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Magnesium in PDB 1aqf: Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate

Enzymatic activity of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate

All present enzymatic activity of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate:
2.7.1.40;

Protein crystallography data

The structure of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate, PDB code: 1aqf was solved by T.M.Larsen, M.M.Benning, G.E.Wesenberg, I.Rayment, G.H.Reed, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 144.400, 112.600, 171.200, 90.00, 93.70, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1aqf:

The structure of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate also contains other interesting chemical elements:

Potassium (K) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate (pdb code 1aqf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate, PDB code: 1aqf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1aqf

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Magnesium binding site 1 out of 8 in the Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg534

b:19.4
occ:1.00
 O1 A:PEQ532 2.0 62.7 1.0
O3P A:PEQ532 2.0 76.7 1.0
OD2 A:ASP295 2.1 94.8 1.0
OE2 A:GLU271 2.1 16.9 1.0
O2 A:PEQ532 2.3 75.9 1.0
P A:PEQ532 2.5 87.8 1.0
C1 A:PEQ532 2.7 16.0 1.0
C2 A:PEQ532 2.9 24.4 1.0
CG A:ASP295 3.1 11.7 1.0
O2P A:PEQ532 3.2 76.5 1.0
CD A:GLU271 3.2 30.6 1.0
CB A:ASP295 3.6 37.8 1.0
O2' A:PEQ532 3.9 39.1 1.0
CG A:GLU271 3.9 34.0 1.0
O1P A:PEQ532 3.9 79.1 1.0
OE1 A:GLU271 4.2 30.1 1.0
OD1 A:ASP295 4.3 22.9 1.0
C3 A:PEQ532 4.3 33.3 1.0
CZ A:PHE243 4.5 49.2 1.0
CE1 A:PHE243 4.6 11.6 1.0
N A:ASP295 4.6 16.5 1.0
NZ A:LYS269 4.7 3.1 1.0
CA A:ASP295 4.7 10.2 1.0

Magnesium binding site 2 out of 8 in 1aqf

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Magnesium binding site 2 out of 8 in the Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg534

b:49.0
occ:1.00
 OE1 B:GLU271 2.3 0.0 1.0
OD2 B:ASP295 2.3 61.3 1.0
CD B:GLU271 3.1 25.9 1.0
OE2 B:GLU271 3.3 83.2 1.0
CG B:ASP295 3.4 0.0 1.0
CB B:ASP295 4.2 38.0 1.0
OD1 B:ASP295 4.3 66.7 1.0
O3P B:PEQ532 4.4 77.5 0.5
CG B:GLU271 4.5 10.3 1.0
OG B:SER242 4.7 13.6 1.0
O2 B:PEQ532 4.8 34.9 0.5
CB B:SER242 4.9 21.8 1.0
O B:LYS114 5.0 30.4 1.0

Magnesium binding site 3 out of 8 in 1aqf

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Magnesium binding site 3 out of 8 in the Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg534

b:42.8
occ:1.00
 OE1 C:GLU271 2.3 74.4 1.0
OD2 C:ASP295 2.4 70.0 1.0
O C:HOH6071 2.9 53.6 1.0
CG C:ASP295 3.3 38.9 1.0
CD C:GLU271 3.4 30.1 1.0
OE2 C:GLU271 4.0 55.7 1.0
CB C:ASP295 4.0 60.3 1.0
OD1 C:ASP295 4.2 99.1 1.0
CG C:GLU271 4.7 8.8 1.0
O3P C:PEQ532 4.7 74.5 0.5
O2P C:PEQ532 4.9 57.3 0.5

Magnesium binding site 4 out of 8 in 1aqf

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Magnesium binding site 4 out of 8 in the Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg534

b:40.8
occ:1.00
 OD2 D:ASP295 2.3 47.4 1.0
OE2 D:GLU271 2.3 56.0 1.0
CG D:ASP295 3.1 0.0 1.0
CD D:GLU271 3.2 23.3 1.0
OD1 D:ASP295 3.7 31.0 1.0
OE1 D:GLU271 3.9 46.5 1.0
CB D:ASP295 4.1 17.9 1.0
CG D:GLU271 4.3 1.0 1.0
O D:HOH6034 4.8 32.2 1.0
CB D:GLU271 4.8 30.0 1.0
O1 D:PEQ532 4.9 51.0 0.5

