Sodium in PDB 2rk8: The Structure of Rat Cytosolic Pepck in Complex with Phosphonoformate

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

The structure of The Structure of Rat Cytosolic Pepck in Complex with Phosphonoformate, PDB code: 2rk8 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)	30.06 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.251, 119.470, 86.870, 90.00, 107.06, 90.00
R / Rfree (%)	19.5 / 24.9

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

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the The Structure of Rat Cytosolic Pepck in Complex with Phosphonoformate (pdb code 2rk8). 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 Phosphonoformate, PDB code: 2rk8:
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 Phosphonoformate


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 Phosphonoformate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na624 b:43.9 occ:1.00 O A:HOH6047 2.2 31.1 1.0 O A:HOH5930 2.3 30.5 1.0 O A:ASN208 2.3 22.0 1.0 O A:LEU79 2.5 17.8 1.0 O A:HOH5839 2.8 47.2 1.0 C A:ASN208 3.5 22.2 1.0 C A:LEU79 3.6 17.2 1.0 O A:VAL65 3.6 23.6 1.0 N A:LEU79 3.8 16.6 1.0 CA A:LEU79 4.0 16.8 1.0 CB A:LEU79 4.1 16.7 1.0 O A:GLY64 4.2 24.6 1.0 CB A:ASN208 4.2 22.6 0.5 CB A:ASN208 4.2 22.4 0.5 CB A:ASN209 4.2 21.3 1.0 O A:HOH6164 4.3 36.4 1.0 C A:ASN209 4.3 20.2 1.0 O A:ASN209 4.4 20.4 1.0 C A:VAL65 4.4 23.6 1.0 N A:ASN209 4.4 21.6 1.0 CA A:ASN208 4.4 22.6 0.5 CA A:ASN208 4.4 22.5 0.5 CA A:ASN209 4.5 21.1 1.0 CA A:VAL65 4.7 23.7 1.0 N A:THR80 4.8 17.1 1.0 N A:TRP210 4.8 19.1 1.0 CB A:TRP210 4.8 17.8 1.0 C A:ALA78 5.0 16.5 1.0

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


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 Phosphonoformate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na624 b:35.9 occ:1.00 O B:ASN208 2.2 22.8 1.0 O B:HOH4249 2.3 24.9 1.0 O B:HOH3970 2.3 34.2 1.0 O B:LEU79 2.5 18.5 1.0 O B:HOH4138 2.5 28.9 1.0 C B:ASN208 3.4 22.7 1.0 C B:LEU79 3.5 18.1 1.0 N B:LEU79 3.8 17.6 1.0 O B:VAL65 3.9 22.4 1.0 CA B:LEU79 4.0 17.9 1.0 CB B:ASN208 4.0 23.2 1.0 CB B:LEU79 4.1 17.7 1.0 CA B:ASN208 4.3 23.2 1.0 CB B:ASN209 4.3 21.6 1.0 C B:ASN209 4.3 20.6 1.0 O B:GLY64 4.3 23.6 1.0 N B:ASN209 4.3 22.0 1.0 O B:ASN209 4.4 20.9 1.0 CA B:ASN209 4.5 21.5 1.0 C B:VAL65 4.6 22.4 1.0 N B:TRP210 4.6 19.6 1.0 N B:THR80 4.7 18.3 1.0 CB B:TRP210 4.8 18.3 1.0 CA B:VAL65 4.8 22.7 1.0 C B:ALA78 5.0 17.5 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