Magnesium in PDB 4hyv: Pyruvate Kinase (Pyk) From Trypanosoma Brucei in the Presence of Magnesium, Pep and F26BP

All present enzymatic activity of Pyruvate Kinase (Pyk) From Trypanosoma Brucei in the Presence of Magnesium, Pep and F26BP:
2.7.1.40;

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei in the Presence of Magnesium, Pep and F26BP, PDB code: 4hyv 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)	65.17 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	103.410, 108.930, 263.340, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 18.8

The structure of Pyruvate Kinase (Pyk) From Trypanosoma Brucei in the Presence of Magnesium, Pep and F26BP also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Pyruvate Kinase (Pyk) From Trypanosoma Brucei in the Presence of Magnesium, Pep and F26BP (pdb code 4hyv). 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 in the Presence of Magnesium, Pep and F26BP, PDB code: 4hyv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyruvate Kinase (Pyk) From Trypanosoma Brucei in the Presence of Magnesium, Pep and F26BP


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 in the Presence of Magnesium, Pep and F26BP within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:24.0 occ:1.00 OD1 A:ASP265 1.9 28.2 1.0 O A:HOH1168 2.0 24.8 1.0 OE1 A:GLU241 2.1 28.0 1.0 O2P A:PEP1003 2.1 31.4 1.0 O1 A:PEP1003 2.2 31.6 1.0 O2 A:PEP1003 2.6 37.1 1.0 P A:PEP1003 2.8 40.4 1.0 CG A:ASP265 3.0 30.9 1.0 C1 A:PEP1003 3.0 28.9 1.0 CD A:GLU241 3.2 29.4 1.0 C2 A:PEP1003 3.2 28.2 1.0 CB A:ASP265 3.5 28.2 1.0 OE2 A:GLU241 3.5 31.5 1.0 O1P A:PEP1003 3.9 38.5 1.0 OD2 A:ASP265 4.1 31.4 1.0 O3P A:PEP1003 4.1 37.9 1.0 N A:ASP265 4.1 25.2 1.0 CZ A:PHE213 4.2 30.0 1.0 O2' A:PEP1003 4.2 30.8 1.0 NZ A:LYS239 4.3 28.6 1.0 CA A:ASP265 4.4 29.2 1.0 CG A:GLU241 4.5 26.6 1.0 O A:HOH1259 4.5 30.8 1.0 CE A:LYS239 4.6 25.1 1.0 CE2 A:PHE213 4.6 30.6 1.0 C3 A:PEP1003 4.7 24.4 1.0 CB A:GLU241 4.7 28.2 1.0 CE1 A:PHE213 4.7 27.8 1.0 O A:HOH1300 4.8 40.5 1.0 CB A:ALA262 4.8 25.8 1.0

Magnesium binding site 2 out of 2 in the Pyruvate Kinase (Pyk) From Trypanosoma Brucei in the Presence of Magnesium, Pep and F26BP


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 in the Presence of Magnesium, Pep and F26BP within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:40.2 occ:1.00 OD1 B:ASP265 1.9 45.7 1.0 O2 B:PEP1003 2.4 50.9 1.0 OE1 B:GLU241 2.5 44.0 1.0 O B:HOH1172 2.5 39.8 1.0 O1 B:PEP1003 2.5 38.8 1.0 O2P B:PEP1003 2.8 59.6 1.0 CG B:ASP265 2.9 38.0 1.0 P B:PEP1003 3.1 41.5 1.0 C2 B:PEP1003 3.2 38.1 1.0 C1 B:PEP1003 3.2 34.9 1.0 O B:HOH1306 3.3 50.7 1.0 CB B:ASP265 3.5 34.2 1.0 CD B:GLU241 3.6 35.3 1.0 OD2 B:ASP265 3.8 42.3 1.0 O1P B:PEP1003 4.0 48.4 1.0 O B:HOH1490 4.0 48.9 1.0 OE2 B:GLU241 4.0 32.9 1.0 N B:ASP265 4.2 25.7 1.0 O B:HOH1390 4.3 50.5 1.0 O B:HOH1344 4.3 46.4 1.0 O2' B:PEP1003 4.4 30.6 1.0 O3P B:PEP1003 4.5 36.2 1.0 CA B:ASP265 4.5 27.4 1.0 O B:HOH1168 4.5 37.5 1.0 NZ B:LYS239 4.5 25.6 1.0 C3 B:PEP1003 4.6 27.4 1.0 CG B:GLU241 4.8 32.9 1.0 CE B:LYS239 4.8 25.5 1.0

W.Zhong, H.P.Morgan, I.W.Mcnae, P.A.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw. `in Crystallo' Substrate Binding Triggers Major Domain Movements and Reveals Magnesium As A Co-Activator of Trypanosoma Brucei Pyruvate Kinase. Acta Crystallogr.,Sect.D V. 69 1768 2013.
ISSN: ISSN 0907-4449
PubMed: 23999300
DOI: 10.1107/S0907444913013875