Manganese in PDB 9ej6: Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (313K)

All present enzymatic activity of Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (313K):
4.1.1.32;

The structure of Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (313K), PDB code: 9ej6 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)	60.10 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.903, 120.204, 60.984, 90, 111.49, 90
R / Rfree (%)	19.9 / 22.5

The binding sites of Manganese atom in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (313K) (pdb code 9ej6). 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 (313K), PDB code: 9ej6:
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 (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 Gtp and Beta-Sulfopyruvate (313K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:29.4 occ:1.00 O1 A:SPV704 2.1 30.1 1.0 OD1 A:ASP311 2.1 32.8 1.0 NE2 A:HIS264 2.3 35.9 1.0 O1G A:GTP705 2.4 32.8 0.8 NZ A:LYS244 2.4 35.2 1.0 O2 A:SPV704 2.5 30.9 1.0 O2G A:GTP705 2.6 35.4 0.2 C1 A:SPV704 2.9 37.2 1.0 C2 A:SPV704 3.0 36.5 1.0 CG A:ASP311 3.1 31.4 1.0 CE1 A:HIS264 3.1 32.5 1.0 OD2 A:ASP311 3.3 31.9 1.0 CD2 A:HIS264 3.3 31.9 1.0 CE A:LYS244 3.4 33.5 1.0 PG A:GTP705 3.7 39.9 0.8 O2G A:GTP705 3.9 38.2 0.8 NZ A:LYS290 4.0 33.3 1.0 PG A:GTP705 4.1 40.9 0.2 O2' A:SPV704 4.1 41.6 1.0 O A:HOH812 4.2 36.7 1.0 ND1 A:HIS264 4.2 33.3 1.0 CE A:LYS290 4.3 32.1 1.0 CG A:HIS264 4.4 32.3 1.0 CB A:ASP311 4.4 31.1 1.0 O A:HOH867 4.5 29.2 1.0 O3G A:GTP705 4.5 41.7 0.8 O3G A:GTP705 4.5 38.2 0.2 C3 A:SPV704 4.5 34.0 1.0 O1G A:GTP705 4.6 41.7 0.2 O3B A:GTP705 4.8 43.6 0.8 CD A:LYS244 4.8 37.8 1.0 OG A:SER286 4.8 48.4 1.0

Manganese binding site 2 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (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 Gtp and Beta-Sulfopyruvate (313K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:32.7 occ:1.00 O1G A:GTP705 2.1 41.7 0.2 OG1 A:THR291 2.2 36.0 1.0 O A:HOH801 2.2 33.8 1.0 O A:HOH812 2.2 36.7 1.0 O3G A:GTP705 2.2 41.7 0.8 O2B A:GTP705 2.3 34.1 0.8 O2B A:GTP705 2.4 35.1 0.2 O A:HOH803 2.4 36.0 1.0 PG A:GTP705 3.4 40.9 0.2 PG A:GTP705 3.4 39.9 0.8 CB A:THR291 3.5 35.9 1.0 OD2 A:ASP310 3.5 30.9 1.0 O1G A:GTP705 3.6 32.8 0.8 PB A:GTP705 3.6 35.2 0.8 PB A:GTP705 3.7 36.2 0.2 O2A A:GTP705 3.7 41.8 0.8 O2G A:GTP705 3.7 35.4 0.2 O A:HOH867 3.9 29.2 1.0 O3B A:GTP705 4.0 43.6 0.8 O3B A:GTP705 4.0 42.5 0.2 N A:THR291 4.1 33.5 1.0 O A:ASP310 4.2 33.5 1.0 CA A:GLY334 4.3 32.6 1.0 CA A:THR291 4.3 34.4 1.0 CG A:ASP310 4.3 36.0 1.0 CG2 A:THR291 4.4 34.5 1.0 O3A A:GTP705 4.4 40.4 0.2 OD1 A:ASP311 4.5 32.8 1.0 O3A A:GTP705 4.5 41.4 0.8 NH1 A:ARG405 4.5 33.0 1.0 PA A:GTP705 4.5 35.2 0.8 O3G A:GTP705 4.5 38.2 0.2 O2G A:GTP705 4.6 38.2 0.8 O A:PHE333 4.7 35.3 1.0 O1B A:GTP705 4.7 40.4 0.8 O1A A:GTP705 4.7 32.3 0.8 O2A A:GTP705 4.7 39.6 0.2 O1B A:GTP705 4.8 39.1 0.2 O1A A:GTP705 4.9 40.0 0.2 O A:HOH859 4.9 37.7 1.0 CB A:LYS290 4.9 35.1 1.0 CB A:ASP310 4.9 31.1 1.0 PA A:GTP705 5.0 40.2 0.2 N A:VAL335 5.0 34.0 1.0

Manganese binding site 3 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (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 Gtp and Beta-Sulfopyruvate (313K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:49.8 occ:1.00 O A:HOH868 2.2 51.9 1.0 OE1 A:GLU63 2.3 60.7 1.0 OE2 A:GLU63 2.9 52.4 1.0 CD A:GLU63 2.9 52.0 1.0 CG A:GLU63 4.4 57.1 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