Manganese in PDB 4gmu: Structure of Rat Cytosolic Pepck LD_1G in Complex with Oxalate and Gtp

All present enzymatic activity of Structure of Rat Cytosolic Pepck LD_1G in Complex with Oxalate and Gtp:
4.1.1.32;

The structure of Structure of Rat Cytosolic Pepck LD_1G in Complex with Oxalate and Gtp, PDB code: 4gmu 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)	26.97 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.546, 85.521, 118.755, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.6

The structure of Structure of Rat Cytosolic Pepck LD_1G 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_1G in Complex with Oxalate and Gtp (pdb code 4gmu). 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_1G in Complex with Oxalate and Gtp, PDB code: 4gmu:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Structure of Rat Cytosolic Pepck LD_1G 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_1G in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:7.3 occ:1.00 O3 A:OXL705 2.1 9.3 1.0 OD1 A:ASP311 2.1 7.6 1.0 O4 A:OXL705 2.2 11.2 1.0 O3G A:GTP701 2.2 7.3 1.0 NE2 A:HIS264 2.2 6.8 1.0 NZ A:LYS244 2.2 5.8 0.7 O A:HOH1671 2.6 18.2 0.7 C2 A:OXL705 2.9 12.4 1.0 C1 A:OXL705 2.9 12.5 1.0 CG A:ASP311 3.0 6.9 1.0 CD2 A:HIS264 3.2 6.9 1.0 CE1 A:HIS264 3.3 6.5 1.0 OD2 A:ASP311 3.3 7.2 1.0 PG A:GTP701 3.3 8.3 1.0 CE A:LYS244 3.4 7.3 0.7 O2G A:GTP701 3.8 8.5 1.0 O1G A:GTP701 3.9 8.4 1.0 NZ A:LYS290 4.0 9.0 1.0 O1 A:OXL705 4.1 12.7 1.0 O2 A:OXL705 4.1 13.9 1.0 O A:HOH915 4.2 8.0 1.0 CE A:LYS290 4.2 9.2 1.0 OG A:SER286 4.2 22.6 1.0 O A:HOH842 4.3 9.8 1.0 CG A:HIS264 4.4 6.4 1.0 ND1 A:HIS264 4.4 6.7 1.0 CB A:ASP311 4.4 6.9 1.0 O3B A:GTP701 4.6 8.5 1.0 CD A:LYS244 4.8 6.8 0.7 CZ A:PHE485 5.0 10.8 1.0 O A:ASP311 5.0 7.5 1.0 CE2 A:PHE485 5.0 10.0 1.0

Manganese binding site 2 out of 3 in the Structure of Rat Cytosolic Pepck LD_1G 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_1G in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn703 b:8.1 occ:1.00 O1G A:GTP701 2.1 8.4 1.0 O1B A:GTP701 2.1 8.1 1.0 O A:HOH884 2.2 9.3 1.0 O A:HOH915 2.2 8.0 1.0 OG1 A:THR291 2.2 8.1 1.0 O A:HOH909 2.2 8.9 1.0 PG A:GTP701 3.3 8.3 1.0 PB A:GTP701 3.3 8.1 1.0 CB A:THR291 3.4 8.0 1.0 O3B A:GTP701 3.5 8.5 1.0 OD2 A:ASP310 3.8 8.4 1.0 O3G A:GTP701 3.8 7.3 1.0 O1A A:GTP701 4.0 10.0 1.0 N A:THR291 4.1 7.7 1.0 O A:HOH842 4.2 9.8 1.0 CA A:THR291 4.3 8.1 1.0 NH1 A:ARG405 4.3 7.8 1.0 O2B A:GTP701 4.4 7.6 1.0 O A:ASP310 4.4 7.7 1.0 O3A A:GTP701 4.4 9.6 1.0 CG2 A:THR291 4.4 9.4 1.0 CA A:GLY334 4.5 8.5 1.0 O2G A:GTP701 4.5 8.5 1.0 CG A:ASP310 4.5 7.4 1.0 OD1 A:ASP311 4.5 7.6 1.0 O A:HOH899 4.6 9.8 1.0 N A:VAL335 4.7 8.8 1.0 PA A:GTP701 4.8 9.2 1.0 O A:PHE333 4.8 8.5 1.0 O3 A:OXL705 4.9 9.3 1.0 CB A:LYS290 5.0 8.0 1.0

Manganese binding site 3 out of 3 in the Structure of Rat Cytosolic Pepck LD_1G 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 3 of Structure of Rat Cytosolic Pepck LD_1G in Complex with Oxalate and Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn706 b:14.0 occ:0.60 O A:HOH1507 2.1 25.0 1.0 OE1 A:GLU63 2.1 18.2 1.0 O A:HOH1130 2.2 21.5 1.0 CD A:GLU63 3.2 18.2 1.0 CG A:GLU63 3.7 18.4 1.0 O A:HOH1315 3.7 39.5 1.0 OE2 A:GLU63 4.3 21.8 1.0 NE2 A:HIS59 4.3 17.7 1.0 O A:HOH1489 4.4 19.9 1.0 O A:HOH1608 4.4 34.6 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