Manganese in PDB 9ej4: Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (273K)

All present enzymatic activity of Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (273K):
4.1.1.32;

The structure of Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (273K), PDB code: 9ej4 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)	51.08 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.855, 119.835, 60.569, 90, 111.21, 90
R / Rfree (%)	16.5 / 19.3

The binding sites of Manganese atom in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (273K) (pdb code 9ej4). 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 (273K), PDB code: 9ej4:
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 (273K)


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 (273K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:19.6 occ:1.00 O1G A:GTP705 2.1 21.6 0.5 OD1 A:ASP311 2.1 18.5 1.0 O1 A:SPV704 2.1 20.7 1.0 NE2 A:HIS264 2.3 16.1 1.0 NZ A:LYS244 2.3 17.8 1.0 O1G A:GTP705 2.3 22.6 0.5 O2 A:SPV704 2.4 20.9 1.0 C1 A:SPV704 3.0 21.6 1.0 C2 A:SPV704 3.0 19.2 1.0 CG A:ASP311 3.1 19.4 1.0 CD2 A:HIS264 3.2 15.6 1.0 PG A:GTP705 3.2 20.4 0.5 CE1 A:HIS264 3.3 17.8 1.0 OD2 A:ASP311 3.3 18.5 1.0 CE A:LYS244 3.3 19.6 1.0 PG A:GTP705 3.6 20.1 0.5 O2G A:GTP705 3.6 20.1 0.5 O3G A:GTP705 3.8 24.1 0.5 O3G A:GTP705 3.9 24.3 0.5 NZ A:LYS290 4.0 15.2 1.0 O2G A:GTP705 4.0 21.9 0.5 CE A:LYS290 4.2 14.8 1.0 O2' A:SPV704 4.2 25.6 1.0 O A:HOH837 4.2 25.1 1.0 ND1 A:HIS264 4.3 16.4 1.0 CG A:HIS264 4.4 16.8 1.0 O A:HOH925 4.4 23.8 1.0 CB A:ASP311 4.5 17.2 1.0 OG A:SER286 4.5 28.4 0.7 C3 A:SPV704 4.5 20.1 1.0 O3B A:GTP705 4.5 19.0 0.5 CD A:LYS244 4.7 16.3 1.0 O A:ASP311 4.9 20.5 1.0 O3B A:GTP705 4.9 23.2 0.5 OG A:SER286 4.9 24.8 0.3 CB A:SER286 4.9 25.8 0.3

Manganese binding site 2 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (273K)


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 (273K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:25.7 occ:1.00 O2B A:GTP705 2.1 20.5 0.5 O3G A:GTP705 2.1 24.1 0.5 O A:HOH837 2.1 25.1 1.0 OG1 A:THR291 2.2 24.5 1.0 O A:HOH887 2.3 23.8 1.0 O2B A:GTP705 2.3 18.6 0.5 O A:HOH809 2.4 24.6 1.0 O3G A:GTP705 2.4 24.3 0.5 PB A:GTP705 3.1 22.7 0.5 PG A:GTP705 3.1 20.4 0.5 O3B A:GTP705 3.3 19.0 0.5 CB A:THR291 3.3 21.7 1.0 PB A:GTP705 3.4 21.9 0.5 PG A:GTP705 3.5 20.1 0.5 O3B A:GTP705 3.7 23.2 0.5 OD2 A:ASP310 3.7 23.8 1.0 O1G A:GTP705 3.8 21.6 0.5 O2A A:GTP705 3.9 27.4 0.5 O3A A:GTP705 4.0 22.8 0.5 O1G A:GTP705 4.0 22.6 0.5 N A:THR291 4.0 20.5 1.0 O A:HOH925 4.1 23.8 1.0 O A:ASP310 4.3 21.2 1.0 CA A:THR291 4.3 20.0 1.0 PA A:GTP705 4.3 25.8 0.5 O2G A:GTP705 4.3 20.1 0.5 O1B A:GTP705 4.3 20.5 0.5 O1A A:GTP705 4.4 24.4 0.5 CG2 A:THR291 4.4 23.8 1.0 O1B A:GTP705 4.4 21.5 0.5 CG A:ASP310 4.4 19.8 1.0 O1A A:GTP705 4.4 21.4 0.5 NH1 A:ARG405 4.5 18.2 1.0 CA A:GLY334 4.5 16.2 1.0 O A:PHE333 4.5 20.4 1.0 O3A A:GTP705 4.6 23.1 0.5 OD1 A:ASP311 4.7 18.5 1.0 O2G A:GTP705 4.8 21.9 0.5 O A:HOH992 4.8 28.5 1.0 N A:VAL335 4.9 19.0 1.0 CB A:LYS290 4.9 18.1 1.0 OD1 A:ASP310 5.0 21.0 1.0

Manganese binding site 3 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (273K)


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 (273K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:44.5 occ:1.00 OE1 A:GLU63 2.3 38.2 1.0 O A:HOH913 2.7 43.4 1.0 OE2 A:GLU63 2.8 47.5 1.0 CD A:GLU63 2.9 38.9 1.0 CG A:GLU63 4.4 42.5 1.0 O A:HOH814 4.5 43.3 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