Sodium in PDB 4ox2: I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp

All present enzymatic activity of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp:
4.1.1.32;

The structure of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 4ox2 was solved by T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.13 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.924, 119.252, 87.397, 90.00, 106.92, 90.00
R / Rfree (%)	18.9 / 23.3

The structure of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Sodium atom in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp (pdb code 4ox2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 4ox2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na706 b:56.2 occ:1.00 O A:HOH964 2.2 46.7 1.0 O A:ASN208 2.2 43.8 1.0 O A:HOH959 2.5 38.0 1.0 O A:LEU79 2.6 35.7 1.0 O A:HOH974 2.9 50.5 1.0 C A:ASN208 3.4 45.7 1.0 C A:LEU79 3.7 34.2 1.0 O A:VAL65 3.9 41.0 1.0 CB A:ASN208 3.9 53.9 1.0 N A:LEU79 3.9 30.7 1.0 CB A:LEU79 4.1 34.1 1.0 CA A:LEU79 4.1 33.5 1.0 O A:GLY64 4.1 44.6 1.0 CA A:ASN208 4.2 50.3 1.0 O A:HOH973 4.2 49.1 1.0 C A:ASN209 4.3 38.2 1.0 CB A:ASN209 4.3 44.5 1.0 O A:ASN209 4.3 42.3 1.0 N A:ASN209 4.4 42.5 1.0 C A:VAL65 4.5 40.5 1.0 CA A:ASN209 4.6 42.4 1.0 N A:TRP210 4.6 35.4 1.0 CB A:TRP210 4.6 31.2 1.0 CA A:VAL65 4.7 41.9 1.0 N A:THR80 4.8 33.2 1.0 CA A:TRP210 5.0 32.4 1.0

Sodium binding site 2 out of 2 in the I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of I45T Cytosolic Phosphoenolpyruvate Carboxykinase in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na706 b:56.0 occ:1.00 O B:HOH1014 2.0 37.1 1.0 O B:HOH1015 2.2 49.7 1.0 O B:ASN208 2.4 41.7 1.0 O B:HOH1013 2.5 39.5 1.0 O B:LEU79 2.7 32.8 1.0 C B:ASN208 3.6 44.1 1.0 O B:VAL65 3.7 36.1 1.0 C B:LEU79 3.8 31.0 1.0 O B:GLY64 3.8 43.7 1.0 N B:LEU79 4.0 27.7 1.0 CB B:ASN209 4.1 41.0 1.0 C B:ASN209 4.2 36.7 1.0 O B:ASN209 4.2 39.0 1.0 CA B:LEU79 4.3 29.4 1.0 CB B:LEU79 4.3 31.3 1.0 CG B:ASN208 4.3 54.3 1.0 CB B:ASN208 4.3 51.5 1.0 C B:VAL65 4.3 38.2 1.0 CA B:VAL65 4.4 39.1 1.0 N B:ASN209 4.4 39.0 1.0 CA B:ASN208 4.5 46.5 1.0 CA B:ASN209 4.5 39.8 1.0 OD1 B:ASN208 4.5 55.9 1.0 N B:TRP210 4.6 33.9 1.0 CB B:TRP210 4.6 29.8 1.0 ND2 B:ASN208 4.7 59.3 1.0 C B:GLY64 4.9 42.6 1.0 N B:THR80 4.9 31.4 1.0 CA B:TRP210 4.9 31.9 1.0 CE3 B:TRP210 4.9 29.3 1.0

D.R.Adams, H.Yuan, T.Holyoak, K.H.Arajs, P.Hakimi, T.C.Markello, L.A.Wolfe, T.Vilboux, B.K.Burton, K.F.Fajardo, G.Grahame, C.Holloman, M.Sincan, A.C.Smith, G.A.Wells, Y.Huang, H.Vega, J.P.Snyder, G.A.Golas, C.J.Tifft, C.F.Boerkoel, R.W.Hanson, S.F.Traynelis, D.S.Kerr, W.A.Gahl. Three Rare Diseases in One Sib Pair: RAI1, PCK1, GRIN2B Mutations Associated with Smith-Magenis Syndrome, Cytosolic Pepck Deficiency and Nmda Receptor Glutamate Insensitivity. Mol.Genet.Metab. 2014.
ISSN: ESSN 1096-7206
PubMed: 24863970
DOI: 10.1016/J.YMGME.2014.04.001