Sodium in PDB 4jk3: Pyld Holoenzyme (Semet)

The structure of Pyld Holoenzyme (Semet), PDB code: 4jk3 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 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.650, 155.400, 39.570, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 25.7

The structure of Pyld Holoenzyme (Semet) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Pyld Holoenzyme (Semet) (pdb code 4jk3). 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 Holoenzyme (Semet), PDB code: 4jk3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pyld Holoenzyme (Semet)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pyld Holoenzyme (Semet) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:43.6 occ:1.00 O A:HOH1019 2.5 37.0 1.0 O A:THR204 2.6 41.3 1.0 O A:PRO227 2.6 66.5 1.0 O A:CYS206 2.7 48.2 1.0 OE2 A:GLU202 3.0 36.0 1.0 OE1 A:GLU202 3.0 33.3 1.0 CD A:GLU202 3.3 33.6 1.0 C A:THR204 3.5 40.7 1.0 CA A:GLY225 3.7 46.7 1.0 N A:CYS206 3.7 49.4 1.0 C A:CYS206 3.7 48.0 1.0 C A:GLY225 3.8 51.8 1.0 N A:ALA229 3.9 53.3 1.0 C A:PRO227 3.9 66.0 1.0 N A:ILE226 4.1 57.1 1.0 CB A:THR204 4.1 39.8 1.0 CA A:ALA229 4.2 48.8 1.0 CB A:ALA229 4.2 47.8 1.0 CA A:THR204 4.2 38.4 1.0 N A:THR204 4.2 34.3 1.0 O A:GLY225 4.2 51.5 1.0 OG1 A:THR223 4.3 37.9 1.0 CA A:CYS206 4.3 49.4 1.0 C A:CYS228 4.3 58.8 1.0 CG2 A:THR204 4.4 39.5 1.0 N A:PRO205 4.5 42.8 1.0 C A:PRO205 4.5 47.4 1.0 CA A:CYS228 4.6 60.7 1.0 CA A:PRO205 4.6 44.6 1.0 N A:PRO227 4.7 71.0 1.0 N A:CYS228 4.7 63.0 1.0 C A:ILE226 4.7 66.7 1.0 N A:GLY225 4.8 44.3 1.0 OG1 A:THR209 4.8 37.4 1.0 CG A:GLU202 4.8 30.8 1.0 N A:ALA207 4.8 49.2 1.0 CA A:ILE226 4.9 64.5 1.0 CA A:PRO227 4.9 69.1 1.0

Sodium binding site 2 out of 2 in the Pyld Holoenzyme (Semet)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pyld Holoenzyme (Semet) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:46.1 occ:1.00 O B:CYS206 2.6 54.8 1.0 O B:HOH1019 2.6 57.5 1.0 O B:THR204 2.6 47.0 1.0 O B:PRO227 2.8 85.0 1.0 OE1 B:GLU202 2.8 42.2 1.0 OE2 B:GLU202 2.9 40.9 1.0 CD B:GLU202 3.2 40.1 1.0 C B:THR204 3.6 46.8 1.0 C B:CYS206 3.7 56.7 1.0 N B:CYS206 3.7 57.4 1.0 N B:ALA229 3.8 70.9 1.0 CA B:GLY225 3.8 61.0 1.0 C B:PRO227 4.0 86.8 1.0 CB B:ALA229 4.0 62.5 1.0 CA B:ALA229 4.0 69.4 1.0 C B:GLY225 4.0 66.0 1.0 CB B:THR204 4.0 44.8 1.0 CA B:THR204 4.2 43.7 1.0 N B:THR204 4.2 40.3 1.0 OG1 B:THR223 4.3 47.1 1.0 CA B:CYS206 4.3 58.6 1.0 C B:CYS228 4.3 74.4 1.0 CG2 B:THR204 4.3 44.2 1.0 N B:ILE226 4.4 75.9 1.0 O B:GLY225 4.4 64.3 1.0 N B:PRO205 4.6 51.3 1.0 OG1 B:THR209 4.6 47.7 1.0 CA B:CYS228 4.6 75.8 1.0 C B:PRO205 4.6 56.9 1.0 CG B:GLU202 4.7 38.5 1.0 CA B:PRO205 4.7 53.0 1.0 N B:ALA207 4.7 57.6 1.0 N B:CYS228 4.8 80.8 1.0 N B:PRO227 4.8 91.2 1.0 N B:GLY225 4.9 54.1 1.0 C B:ILE226 4.9 89.9 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