Manganese in PDB 4ywd: Structure of Rat Cytosolic Pepck in Complex with 2,3-Pyridine Dicarboxylic Acid

All present enzymatic activity of Structure of Rat Cytosolic Pepck in Complex with 2,3-Pyridine Dicarboxylic Acid:
4.1.1.32;

The structure of Structure of Rat Cytosolic Pepck in Complex with 2,3-Pyridine Dicarboxylic Acid, PDB code: 4ywd 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)	57.63 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.340, 119.405, 61.015, 90.00, 109.16, 90.00
R / Rfree (%)	19.5 / 23.7

The structure of Structure of Rat Cytosolic Pepck in Complex with 2,3-Pyridine Dicarboxylic 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 2,3-Pyridine Dicarboxylic Acid (pdb code 4ywd). 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 2,3-Pyridine Dicarboxylic Acid, PDB code: 4ywd:
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 2,3-Pyridine Dicarboxylic 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 2,3-Pyridine Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:38.3 occ:1.00 OD1 A:ASP311 2.1 38.9 1.0 O1 A:NTM704 2.1 40.7 1.0 N1 A:NTM704 2.1 52.2 1.0 NE2 A:HIS264 2.3 37.6 1.0 O A:HOH979 2.4 40.6 1.0 NZ A:LYS244 2.4 37.1 1.0 C7 A:NTM704 2.9 49.8 1.0 C2 A:NTM704 2.9 52.9 1.0 CG A:ASP311 3.0 40.3 1.0 C6 A:NTM704 3.1 54.0 1.0 CD2 A:HIS264 3.2 37.0 1.0 OD2 A:ASP311 3.2 39.2 1.0 CE1 A:HIS264 3.3 37.2 1.0 CE A:LYS244 3.5 37.3 1.0 O2 A:NTM704 4.1 51.4 1.0 C3 A:NTM704 4.2 56.8 1.0 NZ A:LYS290 4.2 61.5 1.0 C5 A:NTM704 4.3 56.1 1.0 CG A:HIS264 4.4 36.8 1.0 CB A:ASP311 4.4 40.6 1.0 ND1 A:HIS264 4.4 37.2 1.0 OG A:SER286 4.7 72.1 1.0 C4 A:NTM704 4.7 57.1 1.0 CD A:LYS244 4.8 36.4 1.0 CE2 A:PHE485 4.9 36.4 1.0 CA A:ASP311 4.9 41.2 1.0 O A:ASP311 4.9 40.9 1.0 CZ A:PHE485 4.9 37.1 1.0

Manganese binding site 2 out of 2 in the Structure of Rat Cytosolic Pepck in Complex with 2,3-Pyridine Dicarboxylic 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 2,3-Pyridine Dicarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:46.8 occ:0.80 O A:HOH862 2.1 51.6 1.0 O A:HOH924 2.1 46.1 1.0 OE2 A:GLU607 2.2 47.9 1.0 NE2 A:HIS502 2.4 55.4 1.0 O A:HOH938 2.6 47.0 1.0 CD A:GLU607 2.9 45.0 1.0 CE1 A:HIS502 3.0 57.6 1.0 OE1 A:GLU607 3.1 44.1 1.0 CD2 A:HIS502 3.6 55.7 1.0 O A:HOH1008 4.2 52.3 1.0 ND1 A:HIS502 4.3 58.6 1.0 CG A:GLU607 4.3 44.1 1.0 O A:HOH995 4.4 52.0 1.0 NE2 A:GLN451 4.5 44.1 1.0 CG A:HIS502 4.6 57.5 1.0 O A:LEU498 4.9 39.8 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