Manganese in PDB 4gmz: Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp

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

The structure of Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 4gmz 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)	30.80 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.624, 83.908, 118.583, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 23.2

The structure of Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate 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_2G in Complex with Beta- Sulfopyruvate and Gtp (pdb code 4gmz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp, PDB code: 4gmz:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate 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 Beta- Sulfopyruvate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:18.6 occ:1.00 O2G A:GTP702 2.1 17.9 1.0 O A:HOH802 2.1 16.4 1.0 O2B A:GTP702 2.1 17.5 1.0 O A:HOH805 2.1 14.8 1.0 OG1 A:THR291 2.2 17.7 1.0 O A:HOH801 2.3 13.9 1.0 CB A:THR291 3.3 17.2 1.0 PG A:GTP702 3.3 17.0 1.0 PB A:GTP702 3.3 18.9 1.0 O3B A:GTP702 3.6 17.6 1.0 OD2 A:ASP310 3.6 15.6 1.0 O1G A:GTP702 3.9 18.5 1.0 O2A A:GTP702 3.9 18.6 1.0 O A:HOH807 4.0 15.2 1.0 N A:THR291 4.1 16.2 1.0 CA A:THR291 4.3 17.1 1.0 CG2 A:THR291 4.3 17.0 1.0 O1B A:GTP702 4.4 17.1 1.0 NH1 A:ARG405 4.4 16.6 1.0 CA A:GLY334 4.4 16.1 1.0 CG A:ASP310 4.4 16.1 1.0 O3A A:GTP702 4.5 18.1 1.0 O A:ASP310 4.5 15.7 1.0 O3G A:GTP702 4.5 17.5 1.0 OD1 A:ASP311 4.6 12.8 1.0 O A:PHE333 4.7 17.2 1.0 O A:HOH803 4.8 14.7 1.0 PA A:GTP702 4.8 18.8 1.0 N A:VAL335 4.8 15.9 1.0 CB A:LYS290 5.0 16.0 1.0

Manganese binding site 2 out of 3 in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate 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 Beta- Sulfopyruvate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn704 b:16.2 occ:1.00 O1G A:GTP702 2.2 18.5 1.0 NE2 A:HIS264 2.2 17.5 1.0 OD1 A:ASP311 2.3 12.8 1.0 NZ A:LYS244 2.3 16.8 1.0 O1 A:SPV705 2.3 15.4 1.0 O2 A:SPV705 2.3 15.8 1.0 C1 A:SPV705 3.1 15.9 1.0 C2 A:SPV705 3.1 16.1 1.0 CE1 A:HIS264 3.1 17.2 1.0 CG A:ASP311 3.1 13.7 1.0 CD2 A:HIS264 3.2 17.4 1.0 OD2 A:ASP311 3.3 13.9 1.0 CE A:LYS244 3.3 16.6 1.0 PG A:GTP702 3.4 17.0 1.0 O3G A:GTP702 3.9 17.5 1.0 NZ A:LYS290 3.9 15.4 1.0 CE A:LYS290 4.1 15.6 1.0 O2G A:GTP702 4.1 17.9 1.0 O A:HOH801 4.2 13.9 1.0 ND1 A:HIS264 4.3 17.6 1.0 O2' A:SPV705 4.3 16.6 1.0 O A:HOH807 4.3 15.2 1.0 CG A:HIS264 4.4 17.6 1.0 OG A:SER286 4.4 18.4 0.5 CB A:ASP311 4.5 14.4 1.0 C3 A:SPV705 4.6 16.3 1.0 O3B A:GTP702 4.6 17.6 1.0 CD A:LYS244 4.7 16.6 1.0 O A:ASP311 4.9 15.5 1.0 OG A:SER286 4.9 18.2 0.5

Manganese binding site 3 out of 3 in the Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Rat Cytosolic Pepck LD_2G in Complex with Beta- Sulfopyruvate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn706 b:30.9 occ:1.00 O A:HOH1130 2.1 27.2 1.0 OE1 A:GLU63 2.2 34.8 1.0 O A:HOH1129 2.3 23.8 1.0 O A:HOH1140 2.4 30.2 1.0 CD A:GLU63 3.0 35.3 1.0 OE2 A:GLU63 3.2 36.4 1.0 O A:HOH1063 3.9 35.6 1.0 CG A:GLU63 4.4 34.7 1.0 O A:HOH1134 4.4 42.4 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