Magnesium in PDB 7qdn: Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted
Enzymatic activity of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted
All present enzymatic activity of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted:
2.7.1.40;
Protein crystallography data
The structure of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted, PDB code: 7qdn
was solved by
A.Lulla,
M.Hyvonen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
103.69 /
1.70
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
207.448,
112.687,
188.333,
90,
91.36,
90
|
R / Rfree (%)
|
20.5 /
21.7
|
Other elements in 7qdn:
The structure of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted
(pdb code 7qdn). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted, PDB code: 7qdn:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 7qdn
Go back to
Magnesium Binding Sites List in 7qdn
Magnesium binding site 1 out
of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg603
b:48.5
occ:1.00
|
O4
|
A:OXD602
|
2.0
|
50.0
|
1.0
|
O
|
A:HOH750
|
2.1
|
45.3
|
1.0
|
OE2
|
A:GLU284
|
2.1
|
44.0
|
1.0
|
OD2
|
A:ASP308
|
2.1
|
48.9
|
1.0
|
O3
|
A:OXD602
|
2.1
|
48.7
|
1.0
|
O
|
A:HOH724
|
2.3
|
40.4
|
1.0
|
C2
|
A:OXD602
|
2.7
|
49.8
|
1.0
|
C1
|
A:OXD602
|
2.7
|
49.0
|
1.0
|
CD
|
A:GLU284
|
3.2
|
45.4
|
1.0
|
CG
|
A:ASP308
|
3.2
|
47.8
|
1.0
|
OE1
|
A:GLU284
|
3.6
|
46.2
|
1.0
|
CB
|
A:ASP308
|
3.7
|
42.6
|
1.0
|
O6
|
A:OXD602
|
3.9
|
50.3
|
1.0
|
O5
|
A:OXD602
|
4.0
|
48.5
|
1.0
|
NZ
|
A:LYS282
|
4.2
|
43.3
|
1.0
|
O
|
A:HOH883
|
4.3
|
49.7
|
1.0
|
OD1
|
A:ASP308
|
4.3
|
48.9
|
1.0
|
O
|
A:HOH844
|
4.3
|
55.6
|
1.0
|
N
|
A:ASP308
|
4.4
|
39.9
|
1.0
|
CE
|
A:LYS282
|
4.4
|
44.2
|
1.0
|
CG
|
A:GLU284
|
4.5
|
43.3
|
1.0
|
O
|
A:HOH755
|
4.5
|
47.2
|
1.0
|
CA
|
A:ASP308
|
4.7
|
40.9
|
1.0
|
CB
|
A:ALA305
|
4.7
|
36.8
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 7qdn
Go back to
Magnesium Binding Sites List in 7qdn
Magnesium binding site 2 out
of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg603
b:42.8
occ:1.00
|
OE2
