Manganese in PDB 4yw8: Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid

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

The structure of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid, PDB code: 4yw8 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)	29.18 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.540, 119.422, 60.488, 90.00, 110.24, 90.00
R / Rfree (%)	18 / 22.1

The structure of Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid 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 (pdb code 4yw8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid, PDB code: 4yw8:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of Rat Cytosolic Pepck in Complex with 3-Mercaptopicolinic Acid


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:14.3 occ:1.00 OD1 A:ASP311 2.0 11.7 1.0 O10 A:1WD704 2.0 12.5 1.0 N4 A:1WD704 2.2 20.6 1.0 O A:HOH1591 2.2 19.2 1.0 NE2 A:HIS264 2.3 16.6 1.0 NZ A:LYS244 2.4 16.1 1.0 C8 A:1WD704 2.8 19.3 1.0 C3 A:1WD704 2.9 21.2 1.0 CG A:ASP311 3.1 16.9 1.0 CE1 A:HIS264 3.2 13.7 1.0 C5 A:1WD704 3.2 24.5 1.0 CD2 A:HIS264 3.2 13.5 1.0 CE A:LYS244 3.3 15.5 1.0 OD2 A:ASP311 3.4 16.7 1.0 NZ A:LYS290 4.0 31.9 1.0 O9 A:1WD704 4.0 22.4 1.0 O A:HOH1655 4.2 22.5 1.0 O A:HOH1627 4.3 30.2 1.0 C2 A:1WD704 4.3 22.1 1.0 ND1 A:HIS264 4.3 13.1 1.0 CG A:HIS264 4.4 13.5 1.0 OG A:SER286 4.4 27.2 1.0 CE A:LYS290 4.4 27.6 1.0 C6 A:1WD704 4.5 24.5 1.0 CB A:ASP311 4.5 16.0 1.0 CD A:LYS244 4.7 14.7 1.0 CB A:SER286 4.9 27.8 1.0 CZ A:PHE485 4.9 12.8 1.0 CE2 A:PHE485 4.9 12.7 1.0 C1 A:1WD704 4.9 25.1 1.0 O A:ASP311 5.0 15.5 1.0 CA A:SER286 5.0 26.9 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:18.6 occ:0.80 O A:HOH1702 2.0 29.5 1.0 OE2 A:GLU607 2.1 18.3 1.0 O A:HOH1726 2.1 30.3 1.0 NE2 A:HIS502 2.1 18.4 1.0 O A:HOH1484 2.5 21.9 1.0 CD A:GLU607 3.1 19.8 1.0 CE1 A:HIS502 3.1 26.4 1.0 CD2 A:HIS502 3.1 24.5 1.0 OE1 A:GLU607 3.4 22.1 1.0 O A:HOH1641 3.9 38.4 1.0 O A:HOH1856 4.2 33.1 1.0 ND1 A:HIS502 4.2 25.5 1.0 CG A:HIS502 4.3 23.5 1.0 O A:HOH1956 4.4 27.4 1.0 CG A:GLU607 4.4 18.3 1.0 O A:HOH1893 4.5 31.6 1.0 NE2 A:GLN451 4.5 20.7 1.0 O A:LEU498 4.8 17.9 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