Sodium in PDB 5v9h: Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp.

All present enzymatic activity of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp.:
4.1.1.32;

The structure of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp., PDB code: 5v9h was solved by T.Holyoak, D.S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.04 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.480, 119.433, 88.166, 90.00, 105.30, 90.00
R / Rfree (%)	24.1 / 28.5

The structure of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Sodium atom in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. (pdb code 5v9h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp., PDB code: 5v9h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:58.9 occ:1.00 O A:HOH847 2.2 40.4 1.0 O A:HOH860 2.2 44.3 1.0 O A:ASN208 2.4 48.0 1.0 O A:LEU79 2.8 46.1 1.0 O A:VAL65 3.1 60.1 1.0 C A:ASN208 3.6 50.0 1.0 O A:GLY64 3.9 63.9 1.0 CB A:ASN209 3.9 49.1 1.0 C A:LEU79 4.0 44.5 1.0 C A:VAL65 4.0 60.6 1.0 C A:ASN209 4.0 42.4 1.0 O A:ASN209 4.0 40.0 1.0 N A:LEU79 4.1 42.5 1.0 CA A:VAL65 4.3 61.5 1.0 CA A:ASN209 4.3 46.7 1.0 N A:ASN209 4.4 47.7 1.0 N A:TRP210 4.5 38.6 1.0 CA A:LEU79 4.5 43.9 1.0 CB A:LEU79 4.6 44.5 1.0 CB A:ASN208 4.6 54.9 1.0 CA A:ASN208 4.7 52.8 1.0 CB A:TRP210 4.7 36.0 1.0 CA A:TRP210 4.9 37.2 1.0 C A:GLY64 4.9 62.9 1.0 CE3 A:TRP210 4.9 33.6 1.0

Sodium binding site 2 out of 2 in the Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Phosphoglycolate and Gdp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na704 b:67.6 occ:1.00 O B:HOH827 2.3 56.5 1.0 O B:HOH884 2.3 42.5 1.0 O B:ASN208 2.4 51.5 1.0 O B:LEU79 2.7 49.0 1.0 O B:VAL65 3.6 57.8 1.0 C B:ASN208 3.6 53.2 1.0 OD1 B:ASN208 3.6 61.8 1.0 C B:LEU79 3.8 47.2 1.0 CB B:ASN209 4.0 52.9 1.0 N B:LEU79 4.0 44.6 1.0 O B:GLY64 4.1 56.8 1.0 C B:ASN209 4.1 47.9 1.0 CA B:LEU79 4.3 46.5 1.0 CB B:LEU79 4.3 46.8 1.0 CA B:ASN209 4.3 51.7 1.0 O B:ASN209 4.3 46.0 1.0 C B:VAL65 4.4 56.1 1.0 N B:ASN209 4.4 52.2 1.0 N B:TRP210 4.5 43.8 1.0 CG B:ASN208 4.5 60.6 1.0 CB B:ASN208 4.6 58.0 1.0 CA B:VAL65 4.6 55.5 1.0 CA B:ASN208 4.6 56.1 1.0 CB B:TRP210 4.8 41.7 1.0 N B:THR80 5.0 46.3 1.0 CA B:TRP210 5.0 42.1 1.0

D.S.Cui, A.Broom, M.J.Mcleod, E.M.Meiering, T.Holyoak. Asymmetric Anchoring Is Required For Efficient Omega-Loop Opening and Closing in Cytosolic Phosphoenolpyruvate Carboxykinase. Biochemistry V. 56 2106 2017.
ISSN: ISSN 1520-4995
PubMed: 28345895
DOI: 10.1021/ACS.BIOCHEM.7B00178