Sodium 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:
Sodium Binding Sites:
The binding sites of Sodium 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 Sodium atom.
In total 6 binding sites of Sodium where determined in the
Structure of Human Liver Pyruvate Kinase From Which the B Domain Has Been Deleted, PDB code: 7qdn:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 7qdn
Go back to
Sodium Binding Sites List in 7qdn
Sodium binding site 1 out
of 6 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 Sodium with other atoms in the Na 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
|
B:Na605
b:40.2
occ:1.00
|
O
|
B:CYS478
|
2.6
|
35.3
|
1.0
|
O
|
B:VAL481
|
2.8
|
38.5
|
1.0
|
O
|
B:HOH774
|
3.0
|
33.4
|
1.0
|
O
|
B:HOH829
|
3.3
|
43.7
|
1.0
|
OG
|
B:SER58
|
3.3
|
37.0
|
1.0
|
N
|
B:VAL481
|
3.3
|
36.7
|
1.0
|
O
|
B:HOH885
|
3.5
|
44.2
|
1.0
|
O
|
B:HIS476
|
3.5
|
40.6
|
1.0
|
C
|
B:CYS478
|
3.6
|
35.9
|
1.0
|
O
|
B:SER56
|
3.7
|
36.2
|
1.0
|
C
|
B:VAL481
|
3.7
|
38.4
|
1.0
|
N
|
B:GLY480
|
3.7
|
34.5
|
1.0
|
O
|
B:VAL475
|
3.8
|
41.8
|
1.0
|
CA
|
B:VAL481
|
3.9
|
37.7
|
1.0
|
CA
|
B:HIS476
|
3.9
|
40.0
|
1.0
|
C
|
B:HIS476
|
4.0
|
39.5
|
1.0
|
C
|
B:ARG479
|
4.1
|
35.0
|
1.0
|
CB
|
B:VAL481
|
4.1
|
39.0
|
1.0
|
CA
|
B:ARG479
|
4.2
|
35.5
|
1.0
|
C
|
B:GLY480
|
4.3
|
36.7
|
1.0
|
N
|
B:ARG479
|
4.3
|
35.6
|
1.0
|
CA
|
B:GLY480
|
4.5
|
35.9
|
1.0
|
N
|
B:CYS478
|
4.5
|
37.1
|
1.0
|
ND1
|
B:HIS476
|
4.5
|
39.4
|
1.0
|
CB
|
B:SER58
|
4.6
|
34.7
|
1.0
|
CA
|
B:CYS478
|
4.6
|
36.8
|
1.0
|
C
|
B:VAL475
|
4.7
|
41.5
|
1.0
|
N
|
B:HIS476
|
4.7
|
40.6
|
1.0
|
C
|
B:SER56
|
4.8
|
36.6
|
1.0
|
N
|
B:SER58
|
4.9
|
33.0
|
1.0
|
CB
|
B:HIS476
|
4.9
|
39.3
|
1.0
|
N
|
B:PHE482
|
4.9
|
38.8
|
1.0
|
O
|
B:ARG479
|
5.0
|
35.5
|
1.0
|
CG2
|
B:VAL481
|
5.0
|
39.2
|
1.0
|
|
Sodium binding site 2 out
of 6 in 7qdn
Go back to
Sodium Binding Sites List in 7qdn
Sodium binding site 2 out
of 6 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 Sodium with other atoms in the Na 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
|
C:Na605
