Sodium in PDB 4zu4: X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans

The structure of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans, PDB code: 4zu4 was solved by J.B.Thoden, E.Vinogradov, M.Gilbert, A.J.Salinger, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.28 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	85.405, 64.579, 112.968, 90.00, 111.39, 90.00
R / Rfree (%)	17.1 / 20.7

The structure of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Sodium atom in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans (pdb code 4zu4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans, PDB code: 4zu4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:23.7 occ:1.00 O A:HOH609 2.2 35.0 1.0 O C:SER160 2.3 19.5 1.0 OG A:SER296 2.3 19.6 1.0 OD2 A:ASP294 2.4 25.5 1.0 CG A:ASP294 3.3 22.7 1.0 C C:SER160 3.5 16.1 1.0 CB A:SER296 3.5 18.6 1.0 CB A:ASP294 3.6 26.2 1.0 N A:SER296 3.8 17.8 1.0 CA C:ASN161 4.1 16.4 1.0 CA A:SER296 4.1 15.5 1.0 N C:ASN161 4.2 17.7 1.0 O C:HOH515 4.3 42.9 1.0 ND2 C:ASN162 4.3 24.9 0.5 OD1 A:ASP294 4.3 32.0 1.0 N A:THR297 4.4 15.3 1.0 N C:SER160 4.4 17.2 1.0 OD1 C:ASN161 4.4 19.6 1.0 N A:TYR295 4.5 16.9 1.0 CA C:SER160 4.5 18.4 1.0 OG1 A:THR297 4.5 18.0 1.0 C A:ASP294 4.6 20.9 1.0 CA A:ASP294 4.7 22.1 1.0 C A:SER296 4.7 17.6 1.0 C C:ASN161 4.9 18.9 1.0 C A:TYR295 4.9 16.3 1.0 CB C:SER160 5.0 19.6 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the 3,4-Ketoisomerase Domain of Fdtd From Shewanella Denitrificans within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:27.0 occ:1.00 O C:GLY157 2.4 29.9 1.0 O C:MET159 2.4 20.9 1.0 O C:HOH601 2.5 35.1 1.0 C C:MET159 3.5 18.3 1.0 C C:GLY157 3.5 28.0 1.0 O C:HOH556 3.9 23.0 1.0 C C:HIS158 4.0 19.1 1.0 N C:MET159 4.1 19.8 1.0 CB C:SER160 4.2 19.6 1.0 N C:GLY157 4.2 37.6 1.0 N C:SER160 4.3 17.2 1.0 CA C:HIS158 4.3 19.0 1.0 N C:HIS158 4.3 22.9 1.0 CA C:SER160 4.4 18.4 1.0 CA C:MET159 4.4 18.5 1.0 O C:HIS158 4.4 20.6 1.0 CA C:GLY157 4.5 30.3 1.0 O C:HOH606 4.5 30.7 1.0 OG C:SER160 4.7 18.5 1.0 O C:HOH574 4.9 23.1 1.0

J.B.Thoden, E.Vinogradov, M.Gilbert, A.J.Salinger, H.M.Holden. Bacterial Sugar 3,4-Ketoisomerases: Structural Insight Into Product Stereochemistry. Biochemistry V. 54 4495 2015.
ISSN: ISSN 0006-2960
PubMed: 26125548
DOI: 10.1021/ACS.BIOCHEM.5B00541