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Magnesium in PDB 6gg6: Crystal Structure of M2 Pyk in Complex with Serine.

Enzymatic activity of Crystal Structure of M2 Pyk in Complex with Serine.

All present enzymatic activity of Crystal Structure of M2 Pyk in Complex with Serine.:
2.7.1.40;

Protein crystallography data

The structure of Crystal Structure of M2 Pyk in Complex with Serine., PDB code: 6gg6 was solved by I.W.Mcnae, M.Yuan, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 116.50 / 2.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 93.350, 108.940, 124.340, 89.72, 71.13, 66.94
R / Rfree (%) 23.6 / 25.2

Other elements in 6gg6:

The structure of Crystal Structure of M2 Pyk in Complex with Serine. also contains other interesting chemical elements:

Potassium (K) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of M2 Pyk in Complex with Serine. (pdb code 6gg6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of M2 Pyk in Complex with Serine., PDB code: 6gg6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6gg6

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Magnesium binding site 1 out of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of M2 Pyk in Complex with Serine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:58.3
occ:1.00
 OE1 A:GLU272 2.3 72.1 1.0
OD2 A:ASP296 2.5 65.6 1.0
CD A:GLU272 3.4 73.4 1.0
NZ A:LYS270 3.5 65.4 1.0
CG A:ASP296 3.6 66.9 1.0
CG A:GLU272 4.0 72.5 1.0
CE A:LYS270 4.1 63.6 1.0
N A:ASP296 4.2 64.0 1.0
CB A:ASP296 4.2 66.2 1.0
CB A:ALA293 4.3 57.1 1.0
OE2 A:GLU272 4.5 76.0 1.0
OD1 A:ASP296 4.6 67.0 1.0
CG2 A:THR328 4.8 66.4 1.0
CA A:ASP296 4.9 64.7 1.0
CA A:GLY295 4.9 61.2 1.0

Magnesium binding site 2 out of 8 in 6gg6

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Magnesium binding site 2 out of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of M2 Pyk in Complex with Serine. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:49.7
occ:1.00
 OE1 B:GLU272 3.0 83.0 1.0
OD2 B:ASP296 3.4 77.0 1.0
NZ B:LYS270 3.5 82.0 1.0
CB B:ALA293 3.6 72.5 1.0
CG2 B:THR328 3.9 60.3 1.0
CD B:GLU272 3.9 87.8 1.0
CE B:LYS270 4.0 83.6 1.0
CG B:GLU272 4.3 87.2 1.0
N B:ASP296 4.3 76.4 1.0
CG B:ASP296 4.5 78.3 1.0
CA B:ALA293 4.5 71.7 1.0
CA B:GLY295 4.6 71.3 1.0
N B:GLY295 4.6 70.2 1.0
O B:ALA293 4.7 70.3 1.0
C B:ALA293 4.7 69.9 1.0
CB B:ASP296 4.8 78.0 1.0

Magnesium binding site 3 out of 8 in 6gg6

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Magnesium binding site 3 out of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of M2 Pyk in Complex with Serine. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:58.0
occ:1.00
 OD2 C:ASP296 2.9 64.8 1.0
OE1 C:GLU272 2.9 65.2 1.0
N C:ASP296 3.7 62.8 1.0
CB C:ALA293 3.8 54.5 1.0
CG C:ASP296 3.8 66.6 1.0
CD C:GLU272 3.8 66.7 1.0
NZ C:LYS270 3.9 62.0 1.0
CG C:GLU272 4.1 64.8 1.0
CG2 C:THR328 4.1 62.7 1.0
CA C:GLY295 4.1 62.2 1.0
CB C:ASP296 4.2 65.8 1.0
N C:GLY295 4.3 61.1 1.0
CE C:LYS270 4.4 61.7 1.0
C C:GLY295 4.4 62.9 1.0
O C:ALA293 4.5 53.2 1.0
CA C:ASP296 4.6 64.1 1.0
C C:ALA293 4.6 53.9 1.0
CA C:ALA293 4.7 54.1 1.0
OD1 C:ASP296 4.9 67.2 1.0
OE2 C:GLU272 5.0 68.9 1.0

Magnesium binding site 4 out of 8 in 6gg6

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Magnesium binding site 4 out of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of M2 Pyk in Complex with Serine. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:57.4
occ:1.00
 OE1 D:GLU272 2.8 80.4 1.0
NZ D:LYS270 3.1 74.5 1.0
OD2 D:ASP296 3.4 79.6 1.0
CE D:LYS270 3.7 74.9 1.0
CB D:ALA293 3.8 67.0 1.0
CD D:GLU272 3.8 82.7 1.0
CG2 D:THR328 4.2 72.4 1.0
CG D:GLU272 4.2 81.4 1.0
CG D:ASP296 4.5 79.5 1.0
N D:ASP296 4.5 74.2 1.0
CA D:ALA293 4.7 65.5 1.0
OE2 D:GLU272 4.8 84.3 1.0
CA D:GLY295 4.9 69.5 1.0
CB D:ASP296 4.9 77.3 1.0
O D:ALA293 4.9 68.0 1.0
N D:GLY295 5.0 67.8 1.0
C D:ALA293 5.0 65.8 1.0