b:37.9
occ:1.00
|
O
|
C:HOH998
|
2.2
|
42.4
|
1.0
|
O
|
C:HOH764
|
2.2
|
29.4
|
1.0
|
O
|
C:SER56
|
2.4
|
29.1
|
1.0
|
OG
|
C:SER58
|
2.4
|
29.8
|
1.0
|
O
|
C:HOH734
|
2.5
|
29.8
|
1.0
|
N
|
C:SER58
|
3.0
|
26.5
|
1.0
|
CB
|
C:SER58
|
3.3
|
27.5
|
1.0
|
C
|
C:SER56
|
3.3
|
28.9
|
1.0
|
O
|
C:HOH845
|
3.4
|
38.2
|
1.0
|
CA
|
C:SER58
|
3.5
|
27.1
|
1.0
|
C
|
C:THR57
|
3.6
|
26.6
|
1.0
|
O
|
C:HIS476
|
3.8
|
29.4
|
1.0
|
O
|
C:CYS478
|
3.9
|
27.6
|
1.0
|
N
|
C:GLY480
|
4.0
|
26.4
|
1.0
|
CA
|
C:THR57
|
4.0
|
27.0
|
1.0
|
N
|
C:THR57
|
4.0
|
27.7
|
1.0
|
CA
|
C:SER56
|
4.3
|
29.9
|
1.0
|
CA
|
C:ARG479
|
4.4
|
26.8
|
1.0
|
O
|
C:VAL481
|
4.4
|
26.1
|
1.0
|
O
|
C:THR57
|
4.4
|
26.5
|
1.0
|
C
|
C:CYS478
|
4.6
|
27.7
|
1.0
|
C
|
C:ARG479
|
4.6
|
25.9
|
1.0
|
O
|
C:ASP369
|
4.7
|
26.6
|
1.0
|
C
|
C:HIS476
|
4.7
|
27.7
|
1.0
|
N
|
C:VAL481
|
4.7
|
26.9
|
1.0
|
CA
|
C:HIS476
|
4.8
|
26.5
|
1.0
|
N
|
C:ARG479
|
4.9
|
27.3
|
1.0
|
CA
|
C:GLY480
|
4.9
|
27.4
|
1.0
|
ND1
|
C:HIS476
|
5.0
|
31.1
|
1.0
|
C
|
C:SER58
|
5.0
|
26.6
|
1.0
|
|
Sodium binding site 3 out
of 6 in 7qdn
Go back to
Sodium Binding Sites List in 7qdn
Sodium binding site 3 out
of 6 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 Sodium with other atoms in the Na 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
|
D:Na605
b:38.1
occ:1.00
|
O
|
D:HOH751
|
2.1
|
29.5
|
1.0
|
OG
|
D:SER58
|
2.3
|
28.0
|
1.0
|
O
|
D:SER56
|
2.4
|
27.6
|
1.0
|
O
|
D:HOH995
|
2.5
|
39.7
|
1.0
|
O
|
D:HOH723
|
2.6
|
28.3
|
1.0
|
N
|
D:SER58
|
2.9
|
24.6
|
1.0
|
CB
|
D:SER58
|
3.2
|
25.8
|
1.0
|
O
|
D:HOH935
|
3.3
|
34.6
|
1.0
|
CA
|
D:SER58
|
3.3
|
24.4
|
1.0
|
C
|
D:SER56
|
3.4
|
28.0
|
1.0
|
C
|
D:THR57
|
3.5
|
25.9
|
1.0
|
O
|
D:HIS476
|
3.8
|
26.7
|
1.0
|
CA
|
D:THR57
|
4.0
|
25.8
|
1.0
|
O
|
D:CYS478
|
4.0
|
26.9
|
1.0
|
N
|
D:GLY480
|
4.1
|
25.9
|
1.0
|
N
|
D:THR57
|
4.1
|
26.7
|
1.0
|
O
|
D:THR57
|
4.3
|
26.2
|
1.0
|
O
|
D:VAL481
|
4.3
|
26.8
|
1.0
|
CA
|
D:SER56
|
4.4
|
29.4
|
1.0
|
CA
|
D:ARG479
|
4.4
|
27.1
|
1.0
|
O
|
D:ASP369
|
4.5
|
24.3
|
1.0
|
N
|
D:VAL481
|
4.7
|
25.6
|
1.0
|
