Manganese in PDB 2rk7: The Structure of Rat Cytosolic Pepck in Complex with Oxalate

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

The structure of The Structure of Rat Cytosolic Pepck in Complex with Oxalate, PDB code: 2rk7 was solved by S.M.Sullivan, R.M.Stiffin, G.M.Carlson, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.82 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.011, 118.945, 86.506, 90.00, 106.95, 90.00
R / Rfree (%)	20.5 / 25.6

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

Sodium

(Na)

2 atoms

The binding sites of Manganese atom in the The Structure of Rat Cytosolic Pepck in Complex with Oxalate (pdb code 2rk7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Structure of Rat Cytosolic Pepck in Complex with Oxalate, PDB code: 2rk7:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Structure of Rat Cytosolic Pepck in Complex with Oxalate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of Rat Cytosolic Pepck in Complex with Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn700 b:13.3 occ:1.00 OD1 A:ASP311 2.1 8.8 1.0 NE2 A:HIS264 2.1 2.9 1.0 O3 A:OXL5575 2.2 14.2 1.0 O A:HOH5887 2.3 15.8 1.0 O4 A:OXL5575 2.3 16.1 1.0 NZ A:LYS244 2.3 7.5 1.0 C1 A:OXL5575 3.0 18.5 1.0 C2 A:OXL5575 3.0 18.5 1.0 CE1 A:HIS264 3.0 2.0 1.0 CG A:ASP311 3.1 8.3 1.0 CD2 A:HIS264 3.2 2.3 1.0 CE A:LYS244 3.3 7.7 1.0 OD2 A:ASP311 3.4 8.5 1.0 O1 A:OXL5575 4.2 20.6 1.0 ND1 A:HIS264 4.2 2.0 1.0 NZ A:LYS290 4.2 16.8 1.0 O2 A:OXL5575 4.2 20.3 1.0 O A:HOH5673 4.3 21.1 1.0 CG A:HIS264 4.3 5.0 1.0 O A:HOH5877 4.3 30.1 1.0 O A:HOH5888 4.3 22.0 1.0 CB A:ASP311 4.4 8.8 1.0 CD A:LYS244 4.7 6.6 1.0 O A:ASP311 4.9 9.2 1.0 CA A:ASP311 4.9 9.0 1.0 CE2 A:PHE485 4.9 4.0 1.0 CZ A:PHE485 5.0 4.7 1.0

Manganese binding site 2 out of 4 in the The Structure of Rat Cytosolic Pepck in Complex with Oxalate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of Rat Cytosolic Pepck in Complex with Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn5576 b:41.3 occ:0.60 N A:PHE530 3.3 8.7 1.0 ND2 A:ASN533 3.4 9.2 1.0 O A:HOH5667 3.7 24.2 1.0 CD1 A:PHE530 3.9 9.8 1.0 CA A:PHE530 3.9 8.6 1.0 CD1 A:TRP516 4.1 8.1 1.0 CE1 A:PHE530 4.3 9.9 1.0 C A:GLY529 4.3 9.0 1.0 CA A:GLY529 4.4 9.2 1.0 CG A:TRP516 4.5 8.0 1.0 O A:HOH5659 4.5 33.7 1.0 CG A:ASN533 4.6 8.0 1.0 CG A:PHE530 4.6 9.4 1.0 NE1 A:TRP516 4.6 9.4 1.0 CB A:TRP516 4.7 7.4 1.0 O A:HOH5677 4.8 29.7 1.0 CB A:PHE530 4.9 8.8 1.0 OD1 A:ASN533 4.9 7.1 1.0 O A:PHE530 5.0 8.2 1.0

Manganese binding site 3 out of 4 in the The Structure of Rat Cytosolic Pepck in Complex with Oxalate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of Rat Cytosolic Pepck in Complex with Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn700 b:10.0 occ:1.00 O4 B:OXL5575 2.1 16.4 1.0 OD1 B:ASP311 2.1 3.7 1.0 NE2 B:HIS264 2.2 3.5 1.0 O B:HOH5794 2.2 12.7 1.0 O3 B:OXL5575 2.3 17.3 1.0 NZ B:LYS244 2.3 6.0 1.0 C2 B:OXL5575 2.9 18.7 1.0 C1 B:OXL5575 3.0 18.8 1.0 CG B:ASP311 3.0 7.9 1.0 CD2 B:HIS264 3.2 3.2 1.0 CE1 B:HIS264 3.2 4.8 1.0 OD2 B:ASP311 3.2 8.6 1.0 CE B:LYS244 3.4 6.7 1.0 NZ B:LYS290 4.1 10.9 1.0 O2 B:OXL5575 4.1 20.9 1.0 O1 B:OXL5575 4.2 19.5 1.0 O B:HOH5770 4.2 19.3 1.0 O B:HOH5714 4.3 10.1 1.0 ND1 B:HIS264 4.3 4.0 1.0 OG B:SER286 4.3 15.7 1.0 CG B:HIS264 4.3 3.3 1.0 CB B:ASP311 4.4 7.9 1.0 O B:HOH5687 4.5 33.1 1.0 CD B:LYS244 4.7 4.0 1.0 CA B:ASP311 4.9 8.4 1.0 CE2 B:PHE485 4.9 4.6 1.0 O B:ASP311 4.9 7.9 1.0 CZ B:PHE485 5.0 5.0 1.0

Manganese binding site 4 out of 4 in the The Structure of Rat Cytosolic Pepck in Complex with Oxalate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Structure of Rat Cytosolic Pepck in Complex with Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn5576 b:45.1 occ:0.60 ND2 B:ASN533 3.6 11.8 1.0 N B:PHE530 3.6 11.9 1.0 O B:HOH5947 3.7 36.0 1.0 CA B:PHE530 4.2 11.9 1.0 CD1 B:TRP516 4.2 12.6 1.0 CD1 B:PHE530 4.2 14.2 1.0 O B:HOH5712 4.3 28.8 1.0 CG B:TRP516 4.5 11.8 1.0 CZ B:PHE517 4.6 12.9 1.0 C B:GLY529 4.6 11.7 1.0 CA B:GLY529 4.6 11.5 1.0 CE1 B:PHE530 4.7 15.4 1.0 CB B:TRP516 4.7 11.4 1.0 CG B:ASN533 4.7 11.6 1.0 OD1 B:ASN292 4.8 20.4 1.0 NE1 B:TRP516 4.8 13.5 1.0 CB B:ASN292 4.9 19.0 1.0 CA B:GLY289 4.9 16.7 1.0 O B:HOH5994 4.9 39.4 1.0 CE1 B:PHE517 4.9 15.6 1.0

R.M.Stiffin, S.M.Sullivan, G.M.Carlson, T.Holyoak. Differential Inhibition of Cytosolic Pepck By Substrate Analogues. Kinetic and Structural Characterization of Inhibitor Recognition. Biochemistry V. 47 2099 2008.
ISSN: ISSN 0006-2960
PubMed: 18197707
DOI: 10.1021/BI7020662