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Magnesium in PDB 4fxf: Structure of M2 Pyruvate Kinase in Complex with Phenylalanine

Enzymatic activity of Structure of M2 Pyruvate Kinase in Complex with Phenylalanine

All present enzymatic activity of Structure of M2 Pyruvate Kinase in Complex with Phenylalanine:
2.7.1.40;

Protein crystallography data

The structure of Structure of M2 Pyruvate Kinase in Complex with Phenylalanine, PDB code: 4fxf was solved by M.D.Walkinshaw, H.P.Morgan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.67 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.600, 139.350, 111.280, 90.00, 90.52, 90.00
R / Rfree (%) 21.2 / 25.4

Other elements in 4fxf:

The structure of Structure of M2 Pyruvate Kinase in Complex with Phenylalanine also contains other interesting chemical elements:

Potassium (K) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of M2 Pyruvate Kinase in Complex with Phenylalanine (pdb code 4fxf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of M2 Pyruvate Kinase in Complex with Phenylalanine, PDB code: 4fxf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4fxf

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Magnesium binding site 1 out of 6 in the Structure of M2 Pyruvate Kinase in Complex with Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of M2 Pyruvate Kinase in Complex with Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:32.5
occ:1.00
 O A:HOH766 1.9 29.1 1.0
OD2 A:ASP296 2.0 33.0 1.0
OE2 A:GLU272 2.2 35.5 1.0
O A:HOH701 2.3 30.4 1.0
O1 A:OXL601 2.3 39.5 1.0
O4 A:OXL601 2.4 38.7 1.0
C1 A:OXL601 3.1 39.5 1.0
C2 A:OXL601 3.1 39.1 1.0
CG A:ASP296 3.2 33.2 1.0
CD A:GLU272 3.2 35.9 1.0
OE1 A:GLU272 3.5 35.8 1.0
CB A:ASP296 3.8 32.9 1.0
CZ A:PHE244 4.1 38.2 1.0
NZ A:LYS270 4.2 30.8 1.0
OD1 A:ASP296 4.2 33.8 1.0
O3 A:OXL601 4.3 39.8 1.0
O2 A:OXL601 4.4 38.8 1.0
O A:HOH768 4.4 41.0 1.0
O A:HOH702 4.4 20.3 1.0
CE1 A:PHE244 4.5 38.1 1.0
CG A:GLU272 4.5 35.9 1.0
CE A:LYS270 4.5 30.9 1.0
N A:ASP296 4.5 32.1 1.0
CE2 A:PHE244 4.6 38.4 1.0
CA A:ASP296 4.8 32.8 1.0
CB A:GLU272 4.8 35.6 1.0

Magnesium binding site 2 out of 6 in 4fxf

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Magnesium binding site 2 out of 6 in the Structure of M2 Pyruvate Kinase in Complex with Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of M2 Pyruvate Kinase in Complex with Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg603

b:56.6
occ:1.00
 OD2 D:ASP296 1.9 39.6 1.0
O2G D:ATP604 2.3 50.5 1.0
O4 D:OXL601 2.3 54.4 1.0
OE2 D:GLU272 2.4 44.3 1.0
O1 D:OXL601 2.6 53.9 1.0
CG D:ASP296 3.1 40.2 1.0
C2 D:OXL601 3.2 54.1 1.0
C1 D:OXL601 3.3 54.2 1.0
CD D:GLU272 3.3 44.6 1.0
PG D:ATP604 3.5 51.2 1.0
OE1 D:GLU272 3.7 45.0 1.0
O1G D:ATP604 3.8 51.0 1.0
O D:HOH716 3.8 46.0 1.0
O D:HOH749 3.8 33.8 1.0
CB D:ASP296 3.9 39.8 1.0
O D:HOH703 3.9 37.2 1.0
NZ D:LYS270 4.0 40.9 1.0
OD1 D:ASP296 4.1 41.1 1.0
O3G D:ATP604 4.3 51.0 1.0
CZ D:PHE244 4.4 45.0 1.0
CE1 D:PHE244 4.4 45.3 1.0
O2 D:OXL601 4.4 53.7 1.0
O D:HOH701 4.5 34.1 1.0
CE D:LYS270 4.5 40.7 1.0
O3 D:OXL601 4.6 54.2 1.0
CG D:GLU272 4.6 44.3 1.0
O3B D:ATP604 4.7 50.8 1.0
N D:ASP296 4.7 38.8 1.0
CA D:ASP296 4.9 39.6 1.0
CB D:GLU272 5.0 43.8 1.0