C
|
D:ARG479
|
4.7
|
26.1
|
1.0
|
C
|
D:CYS478
|
4.7
|
26.9
|
1.0
|
C
|
D:HIS476
|
4.7
|
25.8
|
1.0
|
C
|
D:SER58
|
4.8
|
23.9
|
1.0
|
CA
|
D:HIS476
|
4.9
|
25.3
|
1.0
|
N
|
D:ARG479
|
4.9
|
26.8
|
1.0
|
CA
|
D:GLY480
|
4.9
|
26.4
|
1.0
|
ND1
|
D:HIS476
|
5.0
|
26.9
|
1.0
|
|
Sodium binding site 4 out
of 6 in 7qdn
Go back to
Sodium Binding Sites List in 7qdn
Sodium binding site 4 out
of 6 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 Sodium with other atoms in the Na 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
|
F:Na605
b:40.0
occ:1.00
|
O
|
F:HOH747
|
2.2
|
39.5
|
1.0
|
O
|
F:HOH887
|
2.2
|
42.1
|
1.0
|
O
|
F:SER56
|
2.5
|
34.0
|
1.0
|
OG
|
F:SER58
|
2.5
|
37.1
|
1.0
|
O
|
F:HOH768
|
3.0
|
35.5
|
1.0
|
O
|
F:HOH850
|
3.1
|
46.2
|
1.0
|
N
|
F:SER58
|
3.2
|
32.5
|
1.0
|
C
|
F:SER56
|
3.3
|
34.5
|
1.0
|
CB
|
F:SER58
|
3.5
|
35.0
|
1.0
|
CA
|
F:SER58
|
3.6
|
33.3
|
1.0
|
C
|
F:THR57
|
3.7
|
33.0
|
1.0
|
N
|
F:THR57
|
4.1
|
33.9
|
1.0
|
N
|
F:GLY480
|
4.1
|
33.2
|
1.0
|
CA
|
F:SER56
|
4.1
|
34.8
|
1.0
|
CA
|
F:THR57
|
4.2
|
33.7
|
1.0
|
O
|
F:HIS476
|
4.2
|
38.1
|
1.0
|
O
|
F:VAL481
|
4.2
|
36.8
|
1.0
|
O
|
F:CYS478
|
4.3
|
35.1
|
1.0
|
O
|
F:THR57
|
4.3
|
32.4
|
1.0
|
O
|
F:ARG55
|
4.6
|
37.5
|
1.0
|
N
|
F:VAL481
|
4.7
|
35.4
|
1.0
|
CA
|
F:ARG479
|
4.7
|
34.0
|
1.0
|
ND1
|
F:HIS476
|
4.8
|
43.2
|
1.0
|
OD1
|
F:ASN82
|
4.8
|
37.3
|
1.0
|
C
|
F:ARG479
|
4.9
|
33.2
|
1.0
|
CA
|
F:GLY480
|
4.9
|
34.1
|
1.0
|
|
Sodium binding site 5 out
of 6 in 7qdn
Go back to
Sodium Binding Sites List in 7qdn
Sodium binding site 5 out
of 6 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 Sodium with other atoms in the Na 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
|
G:Na605
b:36.8
occ:1.00
|
O
|
G:HOH995
|
2.2
|
40.5
|
1.0
|
O
|
G:HOH723
|
2.2
|
32.5
|
1.0
|
O
|
G:SER56
|
2.3
|
30.1
|
1.0
|
OG
|
G:SER58
|
2.4
|
28.6
|
1.0
|
O
|
G:HOH801
|
2.5
|
32.4
|
1.0
|
N
|
G:SER58
|
2.9
|
26.8
|
1.0
|
CB
|
G:SER58
|
3.3
|
27.2
|
1.0
|
C
|
G:SER56
|
3.3
|
30.9
|
1.0
|
CA
|
G:SER58
|
3.3
|
26.9
|
1.0
|
O
|
G:HOH949
|
3.4
|
38.5
|
1.0
|
C
|