|
B:GLU284
|
2.0
|
47.7
|
1.0
|
O6
|
B:OXD602
|
2.0
|
41.5
|
1.0
|
OD2
|
B:ASP308
|
2.1
|
43.1
|
1.0
|
O
|
B:HOH816
|
2.1
|
40.0
|
1.0
|
O5
|
B:OXD602
|
2.2
|
39.8
|
1.0
|
O
|
B:HOH758
|
2.3
|
42.4
|
1.0
|
C2
|
B:OXD602
|
2.8
|
41.4
|
1.0
|
C1
|
B:OXD602
|
2.9
|
40.5
|
1.0
|
CD
|
B:GLU284
|
3.0
|
47.5
|
1.0
|
CG
|
B:ASP308
|
3.2
|
41.4
|
1.0
|
OE1
|
B:GLU284
|
3.3
|
49.6
|
1.0
|
CB
|
B:ASP308
|
3.7
|
37.0
|
1.0
|
O4
|
B:OXD602
|
4.1
|
41.2
|
1.0
|
NZ
|
B:LYS282
|
4.1
|
41.0
|
1.0
|
O3
|
B:OXD602
|
4.1
|
40.3
|
1.0
|
O
|
B:HOH887
|
4.2
|
49.4
|
1.0
|
OD1
|
B:ASP308
|
4.3
|
42.3
|
1.0
|
CG
|
B:GLU284
|
4.3
|
42.9
|
1.0
|
N
|
B:ASP308
|
4.4
|
34.8
|
1.0
|
O
|
B:HOH792
|
4.4
|
42.3
|
1.0
|
CE
|
B:LYS282
|
4.4
|
41.0
|
1.0
|
CB
|
B:ALA305
|
4.6
|
34.1
|
1.0
|
CA
|
B:ASP308
|
4.7
|
35.6
|
1.0
|
CE1
|
B:PHE256
|
4.7
|
49.9
|
1.0
|
CB
|
B:GLU284
|
4.8
|
39.1
|
1.0
|
CD1
|
B:PHE256
|
4.9
|
49.0
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 7qdn
Go back to
Magnesium Binding Sites List in 7qdn
Magnesium binding site 3 out
of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg603
b:34.0
occ:1.00
|
OE2
|
C:GLU284
|
2.0
|
34.6
|
1.0
|
O
|
C:HOH718
|
2.1
|
38.0
|
1.0
|
O5
|
C:OXD602
|
2.1
|
35.8
|
1.0
|
OD2
|
C:ASP308
|
2.1
|
35.7
|
1.0
|
O
|
C:HOH787
|
2.2
|
35.6
|
1.0
|
O6
|
C:OXD602
|
2.2
|
36.8
|
1.0
|
C1
|
C:OXD602
|
2.8
|
36.6
|
1.0
|
C2
|
C:OXD602
|
2.9
|
37.5
|
1.0
|
CD
|
C:GLU284
|
3.1
|
33.6
|
1.0
|
CG
|
C:ASP308
|
3.2
|
37.3
|
1.0
|
OE1
|
C:GLU284
|
3.5
|
33.3
|
1.0
|
CB
|
C:ASP308
|
3.6
|
33.3
|
1.0
|
O
|
C:HOH946
|
4.0
|
48.8
|
1.0
|
O3
|
C:OXD602
|
4.1
|
36.4
|
1.0
|
O4
|
C:OXD602
|
4.1
|
38.6
|
1.0
|
NZ
|
C:LYS282
|
4.2
|
29.2
|
1.0
|
OD1
|
C:ASP308
|
4.3
|
39.0
|
1.0
|
N
|
C:ASP308
|
4.3
|
32.1
|
1.0
|
CG
|
C:GLU284
|
4.4
|
33.2
|
1.0
|
O
|
C:HOH879
|
4.4
|
39.5
|
1.0
|
CE
|
C:LYS282
|
4.5
|
28.1
|
1.0
|
CB
|
C:ALA305
|
4.6
|
29.8
|
1.0
|
CA
|
C:ASP308
|
4.6
|
32.5
|
1.0
|
CE1
|
C:PHE256
|
4.7
|
38.6
|
1.0
|
CB
|
C:GLU284
|
4.8
|
31.6
|
1.0
|
CD1
|
C:PHE256
|
5.0
|
37.7
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 7qdn
