Manganese in PDB 5fh5: The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp

All present enzymatic activity of The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp:
4.1.1.32;

The structure of The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp, PDB code: 5fh5 was solved by T.A.Johnson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.50 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.176, 119.717, 60.897, 90.00, 107.29, 90.00
R / Rfree (%)	20.8 / 23.7

The structure of The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp (pdb code 5fh5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp, PDB code: 5fh5:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:28.4 occ:1.00 O2B A:GDP703 2.0 15.1 0.3 O A:HOH807 2.1 32.8 1.0 O A:HOH886 2.1 23.4 1.0 O A:HOH815 2.2 28.5 1.0 O A:HOH994 2.2 27.4 1.0 O2B A:GDP703 2.3 23.0 0.7 OG1 A:THR291 2.3 41.2 1.0 PB A:GDP703 2.9 16.4 0.3 O3B A:GDP703 3.1 15.2 0.3 CB A:THR291 3.5 42.0 1.0 PB A:GDP703 3.6 23.5 0.7 O3B A:GDP703 3.7 25.8 0.7 O2A A:GDP703 3.7 15.6 0.3 OD2 A:ASP310 3.8 36.1 1.0 O3A A:GDP703 4.0 15.5 0.3 O A:HOH973 4.1 27.2 1.0 N A:THR291 4.1 39.4 1.0 O1B A:GDP703 4.1 15.2 0.3 PA A:GDP703 4.2 16.6 0.3 O A:HOH920 4.2 21.0 1.0 CA A:THR291 4.3 41.5 1.0 O A:ASP310 4.4 33.4 1.0 CA A:GLY334 4.5 38.0 1.0 CG2 A:THR291 4.6 43.6 1.0 O2A A:GDP703 4.6 25.5 0.7 O1B A:GDP703 4.6 23.1 0.7 CG A:ASP310 4.6 35.0 1.0 O2P A:PGA704 4.6 27.3 1.0 O3A A:GDP703 4.6 25.3 0.7 O1A A:GDP703 4.7 16.0 0.3 O A:HOH864 4.7 34.6 1.0 O1A A:GDP703 4.8 27.5 0.7 N A:VAL335 4.8 39.7 1.0 PA A:GDP703 4.9 27.4 0.7 O A:PHE333 4.9 34.8 1.0 OD1 A:ASP311 5.0 29.1 1.0 NZ A:LYS290 5.0 34.4 1.0

Manganese binding site 2 out of 2 in the The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of Rat Cytosolic Pepck Variant E89Q in Complex with Phosphoglycolate and Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:22.8 occ:1.00 O3P A:PGA704 2.1 24.4 1.0 O A:HOH819 2.2 24.4 1.0 OD1 A:ASP311 2.2 29.1 1.0 O A:HOH920 2.2 21.0 1.0 NE2 A:HIS264 2.3 18.5 1.0 NZ A:LYS244 2.3 18.9 1.0 CG A:ASP311 3.1 28.7 1.0 P A:PGA704 3.2 26.1 1.0 CD2 A:HIS264 3.2 18.2 1.0 CE1 A:HIS264 3.2 18.3 1.0 OD2 A:ASP311 3.3 28.3 1.0 CE A:LYS244 3.4 18.5 1.0 O4P A:PGA704 3.5 23.3 1.0 O A:HOH973 4.2 27.2 1.0 O2P A:PGA704 4.2 27.3 1.0 CE A:LYS290 4.3 34.7 1.0 NZ A:LYS290 4.3 34.4 1.0 O A:HOH994 4.3 27.4 1.0 O1P A:PGA704 4.3 26.1 1.0 ND1 A:HIS264 4.3 18.0 1.0 O A:HOH815 4.3 28.5 1.0 CG A:HIS264 4.4 17.9 1.0 CB A:ASP311 4.5 29.5 1.0 CD A:LYS244 4.7 18.3 1.0 CZ A:PHE485 4.8 20.8 1.0 O A:HOH1126 4.9 23.2 1.0 CE2 A:PHE485 4.9 19.7 1.0 O A:ASP311 5.0 27.9 1.0

T.A.Johnson, M.J.Mcleod, T.Holyoak. Utilization of Substrate Intrinsic Binding Energy For Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase. Biochemistry V. 55 575 2016.
ISSN: ISSN 0006-2960
PubMed: 26709450
DOI: 10.1021/ACS.BIOCHEM.5B01215