Magnesium in PDB 4kcv: Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid

All present enzymatic activity of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid:
2.7.1.40;

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid, PDB code: 4kcv was solved by W.Zhong, H.P.Morgan, I.W.Mcnae, P.A.M.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.63 / 2.18
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.250, 108.010, 265.820, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 19.3

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid (pdb code 4kcv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid, PDB code: 4kcv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:53.5 occ:1.00 OD2 B:ASP265 1.7 33.5 1.0 O5 B:AKG1003 2.0 52.7 1.0 OE1 B:GLU241 2.3 51.4 1.0 O B:HOH1210 2.4 22.6 1.0 O2 B:AKG1003 2.4 42.9 1.0 C2 B:AKG1003 2.7 51.5 1.0 CG B:ASP265 2.8 31.1 1.0 C1 B:AKG1003 2.9 38.8 1.0 CD B:GLU241 3.3 35.4 1.0 CB B:ASP265 3.5 26.4 1.0 OE2 B:GLU241 3.7 29.5 1.0 OD1 B:ASP265 3.8 40.8 1.0 NZ B:LYS239 3.9 17.8 1.0 O B:HOH1209 3.9 32.2 1.0 O1 B:AKG1003 4.2 34.2 1.0 C3 B:AKG1003 4.2 49.0 1.0 O B:HOH1426 4.3 40.5 1.0 O B:HOH1129 4.3 21.7 1.0 CE B:LYS239 4.4 17.1 1.0 N B:ASP265 4.5 20.4 1.0 CG B:GLU241 4.6 29.4 1.0 CA B:ASP265 4.6 21.1 1.0 O3 B:AKG1003 4.6 63.0 1.0 CB B:ALA262 4.7 15.7 1.0 C4 B:AKG1003 4.8 53.2 1.0 O B:HOH1427 4.9 46.8 1.0 O B:HOH1425 4.9 43.3 1.0

Magnesium binding site 2 out of 2 in the Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with 2- Oxoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:19.2 occ:1.00 OE1 A:GLU241 2.0 17.8 1.0 OD2 A:ASP265 2.0 20.7 1.0 O A:HOH1215 2.1 20.6 1.0 O A:HOH1211 2.1 17.1 1.0 O5 A:AKG1003 2.1 21.7 1.0 O2 A:AKG1003 2.2 23.8 1.0 C2 A:AKG1003 2.8 24.9 1.0 C1 A:AKG1003 2.8 24.4 1.0 CG A:ASP265 3.1 20.8 1.0 CD A:GLU241 3.1 19.3 1.0 CB A:ASP265 3.5 18.0 1.0 OE2 A:GLU241 3.5 20.1 1.0 O1 A:AKG1003 4.1 22.5 1.0 O3 A:AKG1003 4.1 44.5 1.0 N A:ASP265 4.2 16.2 1.0 CZ A:PHE213 4.2 24.3 1.0 OD1 A:ASP265 4.2 19.9 1.0 O A:HOH1135 4.3 20.1 1.0 NZ A:LYS239 4.3 19.0 1.0 C3 A:AKG1003 4.3 26.4 1.0 CG A:GLU241 4.4 18.7 1.0 CA A:ASP265 4.4 17.6 1.0 CE1 A:PHE213 4.5 22.3 1.0 CB A:GLU241 4.6 22.0 1.0 CE A:LYS239 4.6 17.5 1.0 O A:HOH1136 4.7 23.0 1.0 CB A:ALA262 4.7 15.9 1.0 CE2 A:PHE213 4.8 23.8 1.0

W.Zhong, H.P.Morgan, M.W.Nowicki, I.W.Mcnae, M.Yuan, J.Bella, P.A.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw. Pyruvate Kinases Have An Intrinsic and Conserved Decarboxylase Activity. Biochem.J. V. 458 301 2014.
ISSN: ISSN 0264-6021
PubMed: 24328825
DOI: 10.1042/BJ20130790