Go back to
Magnesium Binding Sites List in 7qdn
Magnesium binding site 4 out
of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg603
b:30.3
occ:1.00
|
OD2
|
D:ASP308
|
2.0
|
33.3
|
1.0
|
O
|
D:HOH778
|
2.0
|
30.5
|
1.0
|
OE2
|
D:GLU284
|
2.0
|
29.9
|
1.0
|
O3
|
D:OXD602
|
2.1
|
33.0
|
1.0
|
O
|
D:HOH820
|
2.1
|
34.3
|
1.0
|
O4
|
D:OXD602
|
2.2
|
31.6
|
1.0
|
C1
|
D:OXD602
|
2.9
|
33.4
|
1.0
|
C2
|
D:OXD602
|
2.9
|
32.3
|
1.0
|
CD
|
D:GLU284
|
3.1
|
29.1
|
1.0
|
CG
|
D:ASP308
|
3.1
|
33.5
|
1.0
|
OE1
|
D:GLU284
|
3.5
|
28.5
|
1.0
|
CB
|
D:ASP308
|
3.6
|
28.9
|
1.0
|
O
|
D:HOH962
|
4.0
|
40.5
|
1.0
|
O6
|
D:OXD602
|
4.1
|
32.4
|
1.0
|
NZ
|
D:LYS282
|
4.1
|
30.2
|
1.0
|
O5
|
D:OXD602
|
4.2
|
33.9
|
1.0
|
OD1
|
D:ASP308
|
4.2
|
35.0
|
1.0
|
N
|
D:ASP308
|
4.3
|
28.0
|
1.0
|
CG
|
D:GLU284
|
4.4
|
29.8
|
1.0
|
O
|
D:HOH770
|
4.5
|
33.3
|
1.0
|
CE
|
D:LYS282
|
4.5
|
30.6
|
1.0
|
CA
|
D:ASP308
|
4.6
|
27.8
|
1.0
|
O
|
D:HOH1018
|
4.6
|
49.0
|
1.0
|
CE1
|
D:PHE256
|
4.6
|
43.6
|
1.0
|
CB
|
D:ALA305
|
4.6
|
24.9
|
1.0
|
CB
|
D:GLU284
|
4.8
|
29.1
|
1.0
|
O
|
D:HOH709
|
4.8
|
51.6
|
1.0
|
CD1
|
D:PHE256
|
5.0
|
42.3
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 7qdn
Go back to
Magnesium Binding Sites List in 7qdn
Magnesium binding site 5 out
of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg603
b:47.8
occ:1.00
|
OE2
|
E:GLU284
|
2.0
|
47.2
|
1.0
|
O5
|
E:OXD602
|
2.1
|
49.1
|
1.0
|
OD2
|
E:ASP308
|
2.1
|
44.4
|
1.0
|
O
|
E:HOH800
|
2.1
|
44.3
|
1.0
|
O
|
E:HOH740
|
2.2
|
45.5
|
1.0
|
O6
|
E:OXD602
|
2.3
|
48.5
|
1.0
|
C1
|
E:OXD602
|
2.9
|
49.2
|
1.0
|
C2
|
E:OXD602
|
3.0
|
49.1
|
1.0
|
CD
|
E:GLU284
|
3.0
|
47.0
|
1.0
|
CG
|
E:ASP308
|
3.2
|
43.8
|
1.0
|
OE1
|
E:GLU284
|
3.4
|
44.8
|
1.0
|
CB
|
E:ASP308
|
3.7
|
40.2
|
1.0
|
NZ
|
E:LYS282
|
4.1
|
45.1
|
1.0
|
O3
|
E:OXD602
|
4.1
|
49.4
|
1.0
|
O4
|
E:OXD602
|
4.2
|
49.4
|
1.0
|
OD1
|
E:ASP308
|
4.3
|
45.3
|
1.0
|
CG
|
E:GLU284
|
4.3
|
44.5
|
1.0
|
O
|
E:HOH803
|
4.4
|
46.5
|
1.0
|
CE
|
E:LYS282
|
4.5
|
45.4
|
1.0
|
N
|
E:ASP308
|
