Manganese in PDB 4yw9: Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp

All present enzymatic activity of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp:
4.1.1.32;

The structure of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp, PDB code: 4yw9 was solved by M.D.Balan, T.A.Johnson, M.J.Mcleod, W.R.Lotosky, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.16 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.407, 118.742, 60.248, 90.00, 110.02, 90.00
R / Rfree (%)	16.8 / 19.7

The structure of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp (pdb code 4yw9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp, PDB code: 4yw9:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:10.5 occ:1.00 OD1 A:ASP311 2.0 9.4 1.0 O10 A:1WD706 2.1 11.8 1.0 O1G A:GTP701 2.1 10.7 1.0 N4 A:1WD706 2.3 12.4 1.0 NZ A:LYS244 2.3 9.8 1.0 NE2 A:HIS264 2.3 11.5 1.0 C8 A:1WD706 3.0 11.2 1.0 C3 A:1WD706 3.0 11.9 1.0 C5 A:1WD706 3.1 11.7 1.0 CE1 A:HIS264 3.2 10.0 1.0 CG A:ASP311 3.2 8.3 1.0 PG A:GTP701 3.3 11.4 1.0 CD2 A:HIS264 3.3 11.0 1.0 OD2 A:ASP311 3.4 9.6 1.0 CE A:LYS244 3.4 10.6 1.0 O3G A:GTP701 3.8 12.2 1.0 O2G A:GTP701 3.8 11.9 1.0 NZ A:LYS290 4.0 10.3 1.0 O A:HOH1044 4.1 11.5 1.0 CE A:LYS290 4.1 9.8 1.0 O9 A:1WD706 4.3 14.5 1.0 OG A:SER286 4.3 17.1 1.0 C2 A:1WD706 4.3 13.6 1.0 ND1 A:HIS264 4.3 9.7 1.0 C6 A:1WD706 4.4 13.1 1.0 CG A:HIS264 4.4 8.7 1.0 CB A:ASP311 4.6 9.7 1.0 O3B A:GTP701 4.7 11.3 1.0 CD A:LYS244 4.7 11.4 1.0 C1 A:1WD706 4.9 12.3 1.0 CB A:SER286 4.9 14.6 1.0 O A:ASP311 5.0 11.5 1.0

Manganese binding site 2 out of 3 in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:41.5 occ:0.50 OE2 A:GLU607 1.9 23.4 0.5 CD A:GLU607 2.5 20.0 0.5 NE2 A:HIS502 2.6 35.2 1.0 OE1 A:GLU607 2.6 23.3 0.5 O A:HOH980 2.7 20.8 1.0 OE2 A:GLU607 3.2 18.6 0.5 CE1 A:HIS502 3.4 36.0 1.0 CD2 A:HIS502 3.6 34.4 1.0 O A:HOH827 3.6 41.6 1.0 CG A:GLU607 3.8 15.6 0.5 CG A:GLU607 3.8 17.5 0.5 CD A:GLU607 3.9 16.3 0.5 O A:HOH1335 4.4 33.8 1.0 NE2 A:GLN451 4.5 18.7 1.0 ND1 A:HIS502 4.6 34.6 1.0 CG A:HIS502 4.7 32.8 1.0 O A:LEU498 4.8 14.5 1.0 CG A:GLN451 4.9 16.5 1.0 CB A:GLU607 5.0 15.3 0.5

Manganese binding site 3 out of 3 in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn705 b:11.2 occ:1.00 O3G A:GTP701 2.2 12.2 1.0 O1B A:GTP701 2.2 9.8 1.0 O A:HOH1044 2.2 11.5 1.0 O A:HOH890 2.3 11.9 1.0 O A:HOH859 2.3 11.2 1.0 OG1 A:THR291 2.3 10.4 1.0 PG A:GTP701 3.3 11.4 1.0 PB A:GTP701 3.3 11.7 1.0 CB A:THR291 3.4 11.9 1.0 O3B A:GTP701 3.5 11.3 1.0 OD2 A:ASP310 3.8 14.2 1.0 O1G A:GTP701 4.0 10.7 1.0 O1A A:GTP701 4.0 13.6 1.0 N A:THR291 4.1 11.8 1.0 NH1 A:ARG405 4.2 12.3 1.0 CA A:THR291 4.3 11.1 1.0 CG2 A:THR291 4.4 12.6 1.0 O2B A:GTP701 4.4 10.8 1.0 O3A A:GTP701 4.4 11.8 1.0 O A:ASP310 4.4 11.9 1.0 O A:PHE333 4.5 11.4 1.0 CA A:GLY334 4.5 12.6 1.0 O2G A:GTP701 4.5 11.9 1.0 CG A:ASP310 4.5 11.6 1.0 OD1 A:ASP311 4.6 9.4 1.0 O A:HOH1053 4.6 12.5 1.0 C5 A:1WD706 4.7 11.7 1.0 PA A:GTP701 4.8 13.0 1.0 N A:VAL335 4.8 12.2 1.0

M.D.Balan, M.J.Mcleod, W.R.Lotosky, M.Ghaly, T.Holyoak. Inhibition and Allosteric Regulation of Monomeric Phosphoenolpyruvate Carboxykinase By 3-Mercaptopicolinic Acid. Biochemistry V. 54 5878 2015.
ISSN: ISSN 0006-2960
PubMed: 26322521
DOI: 10.1021/ACS.BIOCHEM.5B00822