Manganese in PDB 9ej5: Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (293K)

All present enzymatic activity of Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (293K):
4.1.1.32;

The structure of Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (293K), PDB code: 9ej5 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)	51.01 / 1.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.818, 119.735, 60.552, 90, 111.39, 90
R / Rfree (%)	16.9 / 20.3

The binding sites of Manganese atom in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (293K) (pdb code 9ej5). 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 Gtp and Beta-Sulfopyruvate (293K), PDB code: 9ej5:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (293K)


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 Gtp and Beta-Sulfopyruvate (293K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:18.6 occ:1.00 O1G A:GTP705 2.1 21.1 0.6 O1 A:SPV704 2.1 21.4 1.0 OD1 A:ASP311 2.2 16.6 1.0 NE2 A:HIS264 2.3 12.1 1.0 NZ A:LYS244 2.4 20.1 1.0 O2G A:GTP705 2.4 20.8 0.4 O2 A:SPV704 2.4 17.3 1.0 C1 A:SPV704 3.0 23.3 1.0 C2 A:SPV704 3.1 22.8 1.0 CG A:ASP311 3.1 17.3 1.0 CD2 A:HIS264 3.2 13.7 1.0 CE1 A:HIS264 3.2 20.2 1.0 OD2 A:ASP311 3.3 19.8 1.0 PG A:GTP705 3.3 20.0 0.6 CE A:LYS244 3.3 17.9 1.0 PG A:GTP705 3.7 20.4 0.4 O2G A:GTP705 3.7 18.8 0.6 O3G A:GTP705 3.7 22.2 0.6 NZ A:LYS290 3.9 17.6 1.0 O3G A:GTP705 4.0 18.0 0.4 CE A:LYS290 4.2 16.3 1.0 O2' A:SPV704 4.2 25.6 1.0 O A:HOH816 4.2 23.3 1.0 ND1 A:HIS264 4.3 15.6 1.0 CG A:HIS264 4.4 14.7 1.0 O A:HOH940 4.5 20.1 1.0 CB A:ASP311 4.5 15.2 1.0 O1G A:GTP705 4.5 23.1 0.4 OG A:SER286 4.5 22.4 0.6 C3 A:SPV704 4.6 18.7 1.0 O3B A:GTP705 4.6 20.3 0.6 CD A:LYS244 4.7 19.7 1.0 OG A:SER286 4.8 23.8 0.4 O3B A:GTP705 4.8 20.4 0.4 CB A:SER286 4.9 23.5 0.4 O A:ASP311 4.9 15.8 1.0 CB A:SER286 4.9 23.5 0.6 CZ A:PHE485 5.0 20.8 1.0

Manganese binding site 2 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (293K)


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 Gtp and Beta-Sulfopyruvate (293K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:20.5 occ:1.00 O A:HOH816 2.0 23.3 1.0 O A:HOH827 2.0 21.1 1.0 O2B A:GTP705 2.0 21.6 0.6 O3G A:GTP705 2.1 22.2 0.6 O1G A:GTP705 2.2 23.1 0.4 O2B A:GTP705 2.2 21.3 0.4 OG1 A:THR291 2.3 17.9 1.0 O A:HOH833 2.4 24.3 1.0 PB A:GTP705 3.1 20.5 0.6 PG A:GTP705 3.2 20.0 0.6 PG A:GTP705 3.3 20.4 0.4 O3B A:GTP705 3.4 20.3 0.6 CB A:THR291 3.5 18.9 1.0 PB A:GTP705 3.5 19.6 0.4 O2G A:GTP705 3.5 20.8 0.4 OD2 A:ASP310 3.7 19.2 1.0 O3B A:GTP705 3.8 20.4 0.4 O2A A:GTP705 4.0 24.6 0.6 O1G A:GTP705 4.0 21.1 0.6 O3A A:GTP705 4.0 21.3 0.6 N A:THR291 4.1 20.7 1.0 O A:HOH940 4.1 20.1 1.0 O A:ASP310 4.3 20.2 1.0 CA A:THR291 4.3 18.9 1.0 PA A:GTP705 4.3 19.1 0.6 O1A A:GTP705 4.3 22.8 0.4 O1B A:GTP705 4.3 21.4 0.4 O1B A:GTP705 4.4 21.6 0.6 O2G A:GTP705 4.4 18.8 0.6 CG A:ASP310 4.4 19.4 1.0 O1A A:GTP705 4.4 20.9 0.6 NH1 A:ARG405 4.4 18.6 1.0 CA A:GLY334 4.5 15.6 1.0 OD1 A:ASP311 4.5 16.6 1.0 CG2 A:THR291 4.6 18.2 1.0 O A:PHE333 4.6 18.3 1.0 O3G A:GTP705 4.6 18.0 0.4 O3A A:GTP705 4.6 22.0 0.4 N A:VAL335 4.9 19.1 1.0 O A:HOH900 5.0 24.9 1.0 CB A:LYS290 5.0 20.5 1.0

Manganese binding site 3 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (293K)


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 Gtp and Beta-Sulfopyruvate (293K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:49.1 occ:1.00 O A:HOH881 2.3 44.5 1.0 OE1 A:GLU63 2.3 39.6 1.0 O A:HOH832 2.8 46.8 1.0 CD A:GLU63 3.0 43.4 1.0 OE2 A:GLU63 3.0 47.0 1.0 CG A:GLU63 4.4 39.9 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