Sodium in PDB 3dtb: The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp

All present enzymatic activity of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp:
4.1.1.32;

The structure of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp, PDB code: 3dtb 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)	28.83 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.154, 119.683, 86.849, 90.00, 107.05, 90.00
R / Rfree (%)	16.8 / 19.3

The structure of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Sodium atom in the The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp (pdb code 3dtb). 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 Phosphoglycolate and Gdp, PDB code: 3dtb:
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 Phosphoglycolate and Gdp


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 Phosphoglycolate and Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1100 b:14.4 occ:1.00 O A:ASN208 2.2 13.2 1.0 O A:HOH3780 2.2 22.4 1.0 O A:LEU79 2.3 10.1 1.0 O A:HOH3508 2.3 14.2 1.0 O A:HOH3782 2.4 15.3 1.0 C A:LEU79 3.4 7.7 1.0 C A:ASN208 3.4 14.4 1.0 N A:LEU79 3.8 7.2 1.0 CB A:LEU79 3.9 7.4 1.0 CA A:LEU79 3.9 7.2 1.0 CB A:ASN208 4.0 16.1 1.0 O A:VAL65 4.0 12.1 1.0 O A:HOH4068 4.2 31.9 1.0 CA A:ASN208 4.2 15.0 1.0 O A:HOH3545 4.2 22.0 1.0 CB A:ASN209 4.3 15.7 1.0 C A:ASN209 4.4 12.7 1.0 N A:ASN209 4.4 13.8 1.0 O A:GLY64 4.5 15.7 1.0 O A:ASN209 4.5 12.9 1.0 N A:THR80 4.5 7.5 1.0 CA A:ASN209 4.6 13.7 1.0 CB A:TRP210 4.6 8.3 1.0 N A:TRP210 4.7 10.6 1.0 C A:VAL65 4.7 11.5 1.0 CA A:THR80 4.8 8.1 1.0 CA A:VAL65 4.9 12.3 0.5 CA A:VAL65 4.9 12.0 0.5 CE3 A:TRP210 5.0 9.4 1.0 CG A:LEU79 5.0 7.6 1.0

Sodium binding site 2 out of 2 in the The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp


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 Phosphoglycolate and Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1100 b:13.9 occ:1.00 O B:LEU79 2.2 11.9 1.0 O B:ASN208 2.3 12.5 1.0 O B:HOH1570 2.3 26.8 1.0 O B:HOH1202 2.4 14.3 1.0 O B:HOH1353 2.5 14.8 1.0 C B:LEU79 3.3 10.8 1.0 C B:ASN208 3.4 11.7 1.0 N B:LEU79 3.8 8.9 1.0 CB B:ASN208 3.9 11.9 1.0 CA B:LEU79 3.9 9.9 1.0 CB B:LEU79 4.0 10.5 1.0 O B:VAL65 4.0 13.1 1.0 O B:HOH1568 4.1 25.4 1.0 CA B:ASN208 4.2 12.4 1.0 O B:HOH1569 4.2 35.4 1.0 CB B:ASN209 4.3 12.6 1.0 O B:GLY64 4.3 18.1 1.0 C B:ASN209 4.3 10.7 1.0 O B:ASN209 4.4 10.5 1.0 N B:ASN209 4.4 12.0 1.0 N B:THR80 4.5 9.3 1.0 O B:HOH1722 4.5 32.8 1.0 CA B:ASN209 4.6 11.5 1.0 CB B:TRP210 4.6 7.5 1.0 N B:TRP210 4.7 9.5 1.0 C B:VAL65 4.7 13.9 1.0 CA B:THR80 4.8 9.4 1.0 CA B:VAL65 4.9 14.3 1.0 C B:ALA78 5.0 9.4 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