4.5
|
37.9
|
1.0
|
O
|
E:HOH819
|
4.6
|
51.1
|
1.0
|
CB
|
E:ALA305
|
4.6
|
37.0
|
1.0
|
CE1
|
E:PHE256
|
4.6
|
54.8
|
1.0
|
CA
|
E:ASP308
|
4.7
|
39.0
|
1.0
|
CB
|
E:GLU284
|
4.8
|
41.8
|
1.0
|
CD1
|
E:PHE256
|
4.9
|
53.7
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 7qdn
Go back to
Magnesium Binding Sites List in 7qdn
Magnesium binding site 6 out
of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg603
b:39.1
occ:1.00
|
OE2
|
F:GLU284
|
2.0
|
37.6
|
1.0
|
O
|
F:HOH733
|
2.0
|
38.0
|
1.0
|
OD2
|
F:ASP308
|
2.1
|
42.8
|
1.0
|
O
|
F:HOH786
|
2.1
|
37.5
|
1.0
|
O4
|
F:OXD602
|
2.1
|
42.3
|
1.0
|
O3
|
F:OXD602
|
2.2
|
40.6
|
1.0
|
C1
|
F:OXD602
|
2.9
|
41.3
|
1.0
|
C2
|
F:OXD602
|
2.9
|
42.6
|
1.0
|
CD
|
F:GLU284
|
3.0
|
38.7
|
1.0
|
CG
|
F:ASP308
|
3.2
|
41.0
|
1.0
|
OE1
|
F:GLU284
|
3.4
|
39.9
|
1.0
|
CB
|
F:ASP308
|
3.6
|
35.4
|
1.0
|
O
|
F:HOH910
|
4.0
|
45.4
|
1.0
|
NZ
|
F:LYS282
|
4.1
|
39.8
|
1.0
|
O5
|
F:OXD602
|
4.1
|
41.0
|
1.0
|
O6
|
F:OXD602
|
4.2
|
43.5
|
1.0
|
OD1
|
F:ASP308
|
4.3
|
41.5
|
1.0
|
O
|
F:HOH758
|
4.3
|
42.4
|
1.0
|
CG
|
F:GLU284
|
4.3
|
38.2
|
1.0
|
N
|
F:ASP308
|
4.4
|
32.7
|
1.0
|
CE
|
F:LYS282
|
4.4
|
38.4
|
1.0
|
CB
|
F:ALA305
|
4.6
|
31.1
|
1.0
|
CA
|
F:ASP308
|
4.7
|
33.5
|
1.0
|
CE1
|
F:PHE256
|
4.7
|
43.9
|
1.0
|
CB
|
F:GLU284
|
4.8
|
35.3
|
1.0
|
CD1
|
F:PHE256
|
5.0
|
43.1
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 7qdn
Go back to
Magnesium Binding Sites List in 7qdn
Magnesium binding site 7 out
of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg603
b:31.6
occ:1.00
|
OE2
|
G:GLU284
|
2.0
|
31.2
|
1.0
|
O3
|
G:OXD602
|
2.0
|
32.5
|
1.0
|
O
|
G:HOH749
|
2.0
|
32.5
|
1.0
|
OD2
|
G:ASP308
|
2.1
|
34.9
|
1.0
|
O4
|
G:OXD602
|
2.1
|
34.5
|
1.0
|
O
|
G:HOH862
|
2.1
|
35.4
|
1.0
|
C1
|
G:OXD602
|
2.8
|
33.7
|
1.0
|
C2
|
G:OXD602
|
2.8
|
34.8
|
1.0
|
CD
|
G:GLU284
|
3.1
|
31.0
|
1.0
|
CG
|
G:ASP308
|
3.2
|
36.1
|
1.0
|
OE1
|
G:GLU284
|
3.4
|
31.1
|
1.0
|
CB
|
G:ASP308
|
3.6
|
31.8
|
1.0
|
O
|
G:HOH942
|
3.9
|
41.9
|
1.0
|
O5
|
G:OXD602
|
4.0
|
33.6
|
1.0
|
O6
|
