Manganese in PDB 5v9g: Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Oxalate and Gtp.

All present enzymatic activity of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Oxalate and Gtp.:
4.1.1.32;

The structure of Structure of the H477R Variant of Rat Cytosolic Pepck in Complex with Oxalate and Gtp., PDB code: 5v9g was solved by T.Holyoak, D.S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.37 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.526, 119.605, 60.679, 90.00, 106.83, 90.00
R / Rfree (%)	18.4 / 21.2

The structure of Structure of the H477R Variant of Rat Cytosolic Pepck 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 the H477R Variant of Rat Cytosolic Pepck in Complex with Oxalate and Gtp. (pdb code 5v9g). 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 the H477R Variant of Rat Cytosolic Pepck in Complex with Oxalate and Gtp., PDB code: 5v9g:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of the H477R Variant of Rat Cytosolic Pepck 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 the H477R Variant of Rat Cytosolic Pepck in Complex with Oxalate and Gtp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn701 b:31.7 occ:1.00 O3 A:OXL704 2.1 30.3 1.0 OD1 A:ASP311 2.2 30.8 1.0 O4 A:OXL704 2.2 31.3 1.0 O1G A:GTP703 2.2 33.6 1.0 NE2 A:HIS264 2.4 30.5 1.0 NZ A:LYS244 2.4 28.3 1.0 C1 A:OXL704 2.9 32.5 1.0 C2 A:OXL704 2.9 32.5 1.0 CG A:ASP311 3.1 30.9 1.0 CD2 A:HIS264 3.3 29.0 1.0 OD2 A:ASP311 3.3 31.6 1.0 CE1 A:HIS264 3.4 28.7 1.0 PG A:GTP703 3.4 37.1 1.0 CE A:LYS244 3.4 29.0 1.0 O2G A:GTP703 3.9 34.9 1.0 O3G A:GTP703 3.9 38.5 1.0 NZ A:LYS290 4.0 32.4 1.0 O1 A:OXL704 4.1 34.2 1.0 O2 A:OXL704 4.1 34.5 1.0 O A:HOH955 4.2 34.6 1.0 CE A:LYS290 4.2 31.5 1.0 O A:HOH814 4.2 34.1 1.0 CG A:HIS264 4.4 29.4 1.0 ND1 A:HIS264 4.4 29.5 1.0 OG A:SER286 4.4 36.0 1.0 CB A:ASP311 4.5 31.8 1.0 O3B A:GTP703 4.8 37.7 1.0 CD A:LYS244 4.8 29.2 1.0 CA A:SER286 4.8 34.4 1.0 CB A:SER286 4.8 34.3 1.0 O A:ASP311 5.0 32.6 1.0

Manganese binding site 2 out of 2 in the Structure of the H477R Variant of Rat Cytosolic Pepck 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 the H477R Variant of Rat Cytosolic Pepck in Complex with Oxalate and Gtp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn702 b:39.8 occ:1.00 O3G A:GTP703 2.1 38.5 1.0 O1B A:GTP703 2.1 37.1 1.0 O A:HOH814 2.1 34.1 1.0 O A:HOH813 2.1 34.6 1.0 O A:HOH825 2.3 36.9 1.0 OG1 A:THR291 2.3 36.1 1.0 PG A:GTP703 3.2 37.1 1.0 PB A:GTP703 3.2 36.6 1.0 CB A:THR291 3.4 33.4 1.0 O3B A:GTP703 3.5 37.7 1.0 OD2 A:ASP310 3.6 35.2 1.0 O1G A:GTP703 3.9 33.6 1.0 O A:HOH955 3.9 34.6 1.0 N A:THR291 4.1 32.4 1.0 O1A A:GTP703 4.1 39.0 1.0 O A:ASP310 4.1 31.9 1.0 CA A:THR291 4.3 34.3 1.0 O3A A:GTP703 4.3 38.3 1.0 CG A:ASP310 4.3 35.3 1.0 O2B A:GTP703 4.4 35.5 1.0 OD1 A:ASP311 4.4 30.8 1.0 CA A:GLY334 4.4 31.9 1.0 NH1 A:ARG405 4.5 33.9 1.0 O2G A:GTP703 4.5 34.9 1.0 O A:PHE333 4.5 30.7 1.0 PA A:GTP703 4.5 40.1 1.0 CG2 A:THR291 4.5 33.8 1.0 O2A A:GTP703 4.7 39.0 1.0 O3 A:OXL704 4.9 30.3 1.0 N A:VAL335 4.9 33.4 1.0 CB A:ASP310 5.0 33.5 1.0 CB A:ASP311 5.0 31.8 1.0 CB A:LYS290 5.0 33.0 1.0 C A:ASP310 5.0 31.2 1.0 CG A:ASP311 5.0 30.9 1.0 O A:HOH909 5.0 39.4 1.0

D.S.Cui, A.Broom, M.J.Mcleod, E.M.Meiering, T.Holyoak. Asymmetric Anchoring Is Required For Efficient Omega-Loop Opening and Closing in Cytosolic Phosphoenolpyruvate Carboxykinase. Biochemistry V. 56 2106 2017.
ISSN: ISSN 1520-4995
PubMed: 28345895
DOI: 10.1021/ACS.BIOCHEM.7B00178