Magnesium in PDB 8qf1: Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp
Enzymatic activity of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp
All present enzymatic activity of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp:
2.7.11.1;
Protein crystallography data
The structure of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp, PDB code: 8qf1
was solved by
C.Werner,
D.Lindenblatt,
K.Niefind,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
58.60 /
1.32
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.628,
71.59,
102.101,
90,
92.09,
90
|
R / Rfree (%)
|
21.4 /
23.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp
(pdb code 8qf1). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp, PDB code: 8qf1:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 8qf1
Go back to
Magnesium Binding Sites List in 8qf1
Magnesium binding site 1 out
of 3 in the Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:25.4
occ:1.00
|
OD1
|
A:ASP176
|
1.9
|
19.5
|
1.0
|
OD2
|
A:ASP176
|
2.0
|
21.5
|
1.0
|
O1B
|
A:GNP401
|
2.0
|
29.6
|
1.0
|
O
|
A:HOH668
|
2.1
|
28.7
|
1.0
|
O
|
A:HOH534
|
2.1
|
16.8
|
1.0
|
O3G
|
A:GNP401
|
2.1
|
28.0
|
1.0
|
CG
|
A:ASP176
|
2.2
|
15.9
|
1.0
|
PG
|
A:GNP401
|
3.3
|
29.7
|
1.0
|
HD2
|
A:TYR51
|
3.3
|
43.7
|
1.0
|
PB
|
A:GNP401
|
3.3
|
30.6
|
1.0
|
N3B
|
A:GNP401
|
3.6
|
28.5
|
1.0
|
H
|
A:GLY178
|
3.7
|
12.2
|
1.0
|
CB
|
A:ASP176
|
3.7
|
12.4
|
1.0
|
O2G
|
A:GNP401
|
3.8
|
25.4
|
1.0
|
HZ1
|
A:LYS69
|
3.8
|
23.8
|
1.0
|
HA3
|
A:GLY178
|
3.9
|
12.2
|
1.0
|
MG
|
A:MG403
|
3.9
|
18.7
|
1.0
|
OD2
|
A:ASP157
|
4.0
|
12.3
|
1.0
|
CD2
|
A:TYR51
|
4.0
|
36.4
|
1.0
|
HB3
|
A:ASP176
|
4.1
|
14.9
|
1.0
|
HB2
|
A:ASP176
|
4.2
|
14.9
|
1.0
|
O2B
|
A:GNP401
|
4.2
|
33.6
|
1.0
|
HG
|
A:LEU179
|
4.3
|
17.3
|
1.0
|
O
|
A:ASP176
|
4.3
|
11.4
|
1.0
|
HE2
|
A:TYR51
|
4.3
|
46.3
|
1.0
|
HNB3
|
A:GNP401
|
4.3
|
34.2
|
1.0
|
HD21
|
A:ASN162
|
4.4
|
11.2
|
1.0
|
HB2
|
A:TYR51
|
4.4
|
39.3
|
1.0
|
N
|
A:GLY178
|
4.4
|
10.2
|
1.0
|
HZ2
|
A:LYS69
|
4.4
|
23.8
|
1.0
|
HA
|
A:ASP176
|
4.4
|
12.6
|
1.0
|
O
|
A:HOH622
|
4.4
|
27.9
|
1.0
|
O1A
|
A:GNP401
|
4.4
|
20.7
|
1.0
|
