Sodium in PDB 3dt7: The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp

All present enzymatic activity of The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp:
4.1.1.32;

The structure of The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 3dt7 was solved by S.M.Sullivan, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.15 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.019, 119.503, 87.283, 90.00, 107.07, 90.00
R / Rfree (%)	17.4 / 20.9

The structure of The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp also contains other interesting chemical elements:

Manganese

(Mn)

5 atoms

The binding sites of Sodium atom in the The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp (pdb code 3dt7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 3dt7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1100 b:22.4 occ:1.00 O A:ASN208 2.1 10.1 1.0 O A:HOH3849 2.1 12.9 1.0 O A:HOH3558 2.2 17.0 1.0 O A:LEU79 2.3 10.4 1.0 O A:HOH3847 2.7 23.8 1.0 C A:ASN208 3.3 11.2 1.0 C A:LEU79 3.4 8.5 1.0 N A:LEU79 3.7 6.6 1.0 O A:VAL65 3.9 13.9 1.0 CA A:LEU79 3.9 7.2 1.0 CB A:LEU79 4.0 7.5 1.0 CB A:ASN208 4.0 13.8 1.0 CB A:ASN209 4.1 12.1 1.0 C A:ASN209 4.1 7.0 1.0 O A:ASN209 4.2 8.9 1.0 CA A:ASN208 4.2 13.1 1.0 N A:ASN209 4.2 10.5 1.0 O A:GLY64 4.3 15.8 1.0 CA A:ASN209 4.3 10.2 1.0 O A:HOH3596 4.4 26.0 1.0 N A:TRP210 4.5 5.5 1.0 CB A:TRP210 4.5 2.4 1.0 C A:VAL65 4.5 12.9 1.0 N A:THR80 4.6 8.0 1.0 CA A:VAL65 4.7 13.3 1.0 CA A:TRP210 4.9 3.5 1.0 C A:ALA78 4.9 6.2 1.0 CA A:THR80 4.9 8.1 1.0 CE3 A:TRP210 5.0 4.2 1.0

Sodium binding site 2 out of 2 in the The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Rat Cytosolic Pepck in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1100 b:16.0 occ:1.00 O B:ASN208 2.1 10.0 1.0 O B:HOH4096 2.2 14.2 1.0 O B:LEU79 2.3 8.9 1.0 O B:HOH3939 2.3 13.6 1.0 O B:HOH4326 2.5 23.1 1.0 C B:ASN208 3.3 12.1 1.0 C B:LEU79 3.4 8.1 1.0 N B:LEU79 3.8 7.1 1.0 CB B:ASN208 3.9 13.8 1.0 CA B:LEU79 3.9 7.7 1.0 O B:VAL65 3.9 12.4 1.0 CB B:LEU79 4.0 7.3 1.0 CA B:ASN208 4.1 13.4 1.0 C B:ASN209 4.2 8.7 1.0 CB B:ASN209 4.2 12.2 1.0 O B:ASN209 4.2 10.8 1.0 N B:ASN209 4.3 10.7 1.0 O B:HOH4324 4.3 26.8 1.0 O B:HOH4325 4.3 25.8 1.0 O B:GLY64 4.4 18.1 1.0 CA B:ASN209 4.4 11.0 1.0 N B:TRP210 4.5 6.7 1.0 CB B:TRP210 4.5 5.3 1.0 N B:THR80 4.6 6.9 1.0 C B:VAL65 4.7 12.4 1.0 CA B:THR80 4.9 6.3 1.0 CA B:TRP210 4.9 5.6 1.0 C B:ALA78 4.9 6.2 1.0 CA B:VAL65 5.0 13.6 1.0

S.M.Sullivan, T.Holyoak. Enzymes with Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead of Conformational Selection. Proc.Natl.Acad.Sci.Usa V. 105 13829 2008.
ISSN: ISSN 0027-8424
PubMed: 18772387
DOI: 10.1073/PNAS.0805364105