Sodium in PDB 4j4h: Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh

The structure of Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh, PDB code: 4j4h 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 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.250, 260.980, 48.600, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.8

The structure of Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Sodium atom in the Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh (pdb code 4j4h). 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 in Complex with Pyrroline-Carboxy-Lysine and Nadh, PDB code: 4j4h:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Pyld in Complex with Pyrroline-Carboxy-Lysine 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 Pyrroline-Carboxy-Lysine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:31.2 occ:1.00 O A:CYS206 2.6 25.5 1.0 O A:THR204 2.6 23.1 1.0 O A:PRO227 2.6 28.5 1.0 OE1 A:GLU202 2.8 25.2 1.0 O A:HOH1034 3.2 25.7 1.0 OE2 A:GLU202 3.4 24.2 1.0 CD A:GLU202 3.5 23.4 1.0 C A:THR204 3.5 23.5 1.0 C A:CYS206 3.6 27.3 1.0 N A:CYS206 3.6 25.3 1.0 C A:GLY225 3.8 21.9 1.0 N A:ALA229 3.8 26.3 1.0 C A:PRO227 3.9 28.2 1.0 CA A:ALA229 3.9 26.2 1.0 N A:ILE226 4.0 23.1 1.0 CA A:GLY225 4.0 21.5 1.0 CB A:ALA229 4.1 25.7 1.0 CA A:CYS206 4.2 26.9 1.0 C A:CYS228 4.2 27.7 1.0 CB A:THR204 4.2 26.7 1.0 CA A:THR204 4.3 24.4 1.0 O A:GLY225 4.3 22.5 1.0 CG2 A:THR204 4.3 27.0 1.0 C A:PRO205 4.3 24.5 1.0 N A:THR204 4.4 22.7 1.0 C A:ILE226 4.4 25.5 1.0 N A:PRO205 4.5 23.2 1.0 N A:PRO227 4.5 27.3 1.0 CA A:PRO205 4.6 23.8 1.0 N A:ALA207 4.6 27.5 1.0 CA A:ILE226 4.6 24.1 1.0 O A:CYS228 4.6 27.1 1.0 OG1 A:THR209 4.7 23.4 1.0 O A:ILE226 4.7 25.0 1.0 OG1 A:THR223 4.7 21.9 1.0 CA A:CYS228 4.7 29.3 1.0 N A:CYS228 4.8 28.1 1.0 CA A:PRO227 4.8 27.7 1.0 CA A:ALA207 4.9 27.4 1.0 CG A:GLU202 4.9 21.4 1.0

Sodium binding site 2 out of 4 in the Pyld in Complex with Pyrroline-Carboxy-Lysine 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 Pyrroline-Carboxy-Lysine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ B:Na903 b:32.6 occ:1.00 O B:CYS206 2.5 28.7 1.0 O B:THR204 2.6 21.0 1.0 OE1 B:GLU202 2.6 27.8 1.0 O B:PRO227 2.8 30.7 1.0 OE2 B:GLU202 3.1 27.8 1.0 O B:HOH1020 3.2 21.3 1.0 CD B:GLU202 3.2 26.2 1.0 C B:THR204 3.5 23.1 1.0 N B:CYS206 3.6 26.4 1.0 C B:CYS206 3.6 29.6 1.0 N B:ALA229 3.9 26.8 1.0 C B:GLY225 4.0 24.1 1.0 CA B:ALA229 4.0 26.9 1.0 C B:PRO227 4.0 28.7 1.0 CA B:GLY225 4.0 22.8 1.0 CB B:THR204 4.0 26.3 1.0 N B:ILE226 4.1 25.8 1.0 CA B:THR204 4.1 24.0 1.0 CA B:CYS206 4.2 28.9 1.0 C B:CYS228 4.2 27.9 1.0 CB B:ALA229 4.2 26.1 1.0 CG2 B:THR204 4.2 27.9 1.0 N B:THR204 4.3 23.1 1.0 O B:GLY225 4.3 24.2 1.0 C B:PRO205 4.3 25.8 1.0 N B:PRO205 4.4 23.6 1.0 CA B:PRO205 4.6 24.5 1.0 C B:ILE226 4.6 26.6 1.0 O B:CYS228 4.6 27.1 1.0 OG1 B:THR209 4.6 28.3 1.0 N B:ALA207 4.6 30.8 1.0 N B:PRO227 4.7 28.1 1.0 OG1 B:THR223 4.7 21.6 1.0 CG B:GLU202 4.7 24.4 1.0 CA B:CYS228 4.8 29.5 1.0 CA B:ILE226 4.8 26.6 1.0 N B:CYS228 4.8 29.9 1.0 O B:ILE226 4.8 25.7 1.0 CG2 B:THR209 4.9 28.4 1.0 CA B:PRO227 5.0 28.7 1.0