O3A
|
A:GNP401
|
4.4
|
28.1
|
1.0
|
H
|
A:LEU179
|
4.5
|
10.9
|
1.0
|
CA
|
A:ASP176
|
4.5
|
10.5
|
1.0
|
NZ
|
A:LYS69
|
4.5
|
19.8
|
1.0
|
C
|
A:ASP176
|
4.5
|
10.8
|
1.0
|
CA
|
A:GLY178
|
4.5
|
10.2
|
1.0
|
O1G
|
A:GNP401
|
4.5
|
29.5
|
1.0
|
CE2
|
A:TYR51
|
4.6
|
38.5
|
1.0
|
PA
|
A:GNP401
|
4.9
|
24.1
|
1.0
|
N
|
A:LEU179
|
4.9
|
9.1
|
1.0
|
O
|
A:HOH522
|
4.9
|
43.7
|
1.0
|
HE3
|
A:LYS69
|
5.0
|
23.6
|
1.0
|
O2A
|
A:GNP401
|
5.0
|
21.2
|
1.0
|
HD12
|
A:LEU179
|
5.0
|
18.5
|
1.0
|
C
|
A:GLY178
|
5.0
|
9.2
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 8qf1
Go back to
Magnesium Binding Sites List in 8qf1
Magnesium binding site 2 out
of 3 in the Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:18.7
occ:1.00
|
OD1
|
A:ASN162
|
2.0
|
11.7
|
1.0
|
O1A
|
A:GNP401
|
2.1
|
20.7
|
1.0
|
OD2
|
A:ASP176
|
2.1
|
21.5
|
1.0
|
O
|
A:HOH663
|
2.1
|
22.6
|
1.0
|
O2G
|
A:GNP401
|
2.1
|
25.4
|
1.0
|
HNB3
|
A:GNP401
|
2.4
|
34.2
|
1.0
|
N3B
|
A:GNP401
|
2.5
|
28.5
|
1.0
|
PG
|
A:GNP401
|
2.8
|
29.7
|
1.0
|
HD21
|
A:ASN162
|
3.0
|
11.2
|
1.0
|
CG
|
A:ASP176
|
3.0
|
15.9
|
1.0
|
CG
|
A:ASN162
|
3.0
|
9.4
|
1.0
|
HB2
|
A:ASP176
|
3.1
|
14.9
|
1.0
|
HB3
|
A:ASP176
|
3.4
|
14.9
|
1.0
|
CB
|
A:ASP176
|
3.4
|
12.4
|
1.0
|
ND2
|
A:ASN162
|
3.4
|
9.3
|
1.0
|
PA
|
A:GNP401
|
3.5
|
24.1
|
1.0
|
O3G
|
A:GNP401
|
3.6
|
28.0
|
1.0
|
H5'2
|
A:GNP401
|
3.6
|
29.4
|
1.0
|
PB
|
A:GNP401
|
3.7
|
30.6
|
1.0
|
MG
|
A:MG402
|
3.9
|
25.4
|
1.0
|
O1B
|
A:GNP401
|
3.9
|
29.6
|
1.0
|
HE3
|
A:LYS159
|
4.0
|
14.7
|
1.0
|
O3A
|
A:GNP401
|
4.0
|
28.1
|
1.0
|
HE2
|
A:LYS159
|
4.0
|
14.7
|
1.0
|
O1G
|
A:GNP401
|
4.1
|
29.5
|
1.0
|
OD1
|
A:ASP176
|
4.2
|
19.5
|
1.0
|
HZ1
|
A:LYS159
|
4.2
|
18.1
|
1.0
|
HD22
|
A:ASN162
|
4.2
|
11.2
|
1.0
|
HO3'
|
A:GNP401
|
4.2
|
27.9
|
1.0
|
HA
|
A:ASN162
|
4.3
|
10.6
|
1.0
|
O2A
|
A:GNP401
|
4.3
|
21.2
|
1.0
|
HB3
|
A:HIS161
|
4.3
|
16.8
|
1.0
|
O3'
|
A:GNP401
|
4.4
|
23.3
|
1.0
|
CB
|
A:ASN162
|
4.4
|
8.9
|
1.0
|
CE
|
A:LYS159
|
4.4
|
12.3
|
1.0
|
C5'
|
A:GNP401
|
4.4
|
24.5
|
1.0
|
O5'
|
A:GNP401
|
4.4
|
23.1
|
1.0
|
H3'
|
A:GNP401
|
4.5
|
29.4
|
1.0
|
OD2
|
A:ASP157
|
4.5
|
12.3
|
1.0
|
O
|
