Manganese in PDB 4gnq: Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp

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

The structure of Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp, PDB code: 4gnq 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)	27.36 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.487, 84.329, 118.971, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 19.7

The structure of Structure of Rat Cytosolic Pepck LD_3G in Complex with Oxalate and Gtp 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 Oxalate and Gtp (pdb code 4gnq). 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 Oxalate and Gtp, PDB code: 4gnq:
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 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_3G in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:9.7 occ:1.00 OD1 A:ASP311 2.1 9.2 1.0 O2 A:OXL705 2.2 12.0 1.0 O1 A:OXL705 2.2 11.9 1.0 O1G A:GTP701 2.2 9.6 1.0 NZ A:LYS244 2.2 9.5 0.7 NE2 A:HIS264 2.3 9.8 1.0 O A:HOH1477 2.6 9.1 0.3 C1 A:OXL705 2.9 13.0 1.0 C2 A:OXL705 2.9 14.2 1.0 CG A:ASP311 3.1 8.9 1.0 CD2 A:HIS264 3.2 9.5 1.0 CE1 A:HIS264 3.3 9.0 1.0 PG A:GTP701 3.3 10.4 1.0 OD2 A:ASP311 3.3 9.0 1.0 CE A:LYS244 3.4 9.9 0.7 O3G A:GTP701 3.8 11.8 1.0 O2G A:GTP701 3.9 10.5 1.0 NZ A:LYS290 4.0 10.3 1.0 O3 A:OXL705 4.1 14.0 1.0 CE A:LYS290 4.1 9.8 1.0 O4 A:OXL705 4.2 15.8 1.0 O A:HOH855 4.2 10.0 1.0 O A:HOH866 4.3 11.4 1.0 OG A:SER286 4.3 12.7 0.3 CG A:HIS264 4.4 9.4 1.0 ND1 A:HIS264 4.4 9.0 1.0 CB A:ASP311 4.5 8.7 1.0 O3B A:GTP701 4.6 11.1 1.0 CD A:LYS244 4.8 9.7 0.7 O A:ASP311 5.0 9.5 1.0 CZ A:PHE485 5.0 11.3 1.0

Manganese binding site 2 out of 2 in the Structure of Rat Cytosolic Pepck LD_3G 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_3G in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:9.3 occ:0.90 O2G A:GTP701 2.1 10.5 1.0 O2B A:GTP701 2.2 10.9 1.0 OG1 A:THR291 2.2 6.9 0.7 O A:HOH821 2.2 10.8 1.0 O A:HOH855 2.2 10.0 1.0 O A:HOH850 2.3 10.3 1.0 PG A:GTP701 3.3 10.4 1.0 CB A:THR291 3.3 8.7 0.7 PB A:GTP701 3.3 10.8 1.0 O3B A:GTP701 3.5 11.1 1.0 CB A:THR291 3.5 11.7 0.3 OD2 A:ASP310 3.7 11.5 1.0 CG2 A:THR291 3.8 12.9 0.3 O1G A:GTP701 3.9 9.6 1.0 O2A A:GTP701 4.0 12.3 1.0 N A:THR291 4.1 10.0 1.0 O A:HOH866 4.2 11.4 1.0 CA A:THR291 4.3 9.6 0.7 CA A:THR291 4.3 11.1 0.3 NH1 A:ARG405 4.4 11.5 1.0 CG2 A:THR291 4.4 9.5 0.7 O3A A:GTP701 4.4 10.9 1.0 O A:ASP310 4.4 9.6 1.0 O1B A:GTP701 4.4 10.4 1.0 CG A:ASP310 4.4 10.0 1.0 CA A:GLY334 4.5 10.7 1.0 O3G A:GTP701 4.5 11.8 1.0 OG1 A:THR291 4.5 12.6 0.3 OD1 A:ASP311 4.5 9.2 1.0 O A:HOH804 4.6 10.8 1.0 O A:PHE333 4.7 10.6 1.0 N A:VAL335 4.7 10.9 1.0 PA A:GTP701 4.8 11.9 1.0 CB A:LYS290 4.9 9.3 1.0 O1 A:OXL705 5.0 11.9 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