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Sodium in PDB 4yw9: Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp

Enzymatic activity of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp

All present enzymatic activity of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp:
4.1.1.32;

Protein crystallography data

The structure of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp, PDB code: 4yw9 was solved by M.D.Balan, T.A.Johnson, M.J.Mcleod, W.R.Lotosky, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.16 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.407, 118.742, 60.248, 90.00, 110.02, 90.00
R / Rfree (%) 16.8 / 19.7

Other elements in 4yw9:

The structure of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp also contains other interesting chemical elements:

Manganese (Mn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp (pdb code 4yw9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp, PDB code: 4yw9:

Sodium binding site 1 out of 1 in 4yw9

Go back to Sodium Binding Sites List in 4yw9
Sodium binding site 1 out of 1 in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na704

b:24.3
occ:1.00
 O A:HOH1209 2.2 20.1 1.0
O A:ASN208 2.3 21.0 1.0
O A:LEU79 2.3 17.5 1.0
O A:HOH959 2.4 24.9 1.0
O A:HOH1306 2.5 36.7 1.0
C A:LEU79 3.5 17.2 1.0
C A:ASN208 3.5 21.8 1.0
N A:LEU79 3.8 15.4 1.0
O A:VAL65 3.8 25.7 1.0
CA A:LEU79 4.0 16.3 1.0
CB A:LEU79 4.0 17.0 1.0
CB A:ASN208 4.0 28.1 1.0
CB A:ASN209 4.2 25.4 1.0
O A:HOH1427 4.3 33.6 1.0
C A:ASN209 4.3 19.8 1.0
O A:ASN209 4.3 20.8 1.0
CA A:ASN208 4.3 25.1 1.0
N A:ASN209 4.4 21.5 1.0
O A:GLY64 4.5 34.3 1.0
CA A:ASN209 4.5 23.5 1.0
CB A:TRP210 4.5 14.9 1.0
N A:THR80 4.6 17.3 1.0
N A:TRP210 4.6 17.6 1.0
C A:VAL65 4.7 26.3 1.0
CE3 A:TRP210 4.8 16.1 1.0
CA A:VAL65 4.9 26.9 1.0
C A:ALA78 4.9 14.8 1.0
O A:HOH1000 5.0 42.9 1.0
CA A:THR80 5.0 16.0 1.0
CA A:TRP210 5.0 15.4 1.0

Reference:

M.D.Balan, M.J.Mcleod, W.R.Lotosky, M.Ghaly, T.Holyoak. Inhibition and Allosteric Regulation of Monomeric Phosphoenolpyruvate Carboxykinase By 3-Mercaptopicolinic Acid. Biochemistry V. 54 5878 2015.
ISSN: ISSN 0006-2960
PubMed: 26322521
DOI: 10.1021/ACS.BIOCHEM.5B00822
Page generated: Sun Aug 17 22:40:30 2025

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