Magnesium binding site 3 out of 6 in 4fxf

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Magnesium binding site 3 out of 6 in the Structure of M2 Pyruvate Kinase in Complex with Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of M2 Pyruvate Kinase in Complex with Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg605

b:70.5
occ:1.00
 O D:HOH701 2.0 34.1 1.0
O2B D:ATP604 2.0 50.3 1.0
O2A D:ATP604 2.0 50.7 1.0
O D:HOH702 2.1 43.5 1.0
O D:HOH748 2.2 47.1 1.0
O3G D:ATP604 2.7 51.0 1.0
PB D:ATP604 3.3 50.6 1.0
PA D:ATP604 3.3 50.4 1.0
O3A D:ATP604 3.7 50.7 1.0
OD2 D:ASP178 3.7 65.6 1.0
PG D:ATP604 3.8 51.2 1.0
O D:HOH727 3.8 39.6 1.0
OG D:SER362 3.8 36.7 1.0
CB D:SER362 3.9 37.0 1.0
O3B D:ATP604 4.0 50.8 1.0
CG2 D:THR328 4.0 37.3 1.0
O5' D:ATP604 4.1 50.8 1.0
O2G D:ATP604 4.1 50.5 1.0
C5' D:ATP604 4.1 51.4 1.0
O D:HOH703 4.3 37.2 1.0
OG1 D:THR328 4.3 37.0 1.0
O1A D:ATP604 4.5 50.5 1.0
O1B D:ATP604 4.5 50.5 1.0
C2 D:OXL601 4.6 54.1 1.0
O2 D:OXL601 4.6 53.7 1.0
NH2 D:ARG73 4.6 40.0 1.0
C1 D:OXL601 4.7 54.2 1.0
CG D:ASP178 4.7 65.8 1.0
CB D:THR328 4.8 36.9 1.0
O3 D:OXL601 4.8 54.2 1.0

Magnesium binding site 4 out of 6 in 4fxf

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Magnesium binding site 4 out of 6 in the Structure of M2 Pyruvate Kinase in Complex with Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of M2 Pyruvate Kinase in Complex with Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:33.2
occ:1.00
 O C:HOH704 2.0 46.2 1.0
OD2 C:ASP296 2.0 32.6 1.0
O1 C:OXL601 2.2 41.1 1.0
O C:HOH703 2.3 17.3 1.0
OE2 C:GLU272 2.3 37.0 1.0
O4 C:OXL601 2.5 41.7 1.0
C1 C:OXL601 3.1 41.1 1.0
CG C:ASP296 3.2 32.8 1.0
C2 C:OXL601 3.2 41.4 1.0
CD C:GLU272 3.4 37.0 1.0
OE1 C:GLU272 3.8 36.8 1.0
CB C:ASP296 3.8 32.5 1.0
O C:HOH792 4.1 31.2 1.0
NZ C:LYS270 4.2 33.0 1.0
CZ C:PHE244 4.2 37.1 1.0
O C:HOH763 4.2 34.3 1.0
OD1 C:ASP296 4.2 33.7 1.0
O3 C:OXL601 4.3 40.6 1.0
O2 C:OXL601 4.4 41.4 1.0
N C:ASP296 4.5 31.9 1.0
CE1 C:PHE244 4.5 37.3 1.0
CE C:LYS270 4.7 33.2 1.0
CG C:GLU272 4.7 36.8 1.0
O C:HOH722 4.8 28.4 1.0
CA C:ASP296 4.8 32.5 1.0
CE2 C:PHE244 4.8 37.1 1.0
O C:HOH791 4.9 31.3 1.0
CB C:GLU272 4.9 36.8 1.0
O C:HOH760 4.9 50.8 1.0
CB C:ALA293 5.0 31.5 1.0

