Sodium in PDB 3dt4: The Structure of Rat Cytosolic Pepck in Complex with Oxalate and Gtp

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

The structure of The Structure of Rat Cytosolic Pepck in Complex with Oxalate and Gtp, PDB code: 3dt4 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)	30.02 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.454, 119.759, 87.300, 90.00, 96.70, 90.00
R / Rfree (%)	17.5 / 20.3

The structure of The Structure of Rat Cytosolic Pepck in Complex with Oxalate and Gtp 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 Oxalate and Gtp (pdb code 3dt4). 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 Oxalate and Gtp, PDB code: 3dt4:
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 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 in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1100 b:12.4 occ:1.00 O A:ASN208 2.2 9.9 1.0 O A:LEU79 2.3 11.0 1.0 O A:HOH1363 2.4 13.2 1.0 O A:HOH1328 2.4 15.3 1.0 O A:HOH1561 2.5 21.4 1.0 C A:LEU79 3.4 9.6 1.0 C A:ASN208 3.4 10.4 1.0 N A:LEU79 3.9 8.2 1.0 CA A:LEU79 3.9 8.6 1.0 CB A:LEU79 3.9 9.0 1.0 CB A:ASN208 3.9 11.8 1.0 O A:VAL65 4.0 14.1 1.0 CA A:ASN208 4.3 11.4 1.0 O A:HOH1518 4.3 18.6 1.0 C A:ASN209 4.3 8.6 1.0 CB A:ASN209 4.4 11.5 1.0 N A:ASN209 4.4 9.7 1.0 O A:ASN209 4.4 9.0 1.0 N A:THR80 4.5 8.8 1.0 O A:GLY64 4.6 17.1 1.0 CB A:TRP210 4.6 5.4 1.0 N A:TRP210 4.6 8.0 1.0 CA A:ASN209 4.6 10.1 1.0 C A:VAL65 4.8 13.4 1.0 CA A:THR80 4.8 9.0 1.0 CE3 A:TRP210 4.9 5.9 1.0 CA A:TRP210 5.0 6.6 1.0 O A:HOH1681 5.0 26.7 1.0

Sodium binding site 2 out of 2 in the The Structure of Rat Cytosolic Pepck 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 in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1100 b:18.8 occ:1.00 O C:ASN208 2.3 6.8 1.0 O C:LEU79 2.3 9.3 1.0 O C:HOH1821 2.4 19.4 1.0 O C:HOH2161 2.4 31.3 1.0 O C:HOH1786 2.5 22.5 1.0 C C:LEU79 3.4 8.7 1.0 C C:ASN208 3.5 8.0 1.0 N C:LEU79 3.9 7.2 1.0 CB C:LEU79 3.9 8.7 1.0 CA C:LEU79 4.0 7.8 1.0 O C:VAL65 4.0 21.1 1.0 CB C:ASN208 4.0 12.0 1.0 C C:ASN209 4.2 4.2 1.0 O C:ASN209 4.3 5.2 1.0 CA C:ASN208 4.3 10.7 1.0 CB C:ASN209 4.4 6.5 1.0 N C:ASN209 4.5 6.7 1.0 CB C:TRP210 4.5 4.5 1.0 O C:HOH2162 4.5 29.2 1.0 N C:TRP210 4.5 4.3 1.0 N C:THR80 4.6 7.1 1.0 CA C:ASN209 4.6 5.8 1.0 CE3 C:TRP210 4.7 6.6 1.0 C C:VAL65 4.8 18.6 1.0 CA C:TRP210 4.8 3.6 1.0 O C:GLY64 4.9 20.5 1.0 CA C:THR80 4.9 6.4 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