Sodium in PDB 2rka: The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate

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

The structure of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate, PDB code: 2rka was solved by S.M.Sullivan, R.M.Stiffin, G.M.Carlson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.92 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.670, 119.660, 90.867, 90.00, 108.90, 90.00
R / Rfree (%)	18.3 / 22.2

The structure of The Structure of Rat Cytosolic Pepck in Complex with Phosphoglycolate 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 (pdb code 2rka). 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, PDB code: 2rka:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na702 b:21.5 occ:1.00 O A:ASN208 2.2 18.9 1.0 O A:HOH914 2.4 21.4 1.0 O A:HOH1021 2.4 15.8 1.0 O A:LEU79 2.4 15.2 1.0 O A:HOH815 2.6 35.0 1.0 C A:ASN208 3.4 19.1 1.0 C A:LEU79 3.5 15.0 1.0 O A:VAL65 3.8 17.8 1.0 N A:LEU79 3.9 14.5 1.0 CB A:ASN208 4.1 18.9 1.0 CA A:LEU79 4.1 14.7 1.0 O A:GLY64 4.2 19.8 1.0 CB A:LEU79 4.2 14.5 1.0 CA A:ASN208 4.3 19.1 1.0 C A:ASN209 4.3 18.2 1.0 CB A:ASN209 4.3 19.2 1.0 N A:ASN209 4.3 18.8 1.0 O A:ASN209 4.4 18.4 1.0 CA A:ASN209 4.5 18.9 1.0 C A:VAL65 4.5 17.7 1.0 CB A:TRP210 4.6 15.9 1.0 N A:THR80 4.7 15.0 1.0 N A:TRP210 4.7 17.2 1.0 CA A:VAL65 4.8 18.2 1.0 CA A:THR80 5.0 14.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na702 b:19.5 occ:1.00 O C:ASN208 2.3 18.8 1.0 O C:LEU79 2.3 15.5 1.0 O C:HOH791 2.3 17.2 1.0 O C:HOH779 2.3 13.8 1.0 C C:LEU79 3.4 15.1 1.0 C C:ASN208 3.4 19.3 1.0 N C:LEU79 3.8 14.7 1.0 O C:VAL65 3.8 18.3 1.0 CA C:LEU79 4.0 14.8 1.0 O C:HOH1107 4.1 30.8 1.0 CB C:ASN208 4.1 20.0 1.0 CB C:LEU79 4.1 14.8 1.0 O C:GLY64 4.3 19.0 1.0 C C:ASN209 4.3 18.3 1.0 O C:ASN209 4.3 17.7 1.0 CB C:ASN209 4.3 18.8 1.0 CA C:ASN208 4.3 19.9 1.0 N C:ASN209 4.4 18.8 1.0 CA C:ASN209 4.5 18.6 1.0 N C:THR80 4.5 15.0 1.0 C C:VAL65 4.6 18.3 1.0 CB C:TRP210 4.6 17.4 1.0 N C:TRP210 4.7 17.6 1.0 CA C:VAL65 4.9 18.5 1.0 CA C:THR80 4.9 14.5 1.0 C C:ALA78 4.9 14.5 1.0 CE3 C:TRP210 5.0 16.7 1.0

R.M.Stiffin, S.M.Sullivan, G.M.Carlson, T.Holyoak. Differential Inhibition of Cytosolic Pepck By Substrate Analogues. Kinetic and Structural Characterization of Inhibitor Recognition. Biochemistry V. 47 2099 2008.
ISSN: ISSN 0006-2960
PubMed: 18197707
DOI: 10.1021/BI7020662