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Magnesium in PDB 3srd: Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate.

Enzymatic activity of Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate.

All present enzymatic activity of Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate.:
2.7.1.40;

Protein crystallography data

The structure of Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate., PDB code: 3srd 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) 54.18 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 95.050, 117.370, 110.460, 90.00, 113.56, 90.00
R / Rfree (%) 25.3 / 27.9

Other elements in 3srd:

The structure of Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate. also contains other interesting chemical elements:

Potassium (K) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate. (pdb code 3srd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate., PDB code: 3srd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3srd

Go back to Magnesium Binding Sites List in 3srd
Magnesium binding site 1 out of 4 in the Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg535

b:31.3
occ:1.00
 OE2 A:GLU272 1.9 60.1 1.0
OD2 A:ASP296 2.0 53.3 1.0
O4 A:OXL533 2.2 52.6 1.0
O1 A:OXL533 2.6 52.7 1.0
O A:HOH555 2.6 28.1 1.0
C2 A:OXL533 3.0 53.0 1.0
C1 A:OXL533 3.1 53.2 1.0
CD A:GLU272 3.2 60.8 1.0
CG A:ASP296 3.2 52.9 1.0
CB A:ASP296 3.9 52.0 1.0
OE1 A:GLU272 3.9 61.3 1.0
O2 A:OXL533 4.1 52.8 1.0
NZ A:LYS270 4.2 56.5 1.0
CG A:GLU272 4.2 60.3 1.0
OD1 A:ASP296 4.2 53.8 1.0
O A:HOH568 4.3 39.2 1.0
O3 A:OXL533 4.3 53.8 1.0
CE1 A:PHE244 4.4 63.0 1.0
CZ A:PHE244 4.4 62.9 1.0
N A:ASP296 4.7 50.9 1.0
CE A:LYS270 4.7 56.7 1.0
CA A:ASP296 4.9 51.8 1.0

Magnesium binding site 2 out of 4 in 3srd

Go back to Magnesium Binding Sites List in 3srd
Magnesium binding site 2 out of 4 in the Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:0.7
occ:1.00
 OE2 B:GLU272 2.2 74.6 1.0
OD2 B:ASP296 2.2 67.2 1.0
O1 B:OXL533 2.4 83.9 1.0
O4 B:OXL533 2.7 82.9 1.0
C1 B:OXL533 3.2 84.0 1.0
C2 B:OXL533 3.3 83.9 1.0
CD B:GLU272 3.4 75.5 1.0
CG B:ASP296 3.4 66.4 1.0
OE1 B:GLU272 4.1 76.6 1.0
NZ B:LYS270 4.2 71.8 1.0
CB B:ASP296 4.2 65.2 1.0
OD1 B:ASP296 4.4 67.2 1.0
O3 B:OXL533 4.4 84.3 1.0
CG B:GLU272 4.5 74.6 1.0
CE1 B:PHE244 4.5 78.7 1.0
O2 B:OXL533 4.6 83.9 1.0
CZ B:PHE244 4.6 78.0 1.0
CE B:LYS270 4.8 72.2 1.0
N B:ASP296 4.9 62.9 1.0

Magnesium binding site 3 out of 4 in 3srd

Go back to Magnesium Binding Sites List in 3srd
Magnesium binding site 3 out of 4 in the Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:50.1
occ:1.00
 OE2 C:GLU272 1.9 68.1 1.0
OD2 C:ASP296 2.0 59.9 1.0
O3 C:OXL533 2.1 66.4 1.0
O2 C:OXL533 2.5 66.9 1.0
C1 C:OXL533 3.0 66.7 1.0
O C:HOH544 3.1 28.1 1.0
CD C:GLU272 3.2 68.5 1.0
C2 C:OXL533 3.2 66.8 1.0
CG C:ASP296 3.2 59.0 1.0
CB C:ASP296 3.9 57.5 1.0
OE1 C:GLU272 3.9 69.1 1.0
CG C:GLU272 4.2 67.9 1.0
NZ C:LYS270 4.2 65.1 1.0
O1 C:OXL533 4.2 67.0 1.0
OD1 C:ASP296 4.2 60.1 1.0
O4 C:OXL533 4.4 66.2 1.0
CE1 C:PHE244 4.5 70.5 1.0
CZ C:PHE244 4.5 70.2 1.0
N C:ASP296 4.6 56.2 1.0
K C:K703 4.7 78.7 1.0
CE C:LYS270 4.7 65.1 1.0
CA C:ASP296 4.9 57.0 1.0

Magnesium binding site 4 out of 4 in 3srd

Go back to Magnesium Binding Sites List in 3srd
Magnesium binding site 4 out of 4 in the Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human M2 Pyruvate Kinase in Complex with Fructose 1-6 Bisphosphate and Oxalate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:53.8
occ:1.00
 O1 D:OXL533 1.9 43.4 1.0
OE2 D:GLU272 2.0 61.9 1.0
OD2 D:ASP296 2.2 55.7 1.0
O4 D:OXL533 2.5 43.4 1.0
C1 D:OXL533 2.9 43.4 1.0
C2 D:OXL533 3.2 42.8 1.0
CD D:GLU272 3.3 62.5 1.0
CG D:ASP296 3.3 55.3 1.0
CB D:ASP296 3.9 54.4 1.0
O3 D:OXL533 4.0 43.5 1.0
OE1 D:GLU272 4.1 63.1 1.0
NZ D:LYS270 4.2 57.6 1.0
CG D:GLU272 4.2 62.0 1.0
OD1 D:ASP296 4.4 56.5 1.0
O2 D:OXL533 4.4 42.5 1.0
N D:ASP296 4.5 53.1 1.0
CE D:LYS270 4.7 57.8 1.0
CE1 D:PHE244 4.8 65.7 1.0
CZ D:PHE244 4.8 65.6 1.0
CA D:ASP296 4.9 54.3 1.0
CB D:ALA293 5.0 50.3 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 03:13:20 2025

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