Sodium binding site 3 out of 4 in the Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ C:Na903 b:40.1 occ:1.00 O C:THR204 2.5 30.5 1.0 O C:CYS206 2.5 31.2 1.0 O C:PRO227 2.6 33.9 1.0 O C:HOH1003 3.2 31.0 1.0 OE1 C:GLU202 3.3 34.1 1.0 C C:THR204 3.4 29.2 1.0 OE2 C:GLU202 3.5 33.6 1.0 N C:CYS206 3.5 29.8 1.0 C C:CYS206 3.5 31.0 1.0 CD C:GLU202 3.8 34.4 1.0 C C:PRO227 3.8 33.4 1.0 C C:GLY225 3.8 30.8 1.0 N C:ILE226 3.8 31.6 1.0 N C:ALA229 3.9 35.0 1.0 CA C:GLY225 3.9 29.3 1.0 CA C:ALA229 4.1 34.9 1.0 CA C:CYS206 4.1 30.6 1.0 CB C:THR204 4.2 32.4 1.0 C C:PRO205 4.2 28.4 1.0 C C:ILE226 4.2 33.2 1.0 CA C:THR204 4.2 29.6 1.0 C C:CYS228 4.2 34.8 1.0 O C:GLY225 4.2 29.1 1.0 N C:PRO205 4.3 27.6 1.0 CB C:ALA229 4.3 37.4 1.0 N C:PRO227 4.3 33.7 1.0 O C:ILE226 4.4 30.7 1.0 CG2 C:THR204 4.4 33.0 1.0 CA C:PRO205 4.4 27.8 1.0 N C:THR204 4.4 30.1 1.0 CA C:ILE226 4.4 32.7 1.0 N C:ALA207 4.6 31.9 1.0 O C:CYS228 4.7 34.4 1.0 N C:CYS228 4.7 35.3 1.0 CA C:CYS228 4.7 36.2 1.0 CA C:PRO227 4.7 34.8 1.0 OG1 C:THR223 4.9 37.1 1.0 CA C:ALA207 4.9 34.7 1.0 OG1 C:THR209 5.0 34.0 1.0 CD C:PRO227 5.0 34.7 1.0

Sodium binding site 4 out of 4 in the Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Pyld in Complex with Pyrroline-Carboxy-Lysine and Nadh within 5.0Å range: probe atom residue distance (Å) B Occ D:Na903 b:42.9 occ:1.00 O D:CYS206 2.4 33.7 1.0 O D:PRO227 2.5 33.9 1.0 O D:THR204 2.6 31.3 1.0 O D:HOH1010 3.1 32.4 1.0 OE1 D:GLU202 3.2 34.1 1.0 C D:CYS206 3.4 33.5 1.0 N D:CYS206 3.5 33.7 1.0 C D:THR204 3.6 32.9 1.0 OE2 D:GLU202 3.6 37.6 1.0 C D:PRO227 3.7 35.6 1.0 CD D:GLU202 3.8 35.9 1.0 C D:GLY225 3.8 33.2 1.0 N D:ALA229 3.8 35.6 1.0 N D:ILE226 4.0 32.3 1.0 CA D:ALA229 4.0 36.8 1.0 CA D:CYS206 4.0 33.8 1.0 CA D:GLY225 4.1 33.6 1.0 C D:CYS228 4.1 36.6 1.0 C D:PRO205 4.1 31.6 1.0 O D:GLY225 4.1 34.9 1.0 CB D:ALA229 4.2 37.0 1.0 C D:ILE226 4.2 33.9 1.0 N D:PRO227 4.3 33.8 1.0 CA D:THR204 4.4 33.7 1.0 CB D:THR204 4.4 34.8 1.0 N D:PRO205 4.4 32.3 1.0 N D:ALA207 4.4 34.1 1.0 O D:ILE226 4.4 32.1 1.0 CG2 D:THR204 4.4 36.3 1.0 CA D:PRO205 4.5 32.4 1.0 CA D:ILE226 4.5 34.3 1.0 O D:CYS228 4.5 36.3 1.0 N D:THR204 4.6 32.9 1.0 N D:CYS228 4.6 35.5 1.0 CA D:PRO227 4.6 35.3 1.0 CA D:CYS228 4.7 37.5 1.0 CA D:ALA207 4.8 35.4 1.0 CD D:PRO227 4.9 34.2 1.0 O D:PRO205 4.9 30.6 1.0 OG1 D:THR223 5.0 32.8 1.0 CG2 D:THR209 5.0 37.1 1.0 OG1 D:THR209 5.0 36.4 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