Magnesium binding site 5 out of 8 in 6gg6

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Magnesium binding site 5 out of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of M2 Pyk in Complex with Serine. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg602

b:58.1
occ:1.00
 OE1 E:GLU272 3.0 74.9 1.0
OD2 E:ASP296 3.2 64.8 1.0
NZ E:LYS270 3.6 75.5 1.0
CB E:ALA293 3.8 65.6 1.0
CG2 E:THR328 3.9 67.7 1.0
CD E:GLU272 4.0 77.2 1.0
CE E:LYS270 4.2 74.9 1.0
N E:ASP296 4.2 64.5 1.0
CG E:ASP296 4.3 66.1 1.0
CG E:GLU272 4.3 74.5 1.0
CA E:GLY295 4.5 62.0 1.0
N E:GLY295 4.5 61.4 1.0
CA E:ALA293 4.6 63.5 1.0
O E:ALA293 4.7 59.0 1.0
CB E:ASP296 4.7 65.5 1.0
C E:ALA293 4.7 61.7 1.0
C E:GLY295 4.9 62.4 1.0

Magnesium binding site 6 out of 8 in 6gg6

Go back to Magnesium Binding Sites List in 6gg6
Magnesium binding site 6 out of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of M2 Pyk in Complex with Serine. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:66.7
occ:1.00
 OE1 F:GLU272 2.4 75.5 1.0
OD2 F:ASP296 2.6 70.2 1.0
CD F:GLU272 3.5 75.4 1.0
NZ F:LYS270 3.5 71.0 1.0
CG F:ASP296 3.7 71.8 1.0
CG F:GLU272 4.0 73.0 1.0
N F:ASP296 4.1 69.4 1.0
CB F:ALA293 4.1 61.0 1.0
CE F:LYS270 4.1 70.3 1.0
CB F:ASP296 4.2 71.0 1.0
OE2 F:GLU272 4.5 78.0 1.0
CG2 F:THR328 4.7 66.0 1.0
OD1 F:ASP296 4.7 72.3 1.0
CA F:GLY295 4.7 65.5 1.0
CA F:ASP296 4.8 70.0 1.0
C F:GLY295 4.9 66.6 1.0
N F:GLY295 5.0 63.6 1.0
O F:ALA293 5.0 59.9 1.0

Magnesium binding site 7 out of 8 in 6gg6

Go back to Magnesium Binding Sites List in 6gg6
Magnesium binding site 7 out of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of M2 Pyk in Complex with Serine. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg602

b:61.0
occ:1.00
 OE1 G:GLU272 2.5 78.3 1.0
OD2 G:ASP296 2.5 65.0 1.0
NZ G:LYS270 3.5 68.5 1.0
CD G:GLU272 3.6 78.3 1.0
CG G:ASP296 3.7 67.0 1.0
CG G:GLU272 4.2 77.5 1.0
CE G:LYS270 4.2 68.1 1.0
N G:ASP296 4.2 67.7 1.0
CB G:ASP296 4.4 68.0 1.0
CB G:ALA293 4.4 65.0 1.0
OE2 G:GLU272 4.6 79.4 1.0
OD1 G:ASP296 4.7 66.4 1.0
CG2 G:THR328 4.8 61.5 1.0
CA G:GLY295 4.9 65.1 1.0
CA G:ASP296 5.0 68.3 1.0

Magnesium binding site 8 out of 8 in 6gg6

Go back to Magnesium Binding Sites List in 6gg6
Magnesium binding site 8 out of 8 in the Crystal Structure of M2 Pyk in Complex with Serine.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of M2 Pyk in Complex with Serine. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg602

b:61.0
occ:1.00
 OE1 H:GLU272 2.6 78.0 1.0
OD2 H:ASP296 2.8 70.3 1.0
CD H:GLU272 3.5 79.5 1.0
NZ H:LYS270 3.7 70.2 1.0
CB H:ALA293 3.7 63.4 1.0
CG H:ASP296 3.8 71.5 1.0
N H:ASP296 3.8 67.5 1.0
CG H:GLU272 3.9 78.3 1.0
CE H:LYS270 4.2 70.3 1.0
CB H:ASP296 4.2 70.4 1.0
CG2 H:THR328 4.4 56.0 1.0
CA H:GLY295 4.4 63.7 1.0
O H:ALA293 4.5 63.7 1.0
N H:GLY295 4.5 61.8 1.0
CA H:ALA293 4.6 63.2 1.0
C H:GLY295 4.6 64.9 1.0
OE2 H:GLU272 4.7 80.0 1.0
CA H:ASP296 4.7 69.5 1.0
C H:ALA293 4.7 63.0 1.0
OD1 H:ASP296 4.9 72.1 1.0

Reference:

M.Yuan, I.W.Mcnae, Y.Chen, E.A.Blackburn, M.A.Wear, P.A.M.Michels, L.A.Fothergill-Gilmore, T.Hupp, M.D.Walkinshaw. An Allostatic Mechanism For M2 Pyruvate Kinase As An Amino-Acid Sensor. Biochem. J. V. 475 1821 2018.
ISSN: ESSN 1470-8728
PubMed: 29748232
DOI: 10.1042/BCJ20180171
Page generated: Tue Oct 1 01:10:26 2024

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