Atomistry » Magnesium » PDB 7r41-7rax » 7r6y
Atomistry »
  Magnesium »
    PDB 7r41-7rax »
      7r6y »

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

Enzymatic activity of E117K Mutant Pyruvate Kinase From Rabbit Muscle

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

Protein crystallography data

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

Magnesium Binding Sites:

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 7r6y

Go back to Magnesium Binding Sites List in 7r6y
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 7r6y

Go back to Magnesium Binding Sites List in 7r6y
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 7r6y

Go back to Magnesium Binding Sites List in 7r6y
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 7r6y

Go back to Magnesium Binding Sites List in 7r6y
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

Reference:

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
Page generated: Thu Oct 3 07:29:10 2024

Last articles

Na in 6BQ9
Na in 6BWI
Na in 6C02
Na in 6C01
Na in 6BG4
Na in 6C0L
Na in 6BXR
Na in 6BZX
Na in 6BZ2
Na in 6BX5
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy