Sodium in PDB 5dip: Crystal Structure of LPG0406 in Reduced Form From Legionella Pneumophila

All present enzymatic activity of Crystal Structure of LPG0406 in Reduced Form From Legionella Pneumophila:
1.11.1.15;

The structure of Crystal Structure of LPG0406 in Reduced Form From Legionella Pneumophila, PDB code: 5dip was solved by X.Chen, X.Gong, N.Zhang, H.Ge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.58 / 2.10
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	145.712, 145.712, 145.712, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 15.8

The binding sites of Sodium atom in the Crystal Structure of LPG0406 in Reduced Form From Legionella Pneumophila (pdb code 5dip). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of LPG0406 in Reduced Form From Legionella Pneumophila, PDB code: 5dip:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of LPG0406 in Reduced Form From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of LPG0406 in Reduced Form From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:29.3 occ:1.00 O A:HOH387 2.7 32.0 1.0 CE B:MET92 2.8 15.1 0.5 O B:HOH340 3.0 37.9 1.0 NE2 A:HIS68 3.1 26.9 1.0 SG A:CYS64 3.4 28.8 1.0 CG B:MET92 3.8 14.2 0.5 OH B:TYR91 3.8 30.8 1.0 CE B:MET92 3.9 15.1 0.5 SD B:MET92 4.0 38.5 0.5 CD2 A:HIS68 4.0 22.3 1.0 CE1 A:HIS68 4.0 22.8 1.0 CZ B:TYR91 4.2 26.8 1.0 CB A:CYS64 4.2 19.5 1.0 SD B:MET92 4.4 23.7 0.5 O B:HOH400 4.4 40.4 1.0 CE1 B:TYR91 4.5 22.9 1.0 CA A:CYS64 4.7 18.9 1.0 CE2 B:TYR91 4.8 29.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of LPG0406 in Reduced Form From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of LPG0406 in Reduced Form From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:16.0 occ:1.00 N A:GLU25 3.2 15.9 1.0 C A:MET23 3.4 15.1 1.0 CA A:MET23 3.5 19.6 1.0 N A:LEU26 3.5 14.2 1.0 CB A:GLU25 3.5 14.8 1.0 N A:PRO24 3.6 17.2 1.0 O A:MET23 3.8 17.6 1.0 CA A:GLU25 3.8 18.6 1.0 CB A:MET23 3.9 18.0 1.0 CD A:PRO24 3.9 16.3 1.0 C A:GLU25 4.1 16.3 1.0 CB A:LEU26 4.1 17.2 1.0 C A:PRO24 4.2 19.0 1.0 CA A:LEU26 4.4 19.9 1.0 CA A:PRO24 4.5 17.3 1.0 CG A:PRO24 4.7 18.8 1.0 OE2 A:GLU25 4.8 20.8 1.0 N A:MET23 4.8 22.6 1.0 O A:GLU22 4.8 18.1 1.0 CG A:GLU25 4.9 16.0 1.0 CG A:MET23 4.9 28.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of LPG0406 in Reduced Form From Legionella Pneumophila


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of LPG0406 in Reduced Form From Legionella Pneumophila within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:24.1 occ:1.00 O B:HOH388 2.8 32.7 1.0 CE A:MET92 2.8 17.2 0.4 O A:HOH375 2.9 37.4 1.0 NE2 B:HIS68 3.1 24.2 1.0 SG B:CYS64 3.5 32.1 1.0 CG A:MET92 3.9 13.4 0.6 CE A:MET92 3.9 14.9 0.6 CD2 B:HIS68 4.0 19.6 1.0 OH A:TYR91 4.0 25.6 1.0 CE1 B:HIS68 4.1 23.2 1.0 SD A:MET92 4.2 37.0 0.6 O A:HOH403 4.3 40.8 1.0 CB B:CYS64 4.3 17.1 1.0 CZ A:TYR91 4.4 26.6 1.0 SD A:MET92 4.4 26.0 0.4 CE1 A:TYR91 4.6 21.1 1.0 CA B:CYS64 4.8 17.3 1.0

X.Chen, Y.Hu, B.Yang, X.Gong, N.Zhang, L.Niu, Y.Wu, H.Ge. Structure of LPG0406, A Carboxymuconolactone Decarboxylase Family Protein Possibly Involved in Antioxidative Response From Legionella Pneumophila Protein Sci. V. 24 2070 2015.
ISSN: ESSN 1469-896X
PubMed: 26402328
DOI: 10.1002/PRO.2811