Cobalt in PDB 6k31: Crystal Structure of Pyrophosphate-Dependent Phosphoenolpyruvate Carboxykinase (Ppi-Pepck)

All present enzymatic activity of Crystal Structure of Pyrophosphate-Dependent Phosphoenolpyruvate Carboxykinase (Ppi-Pepck):
4.1.1.38;

The structure of Crystal Structure of Pyrophosphate-Dependent Phosphoenolpyruvate Carboxykinase (Ppi-Pepck), PDB code: 6k31 was solved by Y.Chiba, T.Miyakawa, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.12 / 2.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	160.439, 160.439, 200.160, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 24.1

The binding sites of Cobalt atom in the Crystal Structure of Pyrophosphate-Dependent Phosphoenolpyruvate Carboxykinase (Ppi-Pepck) (pdb code 6k31). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Pyrophosphate-Dependent Phosphoenolpyruvate Carboxykinase (Ppi-Pepck), PDB code: 6k31:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Pyrophosphate-Dependent Phosphoenolpyruvate Carboxykinase (Ppi-Pepck)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Pyrophosphate-Dependent Phosphoenolpyruvate Carboxykinase (Ppi-Pepck) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1201 b:37.8 occ:1.00 OD1 A:ASP656 2.0 36.4 1.0 NE2 A:HIS352 2.1 34.6 1.0 NZ A:LYS332 2.2 34.5 1.0 O A:HOH1470 2.3 31.3 1.0 CE1 A:HIS352 2.9 30.9 1.0 CG A:ASP656 3.1 31.6 1.0 CE A:LYS332 3.2 37.1 1.0 CD2 A:HIS352 3.3 35.8 1.0 OD2 A:ASP656 3.4 32.6 1.0 NZ A:LYS490 3.9 36.2 1.0 ND1 A:HIS352 4.1 31.6 1.0 CG A:HIS352 4.3 32.3 1.0 CB A:ASP656 4.4 30.8 1.0 CE A:LYS490 4.5 36.2 1.0 CD A:LYS332 4.6 35.6 1.0 CZ A:PHE881 4.8 33.9 1.0 CE2 A:PHE881 4.9 34.3 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Pyrophosphate-Dependent Phosphoenolpyruvate Carboxykinase (Ppi-Pepck)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Pyrophosphate-Dependent Phosphoenolpyruvate Carboxykinase (Ppi-Pepck) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1201 b:45.3 occ:1.00 OD1 B:ASP656 2.1 42.4 1.0 NE2 B:HIS352 2.1 42.7 1.0 NZ B:LYS332 2.1 61.9 1.0 CE1 B:HIS352 2.9 41.4 1.0 CG B:ASP656 3.1 42.2 1.0 CE B:LYS332 3.1 58.1 1.0 CD2 B:HIS352 3.3 45.4 1.0 OD2 B:ASP656 3.4 50.1 1.0 NZ B:LYS490 4.0 47.9 1.0 ND1 B:HIS352 4.1 38.8 1.0 CG B:HIS352 4.3 38.6 1.0 CB B:ASP656 4.5 37.1 1.0 CD B:LYS332 4.5 57.2 1.0 CE B:LYS490 4.6 48.4 1.0 O B:HOH1383 4.6 44.3 1.0 O B:HOH1436 4.7 45.3 1.0 CZ B:PHE881 4.7 56.7 1.0 CE2 B:PHE881 4.8 52.3 1.0

Y.Chiba, T.Miyakawa, Y.Shimane, K.Takai, M.Tanokura, T.Nozaki. Structural Comparisons of Phosphoenolpyruvate Carboxykinases Reveal the Evolutionary Trajectories of These Phosphodiester Energy-Conversion Enzymes. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31662435
DOI: 10.1074/JBC.RA119.010920