Sodium in PDB 2qf2: Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.

All present enzymatic activity of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.:
4.1.1.32;

The structure of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp., PDB code: 2qf2 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)	33.33 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.506, 119.112, 86.710, 90.00, 107.35, 90.00
R / Rfree (%)	20.4 / 23.8

The structure of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp. also contains other interesting chemical elements:

Manganese

(Mn)

7 atoms

The binding sites of Sodium atom in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp. (pdb code 2qf2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp., PDB code: 2qf2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na700 b:28.1 occ:1.00 O A:HOH4233 2.2 22.4 1.0 O A:HOH4235 2.3 24.5 1.0 O A:ASN208 2.4 17.4 1.0 O A:LEU79 2.4 19.4 1.0 C A:LEU79 3.5 18.7 1.0 C A:ASN208 3.6 17.7 1.0 O A:VAL65 3.8 20.3 1.0 N A:LEU79 3.9 17.9 1.0 CA A:LEU79 4.1 18.4 1.0 O A:HOH4681 4.1 36.2 1.0 CB A:ASN208 4.2 18.6 1.0 CB A:LEU79 4.2 18.5 1.0 O A:GLY64 4.3 22.1 1.0 C A:ASN209 4.4 16.2 1.0 O A:ASN209 4.4 15.9 1.0 CB A:ASN209 4.4 17.3 1.0 CA A:ASN208 4.4 18.3 1.0 N A:ASN209 4.5 17.2 1.0 C A:VAL65 4.5 20.7 1.0 CA A:ASN209 4.6 16.8 1.0 N A:THR80 4.6 18.8 1.0 CB A:TRP210 4.7 15.1 1.0 N A:TRP210 4.7 15.6 1.0 CA A:VAL65 4.8 21.0 1.0 CA A:THR80 4.9 19.1 1.0 C A:ALA78 5.0 17.9 1.0

Sodium binding site 2 out of 2 in the Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rat Cytosolic Pepck in Complex with Oxaloacetic Acid and Gdp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na800 b:27.9 occ:1.00 O B:HOH4183 2.2 22.1 1.0 O B:ASN208 2.3 14.2 1.0 O B:LEU79 2.3 17.8 1.0 O B:HOH4351 2.3 28.9 1.0 O B:HOH4368 2.4 41.1 1.0 C B:LEU79 3.4 17.8 1.0 C B:ASN208 3.5 14.3 1.0 O B:VAL65 3.8 18.4 1.0 N B:LEU79 3.8 17.9 1.0 CA B:LEU79 4.0 17.6 1.0 CB B:ASN208 4.1 14.6 1.0 CB B:ASN209 4.2 14.4 1.0 CB B:LEU79 4.2 17.8 1.0 O B:GLY64 4.3 19.9 1.0 C B:ASN209 4.3 13.5 1.0 CA B:ASN208 4.3 14.6 1.0 O B:HOH4654 4.3 46.0 1.0 N B:ASN209 4.4 14.1 1.0 O B:ASN209 4.4 12.8 1.0 CA B:ASN209 4.5 13.8 1.0 N B:THR80 4.5 17.9 1.0 C B:VAL65 4.6 18.6 1.0 CB B:TRP210 4.6 12.7 1.0 N B:TRP210 4.7 12.9 1.0 CA B:VAL65 4.8 18.9 1.0 CA B:THR80 4.9 17.9 1.0 C B:ALA78 5.0 17.7 1.0

S.M.Sullivan, T.Holyoak. Structures of Rat Cytosolic Pepck: Insight Into the Mechanism of Phosphorylation and Decarboxylation of Oxaloacetic Acid. Biochemistry V. 46 10078 2007.
ISSN: ISSN 0006-2960
PubMed: 17685635
DOI: 10.1021/BI701038X