Chlorine in PDB 7atv: Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2
Enzymatic activity of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2
All present enzymatic activity of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2:
2.7.11.1;
Protein crystallography data
The structure of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2, PDB code: 7atv
was solved by
D.Lindenblatt,
V.Applegate,
A.Nickelsen,
M.Klussmann,
I.Neundorf,
C.Goetz,
J.Jose,
K.Niefind,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.28 /
0.98
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.783,
47.56,
50.998,
66.8,
88.96,
88.75
|
R / Rfree (%)
|
12.7 /
14.1
|
Other elements in 7atv:
The structure of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2 also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2
(pdb code 7atv). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the
Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2, PDB code: 7atv:
Jump to Chlorine binding site number:
1;
2;
3;
Chlorine binding site 1 out
of 3 in 7atv
Go back to
Chlorine Binding Sites List in 7atv
Chlorine binding site 1 out
of 3 in the Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl402
b:11.1
occ:1.00
|
CL1
|
A:RXE402
|
0.0
|
11.1
|
1.0
|
C02
|
A:RXE402
|
1.8
|
10.4
|
1.0
|
C03
|
A:RXE402
|
2.7
|
11.3
|
1.0
|
C07
|
A:RXE402
|
2.7
|
9.5
|
1.0
|
H1
|
A:RXE402
|
2.8
|
13.6
|
1.0
|
HB2
|
A:TYR137
|
2.9
|
10.3
|
1.0
|
HA
|
A:ILE134
|
3.0
|
11.4
|
1.0
|
HG2
|
A:MET138
|
3.1
|
10.1
|
1.0
|
CL2
|
A:RXE402
|
3.2
|
10.8
|
1.0
|
HG3
|
A:MET226
|
3.2
|
13.4
|
1.0
|
HE2
|
A:MET138
|
3.2
|
15.3
|
1.0
|
HG23
|
A:ILE134
|
3.3
|
11.4
|
1.0
|
HE2
|
A:MET226
|
3.3
|
17.6
|
1.0
|
HB3
|
A:TYR137
|
3.7
|
10.3
|
1.0
|
CB
|
A:TYR137
|
3.7
|
8.6
|
1.0
|
HG12
|
A:ILE134
|
3.7
|
13.9
|
1.0
|
O
|
A:ILE134
|
3.8
|
9.0
|
1.0
|
H
|
A:MET138
|
3.8
|
9.1
|
1.0
|
CA
|
A:ILE134
|
3.9
|
9.5
|
1.0
|
HD13
|
A:LEU129
|
4.0
|
25.4
|
1.0
|
C04
|
A:RXE402
|
4.0
|
11.1
|
1.0
|
C06
|
A:RXE402
|
4.0
|
9.6
|
1.0
|
CE
|
A:MET138
|
4.0
|
12.8
|
1.0
|
CG
|
A:MET138
|
4.0
|
8.4
|
1.0
|
HE3
|
A:MET138
|
4.1
|
15.3
|
1.0
|
HD2
|
A:TYR137
|
4.1
|
12.6
|
1.0
|
CG
|
A:MET226
|
4.1
|
11.2
|
1.0
|
CG2
|
A:ILE134
|
4.1
|
9.5
|
1.0
|
N
|
A:MET138
|
4.2
|
7.6
|
1.0
|
CE
|
A:MET226
|
4.2
|
14.7
|
1.0
|
C
|
A:ILE134
|
4.3
|
9.0
|
1.0
|
CB
|
A:ILE134
|
4.4
|
10.3
|
1.0
|
HG3
|
A:MET138
|
4.4
|
10.1
|
1.0
|
CG1
|
A:ILE134
|
4.5
|
11.6
|
1.0
|
C
|
A:TYR137
|
4.5
|
8.1
|
1.0
|
C05
|
A:RXE402
|
4.5
|
9.5
|
1.0
|
HB3
|
A:MET226
|
4.5
|
10.7
|
1.0
|
