Manganese in PDB 9ej3: Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (253K)

All present enzymatic activity of Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (253K):
4.1.1.32;

The structure of Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (253K), PDB code: 9ej3 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)	59.88 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.851, 119.77, 60.546, 90, 111.12, 90
R / Rfree (%)	17 / 21

The binding sites of Manganese atom in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (253K) (pdb code 9ej3). 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 (253K), PDB code: 9ej3:
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 (253K)


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 (253K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:19.2 occ:1.00 O1 A:SPV704 2.1 22.5 1.0 OD1 A:ASP311 2.1 20.4 1.0 O1G A:GTP705 2.1 24.1 0.7 NE2 A:HIS264 2.3 16.7 1.0 O1G A:GTP705 2.3 22.6 0.3 O2 A:SPV704 2.4 19.9 1.0 NZ A:LYS244 2.4 17.6 1.0 C1 A:SPV704 3.0 23.3 1.0 C2 A:SPV704 3.0 23.8 1.0 CG A:ASP311 3.0 16.8 1.0 OD2 A:ASP311 3.2 19.8 1.0 CD2 A:HIS264 3.2 15.0 1.0 CE1 A:HIS264 3.3 14.6 1.0 CE A:LYS244 3.3 20.5 1.0 PG A:GTP705 3.3 20.3 0.7 PG A:GTP705 3.6 21.0 0.3 O3G A:GTP705 3.8 21.5 0.7 O2G A:GTP705 3.8 21.3 0.7 O2G A:GTP705 3.9 21.4 0.3 NZ A:LYS290 3.9 17.7 1.0 O2' A:SPV704 4.2 25.9 1.0 O A:HOH921 4.2 22.1 1.0 CE A:LYS290 4.2 14.8 1.0 O3G A:GTP705 4.3 22.4 0.3 ND1 A:HIS264 4.4 14.4 1.0 OG A:SER286 4.4 36.9 1.0 CG A:HIS264 4.4 14.9 1.0 O A:HOH893 4.4 24.9 1.0 CB A:ASP311 4.5 17.4 1.0 C3 A:SPV704 4.5 18.8 1.0 O3B A:GTP705 4.7 21.9 0.7 CD A:LYS244 4.7 17.2 1.0 O3B A:GTP705 4.8 22.2 0.3 O A:ASP311 4.9 16.8 1.0 CB A:SER286 4.9 29.4 1.0

Manganese binding site 2 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (253K)


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 (253K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:24.4 occ:1.00 O3G A:GTP705 2.1 22.4 0.3 O A:HOH921 2.1 22.1 1.0 O2B A:GTP705 2.2 22.1 0.7 O2B A:GTP705 2.2 21.0 0.3 O3G A:GTP705 2.3 21.5 0.7 OG1 A:THR291 2.3 19.6 1.0 O A:HOH888 2.3 20.1 1.0 O A:HOH910 2.4 25.4 1.0 PG A:GTP705 3.2 21.0 0.3 PG A:GTP705 3.3 20.3 0.7 PB A:GTP705 3.3 23.6 0.7 CB A:THR291 3.4 17.0 1.0 PB A:GTP705 3.4 23.1 0.3 O3B A:GTP705 3.5 21.9 0.7 O1G A:GTP705 3.7 22.6 0.3 O3B A:GTP705 3.7 22.2 0.3 OD2 A:ASP310 3.7 21.9 1.0 O1G A:GTP705 4.0 24.1 0.7 O1A A:GTP705 4.0 22.8 0.7 O A:HOH893 4.1 24.9 1.0 N A:THR291 4.1 18.4 1.0 O2A A:GTP705 4.2 22.6 0.3 CA A:THR291 4.3 18.7 1.0 O1A A:GTP705 4.3 22.2 0.3 O1B A:GTP705 4.3 20.8 0.7 CA A:GLY334 4.3 16.8 1.0 O3A A:GTP705 4.4 21.4 0.3 O A:ASP310 4.4 19.3 1.0 CG2 A:THR291 4.4 19.2 1.0 O3A A:GTP705 4.4 21.8 0.7 O2G A:GTP705 4.5 21.3 0.7 NH1 A:ARG405 4.5 16.3 1.0 O2G A:GTP705 4.5 21.4 0.3 CG A:ASP310 4.5 21.6 1.0 PA A:GTP705 4.5 22.4 0.3 O A:PHE333 4.6 15.8 1.0 O1B A:GTP705 4.6 20.5 0.3 O A:HOH987 4.6 23.4 1.0 N A:VAL335 4.7 18.1 1.0 OD1 A:ASP311 4.8 20.4 1.0 PA A:GTP705 4.9 24.7 0.7 CB A:LYS290 5.0 18.2 1.0

Manganese binding site 3 out of 3 in the Rat Cytosolic Pepck in Complex with Gtp and Beta-Sulfopyruvate (253K)


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 (253K) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:90.4 occ:1.00 O A:HOH1061 2.7 48.3 1.0 OE2 A:GLU607 2.7 46.0 1.0 NE2 A:HIS502 3.3 48.7 1.0 O A:HOH961 3.4 34.7 1.0 CD A:GLU607 3.7 40.1 1.0 CD2 A:HIS502 3.9 43.9 1.0 NE2 A:GLN451 4.0 30.5 1.0 OE1 A:GLU607 4.0 41.0 1.0 CE1 A:HIS502 4.5 46.8 1.0 CD A:GLN451 4.7 33.2 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