Manganese in PDB 4gnm: Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp

All present enzymatic activity of Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp:
4.1.1.32;

The structure of Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp, PDB code: 4gnm 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)	26.66 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.491, 84.706, 118.775, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.2

The structure of Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Manganese atom in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate and Gtp (pdb code 4gnm). 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_2G in Complex with Oxalate and Gtp, PDB code: 4gnm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate 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 LD_2G in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:16.7 occ:1.00 O4 A:OXL706 2.0 17.7 1.0 OD1 A:ASP311 2.1 15.7 1.0 O3 A:OXL706 2.2 20.1 1.0 NE2 A:HIS264 2.2 15.8 1.0 O2G A:GTP701 2.3 19.2 1.0 NZ A:LYS244 2.4 17.2 1.0 C2 A:OXL706 2.8 22.4 1.0 C1 A:OXL706 2.8 22.1 1.0 CG A:ASP311 3.1 14.7 1.0 CD2 A:HIS264 3.2 16.2 1.0 CE1 A:HIS264 3.2 14.9 1.0 PG A:GTP701 3.3 19.0 1.0 OD2 A:ASP311 3.4 15.7 1.0 CE A:LYS244 3.4 19.3 1.0 O3G A:GTP701 3.8 18.8 1.0 O1G A:GTP701 4.0 19.0 1.0 O2 A:OXL706 4.0 25.1 1.0 NZ A:LYS290 4.1 18.1 1.0 O1 A:OXL706 4.1 21.9 1.0 O A:HOH854 4.1 17.8 1.0 OG A:SER286 4.1 30.8 1.0 CE A:LYS290 4.2 16.5 1.0 O A:HOH865 4.2 18.7 1.0 ND1 A:HIS264 4.3 14.3 1.0 CG A:HIS264 4.3 15.1 1.0 CB A:ASP311 4.5 15.1 1.0 O3B A:GTP701 4.6 19.1 1.0 CD A:LYS244 4.7 18.1 1.0 O A:ASP311 4.9 17.9 1.0 CB A:SER286 5.0 24.9 1.0

Manganese binding site 2 out of 2 in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Oxalate 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 LD_2G in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:17.9 occ:0.90 O1G A:GTP701 2.1 19.0 1.0 O1B A:GTP701 2.1 18.8 1.0 O A:HOH854 2.2 17.8 1.0 O A:HOH820 2.2 21.4 1.0 OG1 A:THR291 2.2 16.6 1.0 O A:HOH849 2.3 18.4 1.0 PG A:GTP701 3.3 19.0 1.0 PB A:GTP701 3.3 19.6 1.0 CB A:THR291 3.3 18.9 1.0 O3B A:GTP701 3.5 19.1 1.0 OD2 A:ASP310 3.7 19.7 1.0 O2G A:GTP701 3.9 19.2 1.0 O1A A:GTP701 3.9 21.4 1.0 N A:THR291 4.1 19.1 1.0 O A:HOH865 4.2 18.7 1.0 CA A:THR291 4.3 19.8 1.0 NH1 A:ARG405 4.3 18.8 1.0 O A:ASP310 4.4 18.4 1.0 O3A A:GTP701 4.4 20.9 1.0 O2B A:GTP701 4.4 18.7 1.0 CA A:GLY334 4.5 16.6 1.0 CG2 A:THR291 4.5 20.9 1.0 CG A:ASP310 4.5 17.6 1.0 O A:HOH804 4.6 22.1 1.0 OD1 A:ASP311 4.6 15.7 1.0 O3G A:GTP701 4.6 18.8 1.0 N A:VAL335 4.7 20.4 1.0 PA A:GTP701 4.8 21.4 1.0 O A:PHE333 4.8 19.1 1.0 O3 A:OXL706 4.9 20.1 1.0 CB A:LYS290 4.9 19.3 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