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Magnesium in PDB 3srf: Human M1 Pyruvate Kinase

Enzymatic activity of Human M1 Pyruvate Kinase

All present enzymatic activity of Human M1 Pyruvate Kinase:
2.7.1.40;

Protein crystallography data

The structure of Human M1 Pyruvate Kinase, PDB code: 3srf was solved by H.P.Morgan, F.O'reilly, R.Palmer, I.W.Mcnae, M.W.Nowicki, M.A.Wear, 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) 40.00 / 2.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 238.003, 192.222, 109.060, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 28

Other elements in 3srf:

The structure of Human M1 Pyruvate Kinase also contains other interesting chemical elements:

Potassium (K) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human M1 Pyruvate Kinase (pdb code 3srf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Human M1 Pyruvate Kinase, PDB code: 3srf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3srf

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Magnesium binding site 1 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg533

b:45.9
occ:1.00
 OE1 C:GLU271 2.1 30.1 1.0
OD2 C:ASP295 2.7 32.5 1.0
O2 C:PYR534 2.8 46.1 1.0
CD C:GLU271 3.1 30.0 1.0
C1 C:PYR534 3.3 46.4 1.0
CG C:ASP295 3.4 32.2 1.0
OE2 C:GLU271 3.6 29.9 1.0
NZ C:LYS269 3.8 25.4 1.0
O1 C:PYR534 3.9 46.5 1.0
C2 C:PYR534 4.0 46.4 1.0
O3 C:PYR534 4.0 46.2 1.0
CB C:ASP295 4.1 31.7 1.0
CZ C:PHE243 4.1 33.7 1.0
CE C:LYS269 4.2 26.7 1.0
OD1 C:ASP295 4.2 32.7 1.0
CE1 C:PHE243 4.3 34.0 1.0
CG C:GLU271 4.4 29.7 1.0
CE2 C:PHE243 4.8 33.5 1.0
N C:ASP295 4.9 31.4 1.0

Magnesium binding site 2 out of 8 in 3srf

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Magnesium binding site 2 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg533

b:27.0
occ:1.00
 OD2 A:ASP295 2.1 32.9 1.0
O3 A:PYR534 2.4 39.6 1.0
O2 A:PYR534 2.4 38.3 1.0
OE1 A:GLU271 2.6 30.4 1.0
C2 A:PYR534 3.1 39.1 1.0
C1 A:PYR534 3.2 38.6 1.0
CG A:ASP295 3.3 32.1 1.0
O A:HOH594 3.5 13.5 1.0
CD A:GLU271 3.7 29.9 1.0
NZ A:LYS269 3.9 24.8 1.0
OE2 A:GLU271 4.1 29.6 1.0
CB A:ASP295 4.2 31.6 1.0
OD1 A:ASP295 4.2 32.5 1.0
O A:HOH551 4.2 25.9 1.0
O1 A:PYR534 4.4 38.1 1.0
C3 A:PYR534 4.6 38.8 1.0
O A:HOH587 4.6 37.3 1.0
CE A:LYS269 4.6 24.4 1.0
CE1 A:PHE243 4.7 34.0 1.0
N A:ASP295 4.8 31.6 1.0
CZ A:PHE243 4.8 33.9 1.0
CG A:GLU271 5.0 28.6 1.0

Magnesium binding site 3 out of 8 in 3srf

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Magnesium binding site 3 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg533

