Magnesium in PDB 4kcw: Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with Oxalate

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

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with Oxalate, PDB code: 4kcw 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)	68.44 / 2.50
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.880, 108.560, 264.530, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20.2

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei Soaked with Oxalate 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 Oxalate (pdb code 4kcw). 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 Oxalate, PDB code: 4kcw:
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 Oxalate


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 Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:29.7 occ:1.00 O A:HOH1185 1.9 30.7 1.0 OE1 A:GLU241 2.0 32.5 1.0 OD1 A:ASP265 2.0 33.4 1.0 O3 A:OXL1003 2.0 43.4 1.0 O A:HOH1184 2.2 27.8 1.0 O2 A:OXL1003 2.5 33.9 1.0 C1 A:OXL1003 3.0 48.6 1.0 CD A:GLU241 3.0 31.7 1.0 CG A:ASP265 3.1 35.8 1.0 C2 A:OXL1003 3.2 44.8 1.0 OE2 A:GLU241 3.4 29.9 1.0 CB A:ASP265 3.7 31.4 1.0 O A:HOH1172 3.9 34.0 1.0 NZ A:LYS239 4.1 29.1 1.0 O1 A:OXL1003 4.2 46.9 1.0 OD2 A:ASP265 4.2 31.9 1.0 CG A:GLU241 4.3 33.0 1.0 CZ A:PHE213 4.3 41.9 1.0 O A:HOH1186 4.3 30.3 1.0 CE2 A:PHE213 4.4 37.6 1.0 N A:ASP265 4.4 28.1 1.0 O4 A:OXL1003 4.4 41.7 1.0 CE A:LYS239 4.5 28.1 1.0 O A:HOH1288 4.6 38.8 1.0 CA A:ASP265 4.7 30.5 1.0 CB A:ALA262 4.9 25.1 1.0

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


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 Oxalate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:43.6 occ:1.00 O4 B:OXL1003 1.9 44.4 1.0 O B:HOH1170 2.0 32.8 1.0 OD1 B:ASP265 2.0 30.8 1.0 OE1 B:GLU241 2.1 33.0 1.0 O B:HOH1171 2.3 28.8 1.0 O1 B:OXL1003 2.3 29.2 1.0 C2 B:OXL1003 2.8 44.8 1.0 C1 B:OXL1003 2.9 37.8 1.0 CG B:ASP265 3.1 33.5 1.0 CD B:GLU241 3.1 31.6 1.0 OE2 B:GLU241 3.5 28.8 1.0 CB B:ASP265 3.6 30.8 1.0 O2 B:OXL1003 4.0 38.0 1.0 NZ B:LYS239 4.2 25.2 1.0 O3 B:OXL1003 4.2 36.2 1.0 OD2 B:ASP265 4.2 36.0 1.0 O B:HOH1172 4.3 39.6 1.0 N B:ASP265 4.3 27.8 1.0 CG B:GLU241 4.4 27.2 1.0 O B:HOH1101 4.5 26.8 1.0 CE B:LYS239 4.6 27.1 1.0 CA B:ASP265 4.6 28.5 1.0 CB B:ALA262 4.8 22.2 1.0 CB B:GLU241 4.8 25.9 1.0 CE2 B:PHE213 5.0 35.4 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