Sodium in PDB 3d7j: SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor

The structure of SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor, PDB code: 3d7j was solved by J.E.Spoonamore, S.A.Roberts, A.Heroux, V.Bandarian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.34 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.400, 88.000, 120.900, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 22.4

The structure of SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor (pdb code 3d7j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor, PDB code: 3d7j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na133 b:20.3 occ:1.00 O A:HOH260 2.3 30.7 1.0 O A:ARG109 2.3 16.6 1.0 O A:HOH206 2.5 25.2 1.0 C A:ARG109 3.5 17.0 1.0 O A:HOH207 3.9 24.5 1.0 O A:LEU111 4.0 15.8 1.0 CA A:GLY110 4.1 15.5 1.0 N A:GLY110 4.2 16.1 1.0 O A:HOH205 4.4 25.5 1.0 O A:HOH269 4.4 30.9 1.0 C A:GLY110 4.5 15.3 1.0 OXT A:LEU132 4.5 20.6 1.0 O A:LEU132 4.5 19.7 1.0 CA A:ARG109 4.6 17.1 1.0 O A:HOH277 4.7 40.1 1.0 N A:LEU111 4.8 15.2 1.0 C A:LEU132 4.8 19.1 1.0 O A:GLY110 5.0 15.6 1.0

Sodium binding site 2 out of 2 in the SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of SCO6650, A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na134 b:23.4 occ:1.00 O A:HOH276 2.2 24.6 1.0 O A:GLN25 2.4 15.9 1.0 O A:HOH183 2.4 22.0 1.0 O A:HOH185 2.5 25.7 1.0 O A:HOH273 3.4 30.6 1.0 C A:GLN25 3.4 14.9 1.0 CB A:GLN25 4.1 15.5 1.0 CA A:GLN25 4.2 15.9 1.0 N A:ARG26 4.4 15.1 1.0 O A:PHE16 4.5 16.4 1.0 CA A:ARG26 4.5 15.7 1.0 O A:HOH215 4.6 22.9 1.0 OG A:SER15 4.6 17.5 1.0 CB A:SER15 4.7 15.6 1.0 O A:HOH184 4.8 17.9 1.0

J.E.Spoonamore, S.A.Roberts, A.Heroux, V.Bandarian. Structure of A 6-Pyruvoyltetrahydropterin Synthase Homolog From Streptomyces Coelicolor. Acta Crystallogr.,Sect.F V. 64 875 2008.
ISSN: ESSN 1744-3091
PubMed: 18931427
DOI: 10.1107/S1744309108027048