Magnesium binding site 5 out of 6 in 4fxf

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Magnesium binding site 5 out of 6 in the Structure of M2 Pyruvate Kinase in Complex with Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of M2 Pyruvate Kinase in Complex with Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:40.0
occ:1.00
 O1G B:ATP604 1.9 45.6 1.0
OD2 B:ASP296 2.1 35.3 1.0
O4 B:OXL601 2.2 53.1 1.0
OE2 B:GLU272 2.3 39.7 1.0
O B:HOH703 2.6 46.4 1.0
O1 B:OXL601 2.6 52.6 1.0
C2 B:OXL601 3.1 52.9 1.0
PG B:ATP604 3.1 45.7 1.0
C1 B:OXL601 3.3 52.7 1.0
CG B:ASP296 3.3 35.2 1.0
CD B:GLU272 3.3 40.0 1.0
O3G B:ATP604 3.4 45.2 1.0
O B:HOH704 3.6 36.4 1.0
OE1 B:GLU272 3.7 40.7 1.0
CB B:ASP296 4.0 34.9 1.0
O2G B:ATP604 4.0 45.3 1.0
NZ B:LYS270 4.2 35.8 1.0
O3B B:ATP604 4.3 45.6 1.0
OD1 B:ASP296 4.3 35.4 1.0
CE1 B:PHE244 4.3 38.9 1.0
O2 B:OXL601 4.3 52.7 1.0
O B:HOH701 4.5 49.0 1.0
O3 B:OXL601 4.5 52.8 1.0
CZ B:PHE244 4.6 39.2 1.0
CE B:LYS270 4.7 36.0 1.0
CG B:GLU272 4.7 38.8 1.0
N B:ASP296 4.8 34.4 1.0
K B:K602 4.9 40.0 1.0

Magnesium binding site 6 out of 6 in 4fxf

Go back to Magnesium Binding Sites List in 4fxf
Magnesium binding site 6 out of 6 in the Structure of M2 Pyruvate Kinase in Complex with Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of M2 Pyruvate Kinase in Complex with Phenylalanine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:39.8
occ:1.00
 O B:HOH702 1.9 31.3 1.0
O2G B:ATP604 2.0 45.3 1.0
O B:HOH701 2.0 49.0 1.0
O1B B:ATP604 2.0 45.8 1.0
O2A B:ATP604 2.0 47.2 1.0
O B:HOH763 2.2 31.8 1.0
PB B:ATP604 3.1 45.4 1.0
PA B:ATP604 3.2 46.8 1.0
PG B:ATP604 3.2 45.7 1.0
O3A B:ATP604 3.4 46.1 1.0
O3B B:ATP604 3.6 45.6 1.0
O5' B:ATP604 3.7 47.5 1.0
O1G B:ATP604 3.7 45.6 1.0
OG B:SER362 3.9 36.2 1.0
O B:HOH801 4.1 34.4 1.0
CB B:SER362 4.2 36.5 1.0
C2 B:OXL601 4.2 52.9 1.0
OD2 B:ASP178 4.2 53.5 1.0
CG2 B:THR328 4.2 34.1 1.0
O2 B:OXL601 4.3 52.7 1.0
C1 B:OXL601 4.3 52.7 1.0
OG1 B:THR328 4.4 33.8 1.0
O3G B:ATP604 4.4 45.2 1.0
O2B B:ATP604 4.5 45.4 1.0
O1A B:ATP604 4.5 46.7 1.0
O3 B:OXL601 4.5 52.8 1.0
O B:HOH776 4.5 32.4 1.0
O4 B:OXL601 4.6 53.1 1.0
NH2 B:ARG73 4.7 33.6 1.0
O1 B:OXL601 4.8 52.6 1.0
NH1 B:ARG73 4.9 33.6 1.0
C5' B:ATP604 5.0 48.0 1.0
CB B:THR328 5.0 33.8 1.0

Reference:

H.P.Morgan, F.J.O'reilly, M.A.Wear, J.R.O'neill, L.A.Fothergill-Gilmore, T.Hupp, M.D.Walkinshaw. M2 Pyruvate Kinase Provides A Mechanism For Nutrient Sensing and Regulation of Cell Proliferation. Proc.Natl.Acad.Sci.Usa V. 110 5881 2013.
ISSN: ISSN 0027-8424
PubMed: 23530218
DOI: 10.1073/PNAS.1217157110
Page generated: Fri Aug 16 15:18:48 2024

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