b:26.3
occ:1.00
 O2 B:PYR534 2.0 42.7 1.0
OD2 B:ASP295 2.1 32.6 1.0
OE1 B:GLU271 2.1 34.8 1.0
C1 B:PYR534 2.9 43.0 1.0
O3 B:PYR534 2.9 43.1 1.0
CG B:ASP295 3.2 32.0 1.0
CD B:GLU271 3.3 34.4 1.0
C2 B:PYR534 3.3 43.1 1.0
CB B:ASP295 3.8 31.4 1.0
OE2 B:GLU271 3.8 34.5 1.0
O1 B:PYR534 4.0 43.4 1.0
NZ B:LYS269 4.2 27.3 1.0
OD1 B:ASP295 4.3 32.6 1.0
CE B:LYS269 4.4 28.3 1.0
CB B:ALA292 4.5 27.5 1.0
CG B:GLU271 4.5 33.6 1.0
N B:ASP295 4.6 30.7 1.0
CE1 B:PHE243 4.6 34.4 1.0
K B:K532 4.8 94.2 1.0
C3 B:PYR534 4.8 43.0 1.0
CA B:ASP295 4.8 31.3 1.0
CZ B:PHE243 4.9 34.2 1.0

Magnesium binding site 4 out of 8 in 3srf

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Magnesium binding site 4 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg533

b:51.2
occ:1.00
 OD2 D:ASP295 2.1 34.5 1.0
OE1 D:GLU271 2.2 34.2 1.0
O3 D:PYR534 2.4 51.6 1.0
O2 D:PYR534 2.6 51.8 1.0
O D:HOH556 3.0 10.2 1.0
C2 D:PYR534 3.2 52.1 1.0
CG D:ASP295 3.3 34.4 1.0
C1 D:PYR534 3.3 51.9 1.0
CD D:GLU271 3.4 34.3 1.0
CZ D:PHE243 3.9 36.6 1.0
NZ D:LYS269 4.0 29.4 1.0
OE2 D:GLU271 4.0 34.4 1.0
CE1 D:PHE243 4.0 36.6 1.0
CB D:ASP295 4.0 34.1 1.0
OD1 D:ASP295 4.2 34.6 1.0
CG D:GLU271 4.4 33.8 1.0
O1 D:PYR534 4.5 52.0 1.0
K D:K532 4.7 48.5 1.0
C3 D:PYR534 4.7 52.4 1.0
CE D:LYS269 4.7 29.7 1.0
CE2 D:PHE243 4.8 36.6 1.0
OG D:SER242 4.9 34.1 1.0
CD1 D:PHE243 5.0 36.1 1.0

Magnesium binding site 5 out of 8 in 3srf

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Magnesium binding site 5 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg533

b:58.5
occ:1.00
 OD2 E:ASP295 2.0 49.3 1.0
OE1 E:GLU271 2.0 54.6 1.0
O2 E:PYR534 2.3 62.9 1.0
O3 E:PYR534 2.9 63.2 1.0
CD E:GLU271 3.1 54.6 1.0
CG E:ASP295 3.2 49.5 1.0
C1 E:PYR534 3.2 63.2 1.0
C2 E:PYR534 3.4 63.3 1.0
NZ E:LYS269 3.5 52.2 1.0
OE2 E:GLU271 3.7 54.7 1.0
CB E:ASP295 3.8 49.2 1.0
CE1 E:PHE243 3.9 59.2 1.0
CZ E:PHE243 4.1 59.2 1.0
OD1 E:ASP295 4.1 50.0 1.0
CE E:LYS269 4.2 52.3 1.0
K E:K532 4.3 85.0 1.0
CG E:GLU271 4.3 54.3 1.0
O1 E:PYR534 4.3 63.1 1.0
CD1 E:PHE243 4.8 59.0 1.0
C3 E:PYR534 4.9 63.1 1.0

Magnesium binding site 6 out of 8 in 3srf

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Magnesium binding site 6 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg533

