 2.7 60.9 1.0 O D:CYS206 2.7 43.2 1.0 O D:THR204 3.0 46.4 1.0 OE1 D:GLU202 3.2 44.4 1.0 OE2 D:GLU202 3.4 48.8 1.0 CD D:GLU202 3.7 45.0 1.0 N D:CYS206 3.7 39.1 1.0 C D:CYS206 3.7 42.9 1.0 N D:ALA229 3.8 54.8 1.0 C D:THR204 3.8 43.0 1.0 C D:GLY225 3.9 56.8 1.0 C D:PRO227 3.9 59.9 1.0 CA D:GLY225 3.9 53.6 1.0 CA D:ALA229 3.9 52.6 1.0 N D:ILE226 4.0 59.8 1.0 CB D:ALA229 4.0 51.8 1.0 C D:CYS228 4.1 54.9 1.0 O D:GLY225 4.3 60.1 1.0 CG2 D:THR204 4.3 45.7 1.0 CA D:CYS206 4.3 41.0 1.0 C D:ILE226 4.4 65.6 1.0 C D:PRO205 4.4 38.6 1.0 CB D:THR204 4.5 46.8 1.0 O D:ILE226 4.5 63.0 1.0 N D:PRO227 4.5 61.9 1.0 CA D:CYS228 4.5 60.4 1.0 O D:CYS228 4.6 51.6 1.0 CA D:THR204 4.6 42.5 1.0 OG1 D:THR223 4.6 48.2 1.0 CA D:ILE226 4.6 65.9 1.0 N D:THR204 4.6 42.0 1.0 N D:PRO205 4.7 41.0 1.0 N D:CYS228 4.7 56.5 1.0 CA D:PRO205 4.7 39.9 1.0 N D:ALA207 4.8 39.4 1.0 CA D:PRO227 4.8 60.6 1.0 N D:GLY225 5.0 51.5 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