HG22
|
A:ILE134
|
4.6
|
11.4
|
1.0
|
HD11
|
A:ILE165
|
4.6
|
14.5
|
1.0
|
CA
|
A:TYR137
|
4.6
|
8.2
|
1.0
|
O
|
A:ASP133
|
4.6
|
10.0
|
1.0
|
H
|
A:TYR137
|
4.6
|
10.2
|
1.0
|
SD
|
A:MET226
|
4.6
|
12.7
|
1.0
|
HG2
|
A:MET226
|
4.7
|
13.4
|
1.0
|
CG
|
A:TYR137
|
4.7
|
9.2
|
1.0
|
H2
|
A:RXE402
|
4.7
|
13.3
|
1.0
|
HE1
|
A:MET226
|
4.7
|
17.6
|
1.0
|
CD2
|
A:TYR137
|
4.7
|
10.5
|
1.0
|
H3
|
A:RXE402
|
4.7
|
11.5
|
1.0
|
HE1
|
A:MET138
|
4.8
|
15.3
|
1.0
|
HA
|
A:MET138
|
4.8
|
8.7
|
1.0
|
SD
|
A:MET138
|
4.8
|
10.5
|
1.0
|
CD1
|
A:LEU129
|
4.8
|
21.2
|
1.0
|
HG21
|
A:ILE134
|
4.8
|
11.4
|
1.0
|
HD12
|
A:LEU129
|
4.8
|
25.4
|
1.0
|
HE3
|
A:MET226
|
4.8
|
17.6
|
1.0
|
CB
|
A:MET226
|
4.9
|
8.9
|
1.0
|
HG13
|
A:ILE134
|
4.9
|
13.9
|
1.0
|
HD13
|
A:ILE165
|
4.9
|
14.5
|
1.0
|
N
|
A:ILE134
|
4.9
|
9.7
|
1.0
|
CA
|
A:MET138
|
4.9
|
7.2
|
1.0
|
HD11
|
A:LEU129
|
5.0
|
25.4
|
1.0
|
CB
|
A:MET138
|
5.0
|
7.5
|
1.0
|
|
Chlorine binding site 2 out
of 3 in 7atv
Go back to
Chlorine Binding Sites List in 7atv
Chlorine binding site 2 out
of 3 in the Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl402
b:10.8
occ:1.00
|
CL2
|
A:RXE402
|
0.0
|
10.8
|
1.0
|
C07
|
A:RXE402
|
1.8
|
9.5
|
1.0
|
C06
|
A:RXE402
|
2.7
|
9.6
|
1.0
|
C02
|
A:RXE402
|
2.7
|
10.4
|
1.0
|
H3
|
A:RXE402
|
2.8
|
11.5
|
1.0
|
HE2
|
A:MET138
|
3.0
|
15.3
|
1.0
|
CL1
|
A:RXE402
|
3.2
|
11.1
|
1.0
|
HB3
|
A:TYR137
|
3.3
|
10.3
|
1.0
|
HA
|
A:MET138
|
3.4
|
8.7
|
1.0
|
HD22
|
A:LEU141
|
3.5
|
10.4
|
1.0
|
HD23
|
A:LEU141
|
3.5
|
10.4
|
1.0
|
HD11
|
A:LEU172
|
3.6
|
11.6
|
1.0
|
HB2
|
A:LEU141
|
3.6
|
8.9
|
1.0
|
HG2
|
A:MET138
|
3.6
|
10.1
|
1.0
|
O
|
A:TYR137
|
3.7
|
7.8
|
1.0
|
HE2
|
A:MET222
|
3.7
|
11.6
|
1.0
|
C
|
A:TYR137
|
3.8
|
8.1
|
1.0
|
HD11
|
A:ILE165
|
3.8
|
14.5
|
1.0
|
CE
|
A:MET138
|
3.8
|
12.8
|
1.0
|
HG11
|
A:VAL163
|
3.8
|
12.5
|
1.0
|
N
|
A:MET138
|
3.9
|
7.6
|
1.0
|
HB2
|
A:TYR137
|
3.9
|
10.3
|
1.0
|
CD2
|
A:LEU141
|
3.9
|
8.7
|
1.0
|
HB3
|
A:LEU141
|
4.0
|
8.9
|
1.0
|
CB
|
A:TYR137
|
4.0
|
8.6
|
1.0
|
C03
|
A:RXE402
|
4.0
|
11.3
|
1.0
|
C05
|
A:RXE402
|
4.0
|
9.5
|
1.0
|
SD
|
A:MET138
|
4.1
|
10.5
|
1.0
|
CA
|
A:MET138
|
4.1
|
7.2
|
1.0
|
HD12
|
A:LEU172
|
4.1
|
11.6
|
1.0
|
HE1
|
A:MET138
|
4.2
|
15.3
|
1.0
|
HE1
|
A:MET222
|
4.2
|
11.6
|
1.0
|
CD1
|
A:LEU172
|
4.2
|
9.6
|
1.0
|
CB
|
A:LEU141
|
4.2
|
7.5
|
1.0
|
H
|
A:MET138
|
4.2
|
9.1
|
1.0
|
CG
|
A:MET138
|
4.2
|
8.4
|
1.0
|
HD13
|
A:LEU172
|
4.3
|
11.6
|
1.0
|
CE
|
A:MET222
|
4.4
|
9.7
|
1.0
|
C04
|
A:RXE402
|
4.5
|
11.1
|
1.0
|
CA
|
A:TYR137
|
