Sodium in PDB 3mof: The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp

All present enzymatic activity of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp:
4.1.1.32;

The structure of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate and Gtp, PDB code: 3mof was solved by T.A.Johnson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.24 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.983, 119.601, 87.068, 90.00, 106.87, 90.00
R / Rfree (%)	17.9 / 22.8

The structure of The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate 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 Mutant A467G in Complex with Oxalate and Gtp (pdb code 3mof). 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 Mutant A467G in Complex with Oxalate and Gtp, PDB code: 3mof:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate 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 Mutant A467G in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1100 b:30.2 occ:1.00 O A:HOH940 2.3 13.5 1.0 O A:ASN208 2.3 15.1 1.0 O A:HOH840 2.3 17.4 1.0 O A:LEU79 2.4 9.7 1.0 O A:HOH1035 2.7 29.6 1.0 C A:LEU79 3.4 8.0 1.0 C A:ASN208 3.5 16.0 1.0 N A:LEU79 3.8 5.5 1.0 CA A:LEU79 4.0 6.9 1.0 CB A:LEU79 4.0 6.2 1.0 O A:VAL65 4.0 17.7 1.0 CB A:ASN208 4.1 18.9 1.0 CB A:ASN209 4.4 14.7 1.0 C A:ASN209 4.4 12.6 1.0 CA A:ASN208 4.4 18.1 1.0 O A:HOH1030 4.4 24.5 1.0 O A:ASN209 4.4 14.4 1.0 O A:GLY64 4.5 18.9 1.0 N A:ASN209 4.5 14.5 1.0 N A:THR80 4.6 8.2 1.0 CA A:ASN209 4.6 14.7 1.0 N A:TRP210 4.7 11.7 1.0 CB A:TRP210 4.7 9.9 1.0 C A:VAL65 4.7 16.9 1.0 CE3 A:TRP210 4.9 5.4 1.0 CA A:VAL65 4.9 17.6 1.0 C A:ALA78 5.0 5.8 1.0 CA A:THR80 5.0 8.1 1.0

Sodium binding site 2 out of 2 in the The Structure of Rat Cytosolic Pepck Mutant A467G in Complex with Oxalate 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 Mutant A467G in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1100 b:24.9 occ:1.00 O B:ASN208 2.3 15.6 1.0 O B:LEU79 2.3 7.1 1.0 O B:HOH766 2.4 8.4 1.0 O B:HOH883 2.5 14.8 1.0 O B:HOH930 2.6 18.0 1.0 C B:ASN208 3.4 17.0 1.0 C B:LEU79 3.4 7.2 1.0 N B:LEU79 3.8 6.2 1.0 O B:VAL65 3.9 15.0 1.0 CB B:ASN208 3.9 18.5 1.0 CA B:LEU79 4.0 7.0 1.0 CB B:LEU79 4.0 6.9 1.0 O B:HOH936 4.1 18.8 1.0 CA B:ASN208 4.2 18.1 1.0 C B:ASN209 4.4 12.8 1.0 N B:ASN209 4.4 15.7 1.0 CB B:ASN209 4.4 16.0 1.0 O B:ASN209 4.4 14.4 1.0 O B:GLY64 4.5 17.7 1.0 N B:THR80 4.6 6.9 1.0 CA B:ASN209 4.6 15.1 1.0 N B:TRP210 4.7 10.4 1.0 C B:VAL65 4.8 14.8 1.0 CB B:TRP210 4.8 8.8 1.0 CE3 B:TRP210 4.9 9.1 1.0 CA B:THR80 5.0 7.4 1.0

T.A.Johnson, T.Holyoak. Increasing the Conformational Entropy of the Omega-Loop Lid Domain in Phosphoenolpyruvate Carboxykinase Impairs Catalysis and Decreases Catalytic Fidelity . Biochemistry V. 49 5176 2010.
ISSN: ISSN 0006-2960
PubMed: 20476774
DOI: 10.1021/BI100399E