Magnesium in PDB 7r6y: E117K Mutant Pyruvate Kinase From Rabbit Muscle

All present enzymatic activity of E117K Mutant Pyruvate Kinase From Rabbit Muscle:
2.7.1.40;

The structure of E117K Mutant Pyruvate Kinase From Rabbit Muscle, PDB code: 7r6y was solved by A.Rodriguez-Romero, A.Rodriguez-Hernandez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.97 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	108.34, 121.83, 161.37, 90, 90, 90
R / Rfree (%)	20.1 / 25

The binding sites of Magnesium atom in the E117K Mutant Pyruvate Kinase From Rabbit Muscle (pdb code 7r6y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E117K Mutant Pyruvate Kinase From Rabbit Muscle, PDB code: 7r6y:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the E117K Mutant Pyruvate Kinase From Rabbit Muscle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E117K Mutant Pyruvate Kinase From Rabbit Muscle within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:39.3 occ:1.00 O A:HOH724 2.0 33.9 1.0 OD2 A:ASP295 2.2 31.4 1.0 O4 A:OXL603 2.6 41.3 1.0 O1 A:OXL603 2.8 30.8 1.0 OE1 A:GLU271 2.9 38.2 1.0 CG A:ASP295 3.0 31.1 1.0 CD A:GLU271 3.4 30.9 1.0 C2 A:OXL603 3.5 34.1 1.0 C1 A:OXL603 3.5 25.6 1.0 OE2 A:GLU271 3.5 35.8 1.0 CB A:ASP295 3.6 29.4 1.0 OD1 A:ASP295 3.9 32.5 1.0 O A:HOH802 4.1 38.8 1.0 NZ A:LYS269 4.2 30.1 1.0 CG A:GLU271 4.5 25.9 1.0 N A:ASP295 4.6 27.1 1.0 CE A:LYS269 4.6 28.5 1.0 O2 A:OXL603 4.7 30.3 1.0 O A:HOH877 4.7 38.8 1.0 CA A:ASP295 4.7 23.3 1.0 O3 A:OXL603 4.7 27.5 1.0

Magnesium binding site 2 out of 4 in the E117K Mutant Pyruvate Kinase From Rabbit Muscle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E117K Mutant Pyruvate Kinase From Rabbit Muscle within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:39.9 occ:1.00 OD2 B:ASP295 1.9 33.4 1.0 OE1 B:GLU271 2.2 41.3 1.0 O B:HOH754 2.3 38.8 1.0 O1 B:OXL603 2.3 42.6 1.0 O B:HOH775 2.5 39.2 1.0 CG B:ASP295 3.1 32.0 1.0 CD B:GLU271 3.1 35.7 1.0 OE2 B:GLU271 3.3 34.0 1.0 O B:HOH787 3.5 38.1 1.0 C1 B:OXL603 3.6 49.1 1.0 NZ B:LYS117 3.8 49.4 1.0 CB B:ASP295 3.8 30.5 1.0 O B:HOH808 3.9 33.2 1.0 O2 B:OXL603 4.0 38.9 1.0 OD1 B:ASP295 4.0 34.9 1.0 C2 B:OXL603 4.3 34.8 1.0 CG B:GLU271 4.5 30.5 1.0 O3 B:OXL603 4.5 45.4 1.0 NZ B:LYS269 4.6 32.5 1.0 O B:HOH757 4.7 36.0 1.0 CB B:GLU271 4.9 28.7 1.0 OG B:SER242 5.0 30.9 1.0

Magnesium binding site 3 out of 4 in the E117K Mutant Pyruvate Kinase From Rabbit Muscle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E117K Mutant Pyruvate Kinase From Rabbit Muscle within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg604 b:38.7 occ:1.00 OD2 C:ASP295 1.9 34.1 1.0 OE1 C:GLU271 2.1 30.4 1.0 O C:HOH722 2.2 34.0 1.0 O4 C:OXL603 2.2 32.4 1.0 O C:HOH715 2.3 33.6 1.0 O3 C:OXL603 2.4 33.2 1.0 C2 C:OXL603 3.1 32.9 1.0 CG C:ASP295 3.1 37.1 1.0 CD C:GLU271 3.1 31.6 1.0 C1 C:OXL603 3.1 37.4 1.0 OE2 C:GLU271 3.4 33.5 1.0 CB C:ASP295 3.7 32.3 1.0 O C:HOH803 3.7 37.3 1.0 NZ C:LYS269 3.8 27.8 1.0 O C:HOH782 4.1 35.5 1.0 OD1 C:ASP295 4.1 31.8 1.0 O2 C:OXL603 4.3 37.4 1.0 O1 C:OXL603 4.3 27.8 1.0 CE C:LYS269 4.5 27.0 1.0 CG C:GLU271 4.5 32.7 1.0 CE1 C:PHE243 4.5 34.0 1.0 OG C:SER242 4.6 33.1 1.0 CB C:ALA292 4.6 29.2 1.0 N C:ASP295 4.7 32.0 1.0 CD1 C:PHE243 4.7 34.4 1.0 CB C:GLU271 4.7 31.6 1.0 CA C:ASP295 4.8 31.5 1.0

Magnesium binding site 4 out of 4 in the E117K Mutant Pyruvate Kinase From Rabbit Muscle


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E117K Mutant Pyruvate Kinase From Rabbit Muscle within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg605 b:43.0 occ:1.00 O D:HOH706 1.8 41.7 1.0 OE2 D:GLU271 1.9 42.6 1.0 OD2 D:ASP295 2.1 43.8 1.0 O D:HOH737 2.2 42.2 1.0 O4 D:OXL604 2.2 36.6 1.0 O3 D:OXL604 2.5 37.5 1.0 CD D:GLU271 2.9 38.6 1.0 C2 D:OXL604 3.0 41.0 1.0 CG D:ASP295 3.1 39.1 1.0 C1 D:OXL604 3.1 37.7 1.0 OE1 D:GLU271 3.4 45.0 1.0 CB D:ASP295 3.8 36.2 1.0 NZ D:LYS269 3.9 34.7 1.0 OD1 D:ASP295 4.0 44.6 1.0 CG D:GLU271 4.1 39.2 1.0 O2 D:OXL604 4.2 44.2 1.0 O1 D:OXL604 4.4 32.9 1.0 CE D:LYS269 4.5 33.7 1.0 N D:ASP295 4.7 30.8 1.0 OG D:SER242 4.7 35.3 1.0 CB D:ALA292 4.8 32.5 1.0 CA D:ASP295 4.9 29.8 1.0

L.Ramirez-Silva, G.Hernandez-Alcantara, C.Guerrero-Mendiola, M.Gonzalez-Andrade, A.Rodriguez-Romero, A.Rodriguez-Hernandez, A.Lugo-Munguia, P.A.Gomez-Coronado, C.Rodriguez-Mendez, A.Vega-Segura. The K + -Dependent and -Independent Pyruvate Kinases Acquire the Active Conformation By Different Mechanisms. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 35163274
DOI: 10.3390/IJMS23031347