G:OXD602
|
4.1
|
36.0
|
1.0
|
NZ
|
G:LYS282
|
4.2
|
30.1
|
1.0
|
OD1
|
G:ASP308
|
4.3
|
38.2
|
1.0
|
O
|
G:HOH1023
|
4.3
|
47.6
|
1.0
|
N
|
G:ASP308
|
4.3
|
30.7
|
1.0
|
CG
|
G:GLU284
|
4.4
|
32.3
|
1.0
|
O
|
G:HOH847
|
4.5
|
36.3
|
1.0
|
CE
|
G:LYS282
|
4.6
|
30.7
|
1.0
|
CA
|
G:ASP308
|
4.6
|
30.9
|
1.0
|
CB
|
G:ALA305
|
4.7
|
29.1
|
1.0
|
CE1
|
G:PHE256
|
4.7
|
38.1
|
1.0
|
CB
|
G:GLU284
|
4.8
|
31.3
|
1.0
|
CD1
|
G:PHE256
|
5.0
|
37.2
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 7qdn
Go back to
Magnesium Binding Sites List in 7qdn
Magnesium binding site 8 out
of 8 in the Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg603
b:34.0
occ:1.00
|
OD2
|
H:ASP308
|
2.0
|
35.6
|
1.0
|
OE2
|
H:GLU284
|
2.0
|
31.0
|
1.0
|
O5
|
H:OXD602
|
2.1
|
33.2
|
1.0
|
O
|
H:HOH762
|
2.1
|
37.1
|
1.0
|
O
|
H:HOH786
|
2.1
|
29.9
|
1.0
|
O6
|
H:OXD602
|
2.1
|
33.6
|
1.0
|
C2
|
H:OXD602
|
2.9
|
33.3
|
1.0
|
C1
|
H:OXD602
|
2.9
|
33.9
|
1.0
|
CG
|
H:ASP308
|
3.1
|
34.9
|
1.0
|
CD
|
H:GLU284
|
3.1
|
30.6
|
1.0
|
OE1
|
H:GLU284
|
3.5
|
30.7
|
1.0
|
CB
|
H:ASP308
|
3.5
|
30.4
|
1.0
|
O
|
H:HOH962
|
4.1
|
47.7
|
1.0
|
O
|
H:HOH996
|
4.1
|
44.2
|
1.0
|
O3
|
H:OXD602
|
4.1
|
35.0
|
1.0
|
O4
|
H:OXD602
|
4.1
|
32.5
|
1.0
|
OD1
|
H:ASP308
|
4.2
|
35.1
|
1.0
|
NZ
|
H:LYS282
|
4.2
|
32.4
|
1.0
|
N
|
H:ASP308
|
4.3
|
29.4
|
1.0
|
O
|
H:HOH924
|
4.3
|
38.3
|
1.0
|
O
|
H:HOH1044
|
4.4
|
47.5
|
1.0
|
CG
|
H:GLU284
|
4.4
|
30.2
|
1.0
|
CA
|
H:ASP308
|
4.5
|
29.3
|
1.0
|
CE1
|
H:PHE256
|
4.5
|
39.8
|
1.0
|
CE
|
H:LYS282
|
4.6
|
31.6
|
1.0
|
CB
|
H:ALA305
|
4.6
|
28.0
|
1.0
|
CB
|
H:GLU284
|
4.8
|
30.0
|
1.0
|
CD1
|
H:PHE256
|
4.9
|
38.8
|
1.0
|
|
Reference:
A.Nain-Perez,
A.Foller Fuchtbauer,
L.Haversen,
A.Lulla,
C.Gao,
J.Matic,
L.Monjas,
A.Rodriguez,
P.Brear,
W.Kim,
M.Hyvonen,
J.Boren,
A.Mardinoglu,
M.Uhlen,
M.Grotli.
Anthraquinone Derivatives As Adp-Competitive Inhibitors of Liver Pyruvate Kinase. Eur.J.Med.Chem. V. 234 14270 2022.
ISSN: ISSN 0223-5234
PubMed: 35290845
DOI: 10.1016/J.EJMECH.2022.114270
Page generated: Thu Oct 3 05:05:20 2024
|