b:21.2
occ:1.00
 OE1 F:GLU271 1.9 30.6 1.0
O2 F:PYR534 2.1 38.8 1.0
OD2 F:ASP295 2.1 37.5 1.0
O3 F:PYR534 2.7 39.0 1.0
C1 F:PYR534 3.0 38.9 1.0
CD F:GLU271 3.0 30.4 1.0
CG F:ASP295 3.2 36.7 1.0
C2 F:PYR534 3.2 39.0 1.0
OE2 F:GLU271 3.4 30.8 1.0
CB F:ASP295 3.6 35.8 1.0
CZ F:PHE243 4.1 33.4 1.0
O1 F:PYR534 4.1 38.8 1.0
NZ F:LYS269 4.1 27.2 1.0
CE F:LYS269 4.2 27.3 1.0
OD1 F:ASP295 4.3 37.8 1.0
CG F:GLU271 4.3 29.9 1.0
CE1 F:PHE243 4.5 33.4 1.0
CB F:ALA292 4.5 33.7 1.0
CE2 F:PHE243 4.5 33.5 1.0
O F:HOH581 4.6 13.4 1.0
N F:ASP295 4.7 35.4 1.0
C3 F:PYR534 4.7 38.8 1.0
CB F:GLU271 4.8 29.4 1.0
CA F:ASP295 4.8 35.6 1.0

Magnesium binding site 7 out of 8 in 3srf

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Magnesium binding site 7 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg533

b:33.5
occ:1.00
 OD2 G:ASP295 2.0 36.1 1.0
OE1 G:GLU271 2.0 40.9 1.0
O2 G:PYR534 2.1 67.5 1.0
O G:HOH584 2.5 31.0 1.0
O3 G:PYR534 2.7 66.8 1.0
C1 G:PYR534 3.0 67.2 1.0
CG G:ASP295 3.1 36.2 1.0
CD G:GLU271 3.2 41.3 1.0
C2 G:PYR534 3.3 67.1 1.0
OE2 G:GLU271 3.6 41.5 1.0
CB G:ASP295 3.7 35.9 1.0
NZ G:LYS269 3.9 39.4 1.0
OD1 G:ASP295 4.2 36.6 1.0
O G:HOH585 4.2 6.1 1.0
O1 G:PYR534 4.2 67.1 1.0
CE G:LYS269 4.4 39.6 1.0
CG G:GLU271 4.4 41.3 1.0
CZ G:PHE243 4.5 47.0 1.0
CE1 G:PHE243 4.6 46.9 1.0
N G:ASP295 4.6 35.9 1.0
CA G:ASP295 4.8 35.8 1.0
C3 G:PYR534 4.8 66.9 1.0
CB G:GLU271 4.9 41.4 1.0
K G:K532 4.9 60.7 1.0
CB G:ALA292 4.9 36.8 1.0

Magnesium binding site 8 out of 8 in 3srf

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Magnesium binding site 8 out of 8 in the Human M1 Pyruvate Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human M1 Pyruvate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg533

b:14.2
occ:1.00
 OE1 H:GLU271 2.1 31.0 1.0
OD2 H:ASP295 2.2 34.9 1.0
O2 H:PYR534 2.7 69.8 1.0
C1 H:PYR534 3.1 70.3 1.0
CD H:GLU271 3.2 31.7 1.0
O3 H:PYR534 3.2 70.0 1.0
C2 H:PYR534 3.4 70.1 1.0
CG H:ASP295 3.4 34.8 1.0
NZ H:LYS269 3.5 25.8 1.0
CE H:LYS269 3.6 27.1 1.0
OE2 H:GLU271 3.8 32.3 1.0
O1 H:PYR534 3.9 70.8 1.0
CB H:ASP295 4.2 34.4 1.0
CG H:GLU271 4.3 31.3 1.0
CB H:ALA292 4.3 31.1 1.0
OD1 H:ASP295 4.4 35.5 1.0
C3 H:PYR534 4.6 69.7 1.0
CZ H:PHE243 4.9 35.5 1.0
CB H:GLU271 5.0 31.0 1.0

Reference:

H.P.Morgan, F.O'reilly, R.Palmer, I.W.Mcnae, M.W.Nowicki, M.A.Wear, L.A.Fothergill-Gilmore, M.D.Walkinshaw. Allosetric Regulation of M2 Pyruvate Kinase. To Be Published.
Page generated: Mon Aug 11 03:13:26 2025

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