4.5
|
8.2
|
1.0
|
HE3
|
A:MET138
|
4.5
|
15.3
|
1.0
|
HD21
|
A:LEU141
|
4.7
|
10.4
|
1.0
|
CD1
|
A:ILE165
|
4.7
|
12.1
|
1.0
|
CG1
|
A:VAL163
|
4.7
|
10.4
|
1.0
|
H1
|
A:RXE402
|
4.7
|
13.6
|
1.0
|
CG
|
A:LEU141
|
4.7
|
7.7
|
1.0
|
HE3
|
A:MET222
|
4.8
|
11.6
|
1.0
|
CB
|
A:MET138
|
4.8
|
7.5
|
1.0
|
HG12
|
A:VAL163
|
4.8
|
12.5
|
1.0
|
H
|
A:LEU141
|
4.8
|
8.6
|
1.0
|
HG21
|
A:VAL163
|
4.8
|
12.2
|
1.0
|
HD13
|
A:ILE165
|
4.9
|
14.5
|
1.0
|
HG3
|
A:MET226
|
5.0
|
13.4
|
1.0
|
|
Chlorine binding site 3 out
of 3 in 7atv
Go back to
Chlorine Binding Sites List in 7atv
Chlorine binding site 3 out
of 3 in the Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Bivalent Inhibitor KN2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl403
b:19.0
occ:1.00
|
H
|
A:ASN190
|
2.3
|
13.4
|
1.0
|
HH22
|
A:ARG156
|
2.3
|
11.5
|
1.0
|
HD1
|
A:TYR189
|
2.9
|
12.1
|
1.0
|
N
|
A:ASN190
|
3.2
|
11.2
|
1.0
|
HB2
|
A:ASN190
|
3.2
|
17.2
|
1.0
|
NH2
|
A:ARG156
|
3.2
|
9.6
|
1.0
|
HB3
|
A:TYR189
|
3.3
|
11.4
|
1.0
|
HA
|
A:TYR189
|
3.3
|
12.2
|
1.0
|
O
|
A:HOH819
|
3.3
|
17.6
|
1.0
|
HH12
|
A:ARG156
|
3.4
|
11.0
|
1.0
|
HB3
|
A:ASN190
|
3.4
|
17.2
|
1.0
|
HG3
|
A:GLU181
|
3.5
|
11.3
|
0.5
|
CB
|
A:ASN190
|
3.7
|
14.3
|
1.0
|
HH21
|
A:ARG156
|
3.7
|
11.5
|
1.0
|
CD1
|
A:TYR189
|
3.7
|
10.0
|
1.0
|
CA
|
A:TYR189
|
3.9
|
10.2
|
1.0
|
HG2
|
A:GLU181
|
3.9
|
13.0
|
0.5
|
CB
|
A:TYR189
|
3.9
|
9.5
|
1.0
|
O
|
A:HOH744
|
3.9
|
25.6
|
1.0
|
NH1
|
A:ARG156
|
4.0
|
9.1
|
1.0
|
C
|
A:TYR189
|
4.0
|
10.3
|
1.0
|
CA
|
A:ASN190
|
4.0
|
10.8
|
1.0
|
CZ
|
A:ARG156
|
4.0
|
8.5
|
1.0
|
OE1
|
A:GLU181
|
4.2
|
13.7
|
0.5
|
CG
|
A:TYR189
|
4.3
|
9.2
|
1.0
|
CG
|
A:GLU181
|
4.4
|
9.4
|
0.5
|
HH
|
A:TYR210
|
4.5
|
10.4
|
1.0
|
HG2
|
A:GLU181
|
4.6
|
11.3
|
0.5
|
O
|
A:ASN190
|
4.6
|
10.9
|
1.0
|
HH12
|
A:ARG81
|
4.8
|
18.4
|
1.0
|
HB2
|
A:TYR189
|
4.8
|
11.4
|
1.0
|
CG
|
A:GLU181
|
4.8
|
10.8
|
0.5
|
CE1
|
A:TYR189
|
4.8
|
9.7
|
1.0
|
HA
|
A:ASN190
|
4.8
|
13.0
|
1.0
|
HH11
|
A:ARG156
|
4.8
|
11.0
|
1.0
|
HE1
|
A:TYR189
|
4.8
|
11.6
|
1.0
|
OE2
|
A:GLU181
|
4.8
|
11.0
|
0.5
|
OH
|
A:TYR210
|
4.8
|
8.7
|
1.0
|
C
|
A:ASN190
|
4.9
|
10.0
|
1.0
|
HG11
|
A:VAL193
|
5.0
|
14.2
|
1.0
|
|
Reference:
D.Lindenblatt,
V.Applegate,
A.Nickelsen,
M.Klussmann,
I.Neundorf,
C.Gotz,
J.Jose,
K.Niefind.
Molecular Plasticity of Crystalline CK2 Alpha ' Leads to KN2, A Bivalent Inhibitor of Protein Kinase CK2 with Extraordinary Selectivity J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.1C00063
Page generated: Mon Jul 29 18:42:15 2024
|