A:HIS161
|
4.6
|
10.8
|
1.0
|
HA3
|
A:GLY49
|
4.7
|
42.0
|
1.0
|
O
|
A:HOH534
|
4.7
|
16.8
|
1.0
|
HD11
|
A:ILE175
|
4.7
|
8.6
|
1.0
|
CA
|
A:ASN162
|
4.8
|
8.8
|
1.0
|
HB3
|
A:ASN162
|
4.8
|
10.7
|
1.0
|
NZ
|
A:LYS159
|
4.8
|
15.1
|
1.0
|
HG13
|
A:ILE175
|
4.8
|
9.1
|
1.0
|
CA
|
A:ASP176
|
4.9
|
10.5
|
1.0
|
C3'
|
A:GNP401
|
4.9
|
24.5
|
1.0
|
C
|
A:HIS161
|
4.9
|
10.6
|
1.0
|
O
|
A:HOH522
|
4.9
|
43.7
|
1.0
|
N
|
A:ASN162
|
5.0
|
9.8
|
1.0
|
HD12
|
A:ILE175
|
5.0
|
8.6
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 8qf1
Go back to
Magnesium Binding Sites List in 8qf1
Magnesium binding site 3 out
of 3 in the Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of the Catalytic Subunit of Protein Kinase CK2 (CK2ALPHA') in Complex with the Non-Hydrolyzable Gtp Analogue Gmppnp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg401
b:36.1
occ:1.00
|
OD2
|
B:ASP176
|
2.1
|
33.9
|
1.0
|
OD1
|
B:ASN162
|
2.2
|
29.7
|
1.0
|
O
|
B:HOH637
|
2.6
|
56.5
|
1.0
|
HD21
|
B:ASN162
|
3.0
|
33.2
|
1.0
|
CG
|
B:ASP176
|
3.1
|
32.0
|
1.0
|
CG
|
B:ASN162
|
3.1
|
25.9
|
1.0
|
HB2
|
B:ASP176
|
3.3
|
32.8
|
1.0
|
ND2
|
B:ASN162
|
3.4
|
27.6
|
1.0
|
HB3
|
B:ASP176
|
3.4
|
32.8
|
1.0
|
HE1
|
B:HIS161
|
3.5
|
40.7
|
1.0
|
CB
|
B:ASP176
|
3.5
|
27.4
|
1.0
|
ND1
|
B:HIS161
|
3.6
|
34.1
|
1.0
|
HE3
|
B:LYS159
|
3.8
|
29.7
|
1.0
|
CE1
|
B:HIS161
|
3.8
|
33.9
|
1.0
|
HZ3
|
B:LYS159
|
4.0
|
32.8
|
1.0
|
HE2
|
B:LYS159
|
4.1
|
29.7
|
1.0
|
OD1
|
B:ASP176
|
4.3
|
32.8
|
1.0
|
HD22
|
B:ASN162
|
4.3
|
33.2
|
1.0
|
CE
|
B:LYS159
|
4.3
|
24.8
|
1.0
|
OD2
|
B:ASP157
|
4.4
|
23.0
|
1.0
|
CB
|
B:ASN162
|
4.5
|
24.1
|
1.0
|
HA
|
B:ASN162
|
4.6
|
27.7
|
1.0
|
NZ
|
B:LYS159
|
4.6
|
27.3
|
1.0
|
CG
|
B:HIS161
|
4.8
|
30.1
|
1.0
|
HB3
|
B:ASN162
|
4.8
|
28.9
|
1.0
|
HB3
|
B:HIS161
|
4.9
|
29.8
|
1.0
|
O
|
B:HOH625
|
4.9
|
40.1
|
1.0
|
|
Reference:
C.Werner,
D.Lindenblatt,
K.Viht,
A.Uri,
K.Niefind.
Discovery and Exploration of Protein Kinase CK2 Binding Sites Using CK2ALPHA CYS336SER As An Exquisite Crystallographic Tool Kinases Phosphatases 2023.
DOI: 10.3390/KINASESPHOSPHATASES1040018
Page generated: Fri Oct 4 16:41:37 2024
|