Magnesium binding site 5 out of 8 in 1aqf

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Magnesium binding site 5 out of 8 in the Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg534

b:82.0
occ:1.00
 OE1 E:GLU271 2.9 52.2 1.0
O2P E:PEQ532 3.1 0.0 0.5
OD2 E:ASP295 3.2 77.6 1.0
O E:LYS114 3.5 72.7 1.0
OE2 E:GLU271 3.6 58.2 1.0
CD E:GLU271 3.6 0.0 1.0
K E:K533 4.1 81.8 1.0
CB E:SER242 4.3 30.6 1.0
CG E:ASP295 4.3 0.0 1.0
P E:PEQ532 4.4 82.4 0.5
OG E:SER242 4.5 0.0 1.0
C E:LYS114 4.6 49.2 1.0
O2 E:PEQ532 4.6 86.3 0.5
O3P E:PEQ532 4.8 58.8 0.5

Magnesium binding site 6 out of 8 in 1aqf

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Magnesium binding site 6 out of 8 in the Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg534

b:45.0
occ:1.00
 OD2 F:ASP295 2.2 0.0 1.0
OE2 F:GLU271 2.3 38.4 1.0
CG F:ASP295 3.3 49.3 1.0
CD F:GLU271 3.5 25.1 1.0
OD1 F:ASP295 4.1 83.5 1.0
CB F:ASP295 4.3 24.6 1.0
OE1 F:GLU271 4.4 63.1 1.0
CG F:GLU271 4.5 32.4 1.0
CB F:SER242 4.8 1.0 1.0
O1 F:PEQ532 4.9 55.4 0.5
O3P F:PEQ532 4.9 74.2 0.5
O2P F:PEQ532 4.9 30.0 0.5

Magnesium binding site 7 out of 8 in 1aqf

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Magnesium binding site 7 out of 8 in the Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg534

b:52.5
occ:1.00
 OD2 G:ASP295 2.1 77.0 1.0
OE2 G:GLU271 2.9 43.0 1.0
CG G:ASP295 3.2 0.0 1.0
OD1 G:ASP295 3.8 73.8 1.0
CD G:GLU271 3.9 0.0 1.0
CB G:ASP295 4.3 49.9 1.0
OE1 G:GLU271 4.4 17.5 1.0
O1 G:PEQ532 4.9 50.2 0.5
CD1 G:PHE243 4.9 88.6 1.0
ND2 G:ASN209 5.0 39.3 1.0

Magnesium binding site 8 out of 8 in 1aqf

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Magnesium binding site 8 out of 8 in the Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pyruvate Kinase From Rabbit Muscle with Mg, K, and L- Phospholactate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg534

b:64.3
occ:1.00
 OE1 H:GLU271 2.3 35.4 1.0
OD2 H:ASP295 2.4 92.2 1.0
CD H:GLU271 3.3 19.4 1.0
CG H:ASP295 3.5 37.9 1.0
OE2 H:GLU271 3.8 55.3 1.0
CB H:ASP295 4.3 46.4 1.0
O2P H:PEQ532 4.4 90.0 0.5
OD1 H:ASP295 4.5 83.8 1.0
CG H:GLU271 4.6 3.3 1.0

Reference:

T.M.Larsen, M.M.Benning, G.E.Wesenberg, I.Rayment, G.H.Reed. Ligand-Induced Domain Movement in Pyruvate Kinase: Structure of the Enzyme From Rabbit Muscle with MG2+, K+, and L-Phospholactate at 2.7 A Resolution. Arch.Biochem.Biophys. V. 345 199 1997.
ISSN: ISSN 0003-9861
PubMed: 9308890
DOI: 10.1006/ABBI.1997.0257
Page generated: Tue Aug 13 02:07:24 2024

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