G:THR57
|
3.5
|
27.6
|
1.0
|
O
|
G:HIS476
|
3.9
|
27.8
|
1.0
|
CA
|
G:THR57
|
3.9
|
28.6
|
1.0
|
N
|
G:THR57
|
3.9
|
29.8
|
1.0
|
O
|
G:CYS478
|
4.0
|
28.6
|
1.0
|
N
|
G:GLY480
|
4.0
|
27.0
|
1.0
|
CA
|
G:SER56
|
4.3
|
31.9
|
1.0
|
O
|
G:THR57
|
4.3
|
27.9
|
1.0
|
CA
|
G:ARG479
|
4.3
|
28.4
|
1.0
|
O
|
G:VAL481
|
4.4
|
27.1
|
1.0
|
O
|
G:ASP369
|
4.5
|
26.6
|
1.0
|
C
|
G:ARG479
|
4.7
|
27.2
|
1.0
|
C
|
G:CYS478
|
4.7
|
28.6
|
1.0
|
N
|
G:VAL481
|
4.7
|
27.3
|
1.0
|
C
|
G:HIS476
|
4.8
|
25.8
|
1.0
|
C
|
G:SER58
|
4.8
|
26.5
|
1.0
|
N
|
G:ARG479
|
4.9
|
27.9
|
1.0
|
CA
|
G:GLY480
|
4.9
|
27.8
|
1.0
|
CA
|
G:HIS476
|
4.9
|
25.5
|
1.0
|
|
Sodium binding site 6 out
of 6 in 7qdn
Go back to
Sodium Binding Sites List in 7qdn
Sodium binding site 6 out
of 6 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 Sodium with other atoms in the Na 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
|
H:Na605
b:40.0
occ:1.00
|
O
|
H:HOH720
|
2.1
|
31.3
|
1.0
|
O
|
H:HOH1009
|
2.2
|
38.6
|
1.0
|
O
|
H:SER56
|
2.2
|
28.1
|
1.0
|
OG
|
H:SER58
|
2.5
|
28.1
|
1.0
|
O
|
H:HOH709
|
2.7
|
35.8
|
1.0
|
N
|
H:SER58
|
3.0
|
24.2
|
1.0
|
C
|
H:SER56
|
3.2
|
27.9
|
1.0
|
O
|
H:HOH901
|
3.3
|
32.2
|
1.0
|
CB
|
H:SER58
|
3.4
|
25.2
|
1.0
|
CA
|
H:SER58
|
3.4
|
24.7
|
1.0
|
C
|
H:THR57
|
3.6
|
24.8
|
1.0
|
N
|
H:GLY480
|
3.9
|
25.3
|
1.0
|
N
|
H:THR57
|
3.9
|
26.1
|
1.0
|
CA
|
H:THR57
|
4.0
|
25.0
|
1.0
|
O
|
H:CYS478
|
4.0
|
25.8
|
1.0
|
O
|
H:HIS476
|
4.0
|
27.5
|
1.0
|
CA
|
H:SER56
|
4.2
|
29.1
|
1.0
|
O
|
H:THR57
|
4.3
|
24.2
|
1.0
|
CA
|
H:ARG479
|
4.3
|
26.4
|
1.0
|
O
|
H:VAL481
|
4.3
|
26.1
|
1.0
|
C
|
H:ARG479
|
4.5
|
25.9
|
1.0
|
N
|
H:VAL481
|
4.6
|
25.7
|
1.0
|
O
|
H:ASP369
|
4.6
|
24.2
|
1.0
|
C
|
H:CYS478
|
4.7
|
26.3
|
1.0
|
CA
|
H:GLY480
|
4.7
|
26.2
|
1.0
|
N
|
H:ARG479
|
4.9
|
26.0
|
1.0
|
O
|
H:ARG55
|
4.9
|
30.5
|
1.0
|
C
|
H:HIS476
|
4.9
|
25.6
|
1.0
|
C
|
H:SER58
|
5.0
|
24.5
|
1.0
|
OD1
|
H:ASN82
|
5.0
|
23.6
|
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: Wed Oct 9 08:20:39 2024
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