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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 4kcu:

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

Potassium (K) 2 atoms

Magnesium Binding Sites:

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 4kcu

Go back to Magnesium Binding Sites List in 4kcu
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 4kcu

Go back to Magnesium Binding Sites List in 4kcu
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

Reference:

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
Page generated: Sat Aug 17 03:33:37 2024

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