Sodium in PDB 1zud: Structure of This-Thif Protein Complex

The structure of Structure of This-Thif Protein Complex, PDB code: 1zud was solved by S.E.Ealick, C.Lehmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.23 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.505, 111.171, 114.153, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 22.9

The structure of Structure of This-Thif Protein Complex also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Zinc	(Zn)	2 atoms

The binding sites of Sodium atom in the Structure of This-Thif Protein Complex (pdb code 1zud). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of This-Thif Protein Complex, PDB code: 1zud:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of This-Thif Protein Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of This-Thif Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ 1:Na701 b:25.6 occ:1.00 O 1:VAL116 2.3 28.2 1.0 O 1:ALA119 2.3 28.4 1.0 O 1:HOH755 2.4 46.4 1.0 O 1:ALA117 2.4 27.9 1.0 OG1 1:THR144 2.6 29.4 1.0 O 1:HOH757 2.7 37.6 1.0 C 1:ALA117 3.1 26.3 1.0 C 1:ALA119 3.5 27.4 1.0 C 1:VAL116 3.5 30.4 1.0 CA 1:ALA117 3.5 25.7 1.0 CG2 1:THR144 3.6 22.6 1.0 N 1:ALA119 3.7 24.8 1.0 CB 1:THR144 3.7 28.6 1.0 N 1:ALA117 4.0 25.0 1.0 CA 1:ALA119 4.1 26.1 1.0 N 1:ARG118 4.1 28.5 1.0 C 1:ARG118 4.1 26.9 1.0 CA 1:ARG118 4.5 28.4 1.0 N 1:ASP120 4.6 20.9 1.0 CB 1:ALA119 4.7 20.4 1.0 CA 1:THR144 4.7 22.4 1.0 CA 1:VAL116 4.8 24.9 1.0 O 1:LEU142 4.8 25.3 1.0 O 1:ARG118 4.8 27.9 1.0 O 1:HOH840 4.8 48.7 1.0 CA 1:ASP120 4.9 25.8 1.0 CG1 1:VAL116 4.9 26.6 1.0 CB 1:ALA117 5.0 29.1 1.0

Sodium binding site 2 out of 2 in the Structure of This-Thif Protein Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of This-Thif Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ 3:Na702 b:24.3 occ:1.00 O 3:HOH808 2.4 44.1 1.0 O 3:ALA119 2.4 23.7 1.0 OG1 3:THR144 2.4 26.0 1.0 O 3:VAL116 2.4 21.5 1.0 O 3:HOH796 2.5 33.7 1.0 O 3:ALA117 2.6 23.5 1.0 C 3:ALA117 3.1 21.8 1.0 CA 3:ALA117 3.4 20.3 1.0 CG2 3:THR144 3.5 20.8 1.0 CB 3:THR144 3.5 20.6 1.0 C 3:VAL116 3.5 21.5 1.0 C 3:ALA119 3.6 27.8 1.0 N 3:ALA119 3.9 21.3 1.0 N 3:ALA117 3.9 21.9 1.0 N 3:ARG118 4.1 22.5 1.0 CA 3:ALA119 4.3 23.2 1.0 C 3:ARG118 4.3 23.5 1.0 CA 3:THR144 4.6 24.2 1.0 O 3:LEU142 4.7 25.2 1.0 N 3:ASP120 4.7 21.6 1.0 CA 3:ARG118 4.7 21.1 1.0 CB 3:ALA117 4.8 23.3 1.0 CA 3:VAL116 4.8 19.9 1.0 CG1 3:VAL116 4.8 18.8 1.0 CB 3:ALA119 4.8 20.6 1.0 O 3:ARG118 4.9 25.0 1.0 CA 3:ASP120 4.9 25.6 1.0

C.Lehmann, T.P.Begley, S.E.Ealick. Structure of the Escherichia Coli This-Thif Complex, A Key Component of the Sulfur Transfer System in Thiamin Biosynthesis. Biochemistry V. 45 11 2006.
ISSN: ISSN 0006-2960
PubMed: 16388576
DOI: 10.1021/BI051502Y