Manganese in PDB 9eiy: Rat Cytosolic Pepck in Complex with Gdp and Phosphoglycolic Acid (313K)

All present enzymatic activity of Rat Cytosolic Pepck in Complex with Gdp and Phosphoglycolic Acid (313K):
4.1.1.32;

The structure of Rat Cytosolic Pepck in Complex with Gdp and Phosphoglycolic Acid (313K), PDB code: 9eiy was solved by M.J.Mcleod, S.A.E.Barwell, T.Holyoak, R.E.Thorne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.08 / 2.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.892, 120.165, 61.407, 90, 110.19, 90
R / Rfree (%)	21.3 / 25.5

The binding sites of Manganese atom in the Rat Cytosolic Pepck in Complex with Gdp and Phosphoglycolic Acid (313K) (pdb code 9eiy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Rat Cytosolic Pepck in Complex with Gdp and Phosphoglycolic Acid (313K), PDB code: 9eiy:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Rat Cytosolic Pepck in Complex with Gdp and Phosphoglycolic Acid (313K)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Rat Cytosolic Pepck in Complex with Gdp and Phosphoglycolic Acid (313K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:46.0 occ:1.00 OD1 A:ASP311 2.0 40.1 1.0 O1P A:PGA704 2.1 47.8 0.4 O A:HOH803 2.3 47.4 0.3 NZ A:LYS244 2.3 43.0 1.0 O A:HOH801 2.4 48.0 0.3 NE2 A:HIS264 2.4 37.4 1.0 O4P A:PGA704 2.5 50.4 0.3 O3P A:PGA704 2.6 48.7 0.3 O A:HOH802 2.6 47.8 0.3 O4P A:PGA704 2.8 42.3 0.4 P A:PGA704 2.8 45.0 0.4 CG A:ASP311 3.0 38.5 1.0 O1 A:PGA704 3.0 48.7 0.4 P A:PGA704 3.1 52.2 0.3 O2P A:PGA704 3.1 51.9 0.3 O2P A:PGA704 3.2 49.0 0.4 OD2 A:ASP311 3.3 42.0 1.0 CE1 A:HIS264 3.3 34.0 1.0 C2 A:PGA704 3.3 51.6 0.4 CD2 A:HIS264 3.4 30.9 1.0 CE A:LYS244 3.4 44.6 1.0 C1 A:PGA704 3.6 53.4 0.4 O2P A:PGA704 4.0 51.2 0.3 H22 A:PGA704 4.0 61.9 0.4 H21 A:PGA704 4.0 61.9 0.4 O3P A:PGA704 4.1 51.5 0.3 OG A:SER286 4.1 52.0 1.0 O A:HOH816 4.1 40.0 1.0 P A:PGA704 4.2 54.7 0.3 O3P A:PGA704 4.2 47.6 0.4 NZ A:LYS290 4.3 35.8 1.0 CB A:ASP311 4.3 35.4 1.0 ND1 A:HIS264 4.4 27.4 1.0 O1P A:PGA704 4.4 53.1 0.3 CE A:LYS290 4.4 33.6 1.0 CG A:HIS264 4.4 30.7 1.0 CD A:LYS244 4.7 44.9 1.0 O4P A:PGA704 4.8 55.6 0.3 O2 A:PGA704 4.8 55.7 0.4 H21 A:PGA704 4.9 61.7 0.3 CA A:ASP311 4.9 29.4 1.0

Manganese binding site 2 out of 3 in the Rat Cytosolic Pepck in Complex with Gdp and Phosphoglycolic Acid (313K)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Rat Cytosolic Pepck in Complex with Gdp and Phosphoglycolic Acid (313K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:53.4 occ:1.00 O A:HOH806 2.1 41.8 1.0 O3B A:GDP705 2.2 45.5 1.0 O A:HOH808 2.3 41.2 1.0 OG1 A:THR291 2.3 40.9 1.0 O4P A:PGA704 2.5 42.3 0.4 O3P A:PGA704 2.8 47.6 0.4 P A:PGA704 3.1 45.0 0.4 PB A:GDP705 3.4 46.4 1.0 OD2 A:ASP310 3.5 34.8 1.0 CB A:THR291 3.6 50.0 1.0 O A:ASP310 3.7 36.2 1.0 O2B A:GDP705 3.7 46.4 1.0 O A:HOH801 3.9 48.0 0.3 O2P A:PGA704 3.9 49.0 0.4 O A:HOH816 3.9 40.0 1.0 O1B A:GDP705 4.0 39.7 1.0 N A:THR291 4.1 49.4 1.0 O A:HOH802 4.2 47.8 0.3 CG A:ASP310 4.3 37.6 1.0 CA A:THR291 4.4 45.0 1.0 CA A:GLY334 4.5 42.7 1.0 O1P A:PGA704 4.5 47.8 0.4 O2A A:GDP705 4.6 53.6 1.0 CB A:LYS290 4.7 35.7 1.0 CG2 A:THR291 4.7 42.7 1.0 OD1 A:ASP311 4.7 40.1 1.0 O3A A:GDP705 4.7 49.4 1.0 O A:PHE333 4.8 36.1 1.0 C A:ASP310 4.8 39.2 1.0 CB A:ASP310 4.8 34.2 1.0 O3P A:PGA704 4.9 48.7 0.3 NH1 A:ARG405 4.9 45.3 1.0 CE A:LYS290 4.9 33.6 1.0 OD1 A:ASP310 5.0 39.7 1.0

Manganese binding site 3 out of 3 in the Rat Cytosolic Pepck in Complex with Gdp and Phosphoglycolic Acid (313K)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Rat Cytosolic Pepck in Complex with Gdp and Phosphoglycolic Acid (313K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:104.8 occ:1.00 OE2 A:GLU607 2.1 76.7 1.0 NE2 A:HIS502 2.6 66.9 1.0 CD A:GLU607 3.0 62.5 1.0 OE1 A:GLU607 3.2 64.9 1.0 CE1 A:HIS502 3.3 68.1 1.0 CD2 A:HIS502 3.8 63.5 1.0 CG A:GLU607 4.4 53.3 1.0 ND1 A:HIS502 4.6 68.3 1.0 NE2 A:GLN451 4.7 53.1 1.0 O A:LEU498 4.7 54.9 1.0 CG A:HIS502 4.8 68.5 1.0

M.J.Mcleod, S.A.E.Barwell, T.Holyoak, R.E.Thorne. A Structural Perspective on the Temperature Dependent Activity of Enzymes. Structure 2025.
ISSN: ISSN 0969-2126
PubMed: 40120576
DOI: 10.1016/J.STR.2025.02.013