Magnesium in PDB 4kcu: Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate

All present enzymatic activity of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate:
2.7.1.40;

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate, PDB code: 4kcu 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)	67.18 / 2.35
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.370, 108.270, 265.190, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20.6

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with D-Malate 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 D-Malate (pdb code 4kcu). 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 D-Malate, PDB code: 4kcu:
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 D-Malate


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 D-Malate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:34.4 occ:1.00 O A:HOH1143 2.0 36.3 1.0 OE1 A:GLU241 2.1 33.0 1.0 OD1 A:ASP265 2.1 34.9 1.0 O1 A:MLT1003 2.1 33.4 1.0 O A:HOH1102 2.2 28.9 1.0 O3 A:MLT1003 2.3 38.4 1.0 C2 A:MLT1003 2.6 44.3 1.0 C1 A:MLT1003 2.7 39.9 1.0 CD A:GLU241 3.1 33.8 1.0 CG A:ASP265 3.2 38.0 1.0 OE2 A:GLU241 3.5 38.0 1.0 CB A:ASP265 3.7 30.9 1.0 O A:HOH1242 3.8 32.6 1.0 O2 A:MLT1003 3.9 32.9 1.0 C3 A:MLT1003 4.1 45.1 1.0 NZ A:LYS239 4.1 28.7 1.0 O A:HOH1324 4.2 55.0 1.0 N A:ASP265 4.2 26.7 1.0 O4 A:MLT1003 4.3 50.6 1.0 OD2 A:ASP265 4.3 36.4 1.0 CG A:GLU241 4.4 34.1 1.0 CZ A:PHE213 4.4 38.2 1.0 CE A:LYS239 4.5 25.4 1.0 O A:HOH1101 4.6 30.2 1.0 CA A:ASP265 4.6 29.8 1.0 CB A:ALA262 4.6 26.2 1.0 C4 A:MLT1003 4.7 57.8 1.0 CE2 A:PHE213 4.7 42.0 1.0

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


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 D-Malate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:62.1 occ:1.00 OD1 B:ASP265 2.4 53.9 1.0 OE2 B:GLU241 2.6 60.7 1.0 CG B:ASP265 3.2 46.8 1.0 CD B:GLU241 3.6 45.0 1.0 OD2 B:ASP265 3.7 50.4 1.0 OE1 B:GLU241 4.0 38.9 1.0 O B:HOH601 4.2 32.6 1.0 CB B:ASP265 4.2 38.2 1.0 O3 B:MLT503 4.7 55.1 1.0 CG B:GLU241 4.9 37.5 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