Manganese in PDB 4gnp: Structure of Rat Cytosolic Pepck LD_3G in Complex with Pep and Gdp

All present enzymatic activity of Structure of Rat Cytosolic Pepck LD_3G in Complex with Pep and Gdp:
4.1.1.32;

The structure of Structure of Rat Cytosolic Pepck LD_3G in Complex with Pep and Gdp, PDB code: 4gnp 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)	34.74 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.875, 84.612, 118.842, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 24

The structure of Structure of Rat Cytosolic Pepck LD_3G in Complex with Pep and Gdp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Structure of Rat Cytosolic Pepck LD_3G in Complex with Pep and Gdp (pdb code 4gnp). 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 LD_3G in Complex with Pep and Gdp, PDB code: 4gnp:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of Rat Cytosolic Pepck LD_3G in Complex with Pep and Gdp


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 LD_3G in Complex with Pep and Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:14.8 occ:1.00 O A:HOH844 2.1 14.3 1.0 OD1 A:ASP311 2.2 13.1 1.0 NZ A:LYS244 2.3 14.8 1.0 NE2 A:HIS264 2.3 15.6 1.0 O A:HOH838 2.3 17.6 1.0 O A:HOH865 2.4 19.5 1.0 CG A:ASP311 3.1 13.4 1.0 CD2 A:HIS264 3.2 13.7 1.0 CE A:LYS244 3.2 14.8 1.0 CE1 A:HIS264 3.2 13.0 1.0 OD2 A:ASP311 3.3 13.8 1.0 NZ A:LYS290 4.0 22.1 1.0 O A:HOH930 4.1 25.6 1.0 O1P A:PEP703 4.1 18.1 1.0 O A:HOH869 4.1 24.2 1.0 O3P A:PEP703 4.2 17.9 1.0 ND1 A:HIS264 4.3 14.0 1.0 CG A:HIS264 4.3 13.7 1.0 O A:HOH877 4.4 21.3 1.0 CB A:ASP311 4.5 13.9 1.0 O A:HOH1359 4.5 24.9 1.0 CD A:LYS244 4.6 13.8 1.0 P A:PEP703 4.8 18.8 1.0 CE A:LYS290 4.8 20.2 1.0 O A:HOH912 4.8 19.2 1.0 CZ A:PHE485 4.9 14.6 1.0 CE2 A:PHE485 4.9 14.3 1.0

Manganese binding site 2 out of 2 in the Structure of Rat Cytosolic Pepck LD_3G in Complex with Pep and Gdp


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 LD_3G in Complex with Pep and Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn705 b:32.7 occ:0.25 O A:HOH1360 1.9 18.7 1.0 O A:HOH1357 1.9 24.8 1.0 O A:HOH1358 2.3 31.2 1.0 O A:HOH1359 2.3 24.9 1.0 OG1 A:THR291 2.4 22.3 1.0 O2B A:GDP701 2.6 26.1 1.0 O A:HOH1380 3.5 28.4 1.0 OD2 A:ASP310 3.7 24.4 1.0 CB A:THR291 3.7 21.9 1.0 PB A:GDP701 3.8 25.7 1.0 O1B A:GDP701 3.9 26.6 1.0 CA A:GLY334 4.1 20.3 1.0 O A:HOH869 4.2 24.2 1.0 N A:THR291 4.3 19.4 1.0 CG A:ASP310 4.4 20.0 1.0 O1A A:GDP701 4.4 30.4 1.0 N A:VAL335 4.5 20.3 1.0 O A:HOH930 4.5 25.6 1.0 CA A:THR291 4.5 20.7 1.0 O A:HOH865 4.6 19.5 1.0 CG2 A:THR291 4.7 21.6 1.0 O A:ASP310 4.8 15.5 1.0 O3B A:GDP701 4.8 24.7 1.0 O3A A:GDP701 4.8 26.5 1.0 C A:GLY334 4.9 19.9 1.0 O A:PHE333 4.9 17.2 1.0 OD1 A:ASP310 4.9 20.2 1.0

T.A.Johnson, T.Holyoak. The {Omega}-Loop Lid Domain of Phosphoenolpyruvate Carboxykinase Is Essential For Catalytic Function. Biochemistry V. 51 9547 2012.
ISSN: ISSN 0006-2960
PubMed: 23127136
DOI: 10.1021/BI301278T