Sodium in PDB 4j4b: Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh

The structure of Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh, PDB code: 4j4b 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)	10.00 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	48.383, 142.440, 167.305, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24

The structure of Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Pyld in Complex with L-Lysine-Ne-D-Ornithine and Nadh (pdb code 4j4b). 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 L-Lysine-Ne-D-Ornithine and Nadh, PDB code: 4j4b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pyld in Complex with L-Lysine-Ne-D-Ornithine 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 L-Lysine-Ne-D-Ornithine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:41.5 occ:1.00 O A:THR204 2.3 35.6 1.0 O A:CYS206 2.3 39.0 1.0 OE1 A:GLU202 2.3 38.9 1.0 O A:HOH1001 3.0 43.4 1.0 CD A:GLU202 3.1 36.5 1.0 OE2 A:GLU202 3.1 34.8 1.0 C A:THR204 3.3 35.3 1.0 C A:CYS206 3.4 37.6 1.0 N A:CYS206 3.4 36.0 1.0 CA A:CYS206 3.9 36.8 1.0 CB A:THR204 4.0 37.0 1.0 CA A:THR204 4.0 35.5 1.0 N A:ALA229 4.1 59.0 1.0 CG2 A:THR204 4.1 37.7 1.0 CA A:ALA229 4.1 55.6 1.0 C A:PRO205 4.1 35.3 1.0 CB A:ALA229 4.2 50.8 1.0 N A:THR204 4.2 35.2 1.0 N A:PRO205 4.2 34.5 1.0 CA A:GLY225 4.4 52.2 1.0 CA A:PRO205 4.4 34.4 1.0 O A:PRO227 4.4 74.7 1.0 C A:GLY225 4.4 57.7 1.0 OG1 A:THR209 4.5 37.6 1.0 N A:ALA207 4.5 38.2 1.0 CG A:GLU202 4.5 37.0 1.0 N A:ILE226 4.6 63.8 1.0 C A:CYS228 4.6 62.9 1.0 OG1 A:THR223 4.6 40.6 1.0 C A:ILE226 4.6 71.4 1.0 O A:ILE226 4.7 65.1 1.0 N A:PRO227 4.7 75.3 1.0 C A:PRO227 4.8 75.0 1.0 CD A:PRO227 4.8 77.2 1.0 CG2 A:THR209 4.8 36.5 1.0 CA A:ALA207 4.9 39.1 1.0 O A:GLY225 4.9 55.7 1.0 CB A:CYS206 4.9 37.7 1.0

Sodium binding site 2 out of 2 in the Pyld in Complex with L-Lysine-Ne-D-Ornithine 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 L-Lysine-Ne-D-Ornithine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:25.6 occ:1.00 O B:CYS206 2.3 27.4 1.0 O B:PRO227 2.3 36.8 1.0 O B:THR204 2.3 20.1 1.0 O B:HOH407 3.0 25.4 1.0 OE1 B:GLU202 3.3 18.9 1.0 C B:CYS206 3.3 27.1 1.0 C B:THR204 3.3 19.1 1.0 N B:CYS206 3.4 24.3 1.0 OE2 B:GLU202 3.5 17.2 1.0 C B:PRO227 3.5 40.5 1.0 CD B:GLU202 3.8 17.6 1.0 C B:GLY225 3.9 29.3 1.0 CA B:CYS206 3.9 26.3 1.0 CA B:GLY225 3.9 26.9 1.0 CG2 B:THR204 4.0 17.7 1.0 N B:ILE226 4.0 33.4 1.0 C B:PRO205 4.0 24.3 1.0 N B:ALA229 4.2 37.6 1.0 CA B:THR204 4.2 17.6 1.0 N B:PRO227 4.2 41.3 1.0 CB B:THR204 4.2 18.3 1.0 N B:PRO205 4.2 21.3 1.0 C B:ILE226 4.3 38.7 1.0 CA B:PRO205 4.3 22.5 1.0 C B:CYS228 4.3 41.3 1.0 O B:GLY225 4.3 29.7 1.0 N B:ALA207 4.4 27.4 1.0 N B:THR204 4.4 16.6 1.0 CA B:ALA229 4.4 35.4 1.0 CA B:PRO227 4.4 42.2 1.0 N B:CYS228 4.5 42.8 1.0 CA B:ILE226 4.6 38.1 1.0 CB B:ALA229 4.6 35.3 1.0 CA B:CYS228 4.6 44.1 1.0 O B:ILE226 4.6 39.3 1.0 CD B:PRO227 4.7 42.5 1.0 O B:CYS228 4.7 40.4 1.0 CA B:ALA207 4.8 26.8 1.0 O B:PRO205 4.8 24.9 1.0 OG1 B:THR223 4.9 16.9 1.0 OG1 B:THR209 5.0 21.9 1.0

F.Quitterer, P.Beck, A.Bacher, M.Groll. Structure and Reaction Mechanism of Pyrrolysine Synthase (Pyld). Angew.Chem.Int.Ed.Engl. V. 52 7033 2013.
ISSN: ISSN 1433-7851
PubMed: 23720358
DOI: 10.1002/ANIE.201301164