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Chlorine in PDB 8qbu: Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa)

Enzymatic activity of Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa)

All present enzymatic activity of Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa):
2.7.11.1;

Protein crystallography data

The structure of Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa), PDB code: 8qbu was solved by C.Werner, K.Niefind, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.17 / 1.09
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.173, 47.715, 50.586, 66.05, 89.72, 88.97
R / Rfree (%) 15.9 / 17.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa) (pdb code 8qbu). 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 (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa), PDB code: 8qbu:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 8qbu

Go back to Chlorine Binding Sites List in 8qbu
Chlorine binding site 1 out of 3 in the Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa)


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 (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:22.7
occ:1.00
CL1 A:42J404 0.0 22.7 1.0
C6 A:42J404 1.7 21.4 1.0
C7 A:42J404 2.7 20.1 1.0
C5 A:42J404 2.7 23.2 1.0
H3 A:42J404 2.8 24.1 1.0
HE2 A:MET138 2.8 25.3 1.0
HB3 A:TYR137 3.2 13.0 1.0
CL A:42J404 3.2 24.7 1.0
HG11 A:VAL163 3.4 14.9 1.0
HD22 A:LEU141 3.4 11.9 1.0
HE2 A:MET222 3.5 13.8 1.0
HD11 A:ILE165 3.5 17.8 1.0
HA A:MET138 3.5 10.2 1.0
HD11 A:LEU172 3.7 12.6 1.0
HD23 A:LEU141 3.7 11.9 1.0
CE A:MET138 3.7 21.1 1.0
HG2 A:MET138 3.7 15.4 1.0
HB2 A:LEU141 3.8 11.6 1.0
C A:TYR137 3.8 9.5 1.0
O A:TYR137 3.8 10.4 1.0
HB2 A:TYR137 3.9 13.0 1.0
CB A:TYR137 3.9 10.8 1.0
C2 A:42J404 4.0 19.6 1.0
C4 A:42J404 4.0 23.4 1.0
N A:MET138 4.0 9.2 1.0
CD2 A:LEU141 4.0 9.9 1.0
SD A:MET138 4.1 17.7 1.0
HE1 A:MET222 4.1 13.8 1.0
HB3 A:LEU141 4.1 11.6 1.0
HD12 A:LEU172 4.2 12.6 1.0
CE A:MET222 4.2 11.4 1.0
HE1 A:MET138 4.2 25.3 1.0
CA A:MET138 4.2 8.5 1.0
CG1 A:VAL163 4.3 12.4 1.0
CD1 A:LEU172 4.3 10.5 1.0
HE3 A:MET138 4.3 25.3 1.0
CB A:LEU141 4.4 9.6 1.0
CG A:MET138 4.4 12.8 1.0
CD1 A:ILE165 4.4 14.8 1.0
H A:MET138 4.4 11.1 1.0
HG12 A:VAL163 4.4 14.9 1.0
C3 A:42J404 4.5 22.0 1.0
CA A:TYR137 4.5 10.0 1.0
HD13 A:LEU172 4.5 12.6 1.0
HE3 A:MET222 4.6 13.8 1.0
HD12 A:ILE165 4.6 17.8 1.0
HD13 A:ILE165 4.7 17.8 1.0
H1 A:42J404 4.7 28.1 1.0
HD21 A:LEU141 4.7 11.9 1.0
HG13 A:VAL163 4.8 14.9 1.0
HG21 A:VAL163 4.9 14.1 1.0
HG3 A:MET226 4.9 17.6 1.0
CG A:LEU141 4.9 9.6 1.0
HB A:VAL163 4.9 13.8 1.0
CB A:MET138 4.9 10.5 1.0

Chlorine binding site 2 out of 3 in 8qbu

Go back to Chlorine Binding Sites List in 8qbu
Chlorine binding site 2 out of 3 in the Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa)


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 (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:24.7
occ:1.00
CL A:42J404 0.0 24.7 1.0
C5 A:42J404 1.7 23.2 1.0
C4 A:42J404 2.7 23.4 1.0
C6 A:42J404 2.7 21.4 1.0
H1 A:42J404 2.8 28.1 1.0
HB2 A:TYR137 2.8 13.0 1.0
HA A:ILE134 3.0 13.5 1.0
HG3 A:MET226 3.1 17.6 1.0
CL1 A:42J404 3.2 22.7 1.0
HE2 A:MET138 3.2 25.3 1.0
HG23 A:ILE134 3.3 13.7 1.0
HG2 A:MET138 3.3 15.4 1.0
HB3 A:TYR137 3.5 13.0 1.0
HE2 A:MET226 3.6 33.6 1.0
CB A:TYR137 3.6 10.8 1.0
HG12 A:ILE134 3.7 16.0 1.0
HE3 A:MET138 3.8 25.3 1.0
HD2 A:TYR137 3.8 14.3 1.0
HD13 A:LEU129 3.8 35.9 1.0
CE A:MET138 3.9 21.1 1.0
CA A:ILE134 3.9 11.2 1.0
C3 A:42J404 4.0 22.0 1.0
C7 A:42J404 4.0 20.1 1.0
O A:ILE134 4.0 10.0 1.0
CG A:MET226 4.1 14.7 1.0
H A:MET138 4.2 11.1 1.0
CG2 A:ILE134 4.2 11.4 1.0
CG A:MET138 4.2 12.8 1.0
HB3 A:MET226 4.3 14.3 1.0
N A:MET138 4.4 9.2 1.0
HD22 A:LEU129 4.4 35.4 1.0
CE A:MET226 4.4 28.0 1.0
CB A:ILE134 4.5 11.6 1.0
C A:ILE134 4.5 10.4 1.0
CD2 A:TYR137 4.5 11.9 1.0
CG1 A:ILE134 4.5 13.3 1.0
CG A:TYR137 4.5 11.2 1.0
HD11 A:ILE165 4.5 17.8 1.0
C2 A:42J404 4.5 19.6 1.0
C A:TYR137 4.6 9.5 1.0
CA A:TYR137 4.6 10.0 1.0
HG2 A:MET226 4.6 17.6 1.0
O A:ASP133 4.6 11.2 1.0
HG3 A:MET138 4.6 15.4 1.0
HE1 A:MET138 4.7 25.3 1.0
H A:TYR137 4.7 12.2 1.0
HG22 A:ILE134 4.7 13.7 1.0
SD A:MET226 4.7 23.1 1.0
CB A:MET226 4.7 11.9 1.0
H2 A:42J404 4.7 26.4 1.0
H3 A:42J404 4.7 24.1 1.0
CD1 A:LEU129 4.8 29.9 1.0
HG21 A:ILE134 4.8 13.7 1.0
HD13 A:ILE165 4.8 17.8 1.0
HD12 A:ILE165 4.9 17.8 1.0
SD A:MET138 4.9 17.7 1.0
HB2 A:MET226 4.9 14.3 1.0
HE1 A:MET226 4.9 33.6 1.0
N A:ILE134 4.9 11.9 1.0
HD11 A:LEU129 4.9 35.9 1.0
HA A:MET138 4.9 10.2 1.0
HG13 A:ILE134 4.9 16.0 1.0
CD1 A:ILE165 4.9 14.8 1.0

Chlorine binding site 3 out of 3 in 8qbu

Go back to Chlorine Binding Sites List in 8qbu
Chlorine binding site 3 out of 3 in the Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa)


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 (Isoform CK2ALPHA'; CSNK2A2 Gene Product) in Complex with the Inhibitor Cx-4945 and the Alpha-D-Pocket Ligand 3,4-Dichloro Phenethylamine (Dpa) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:19.9
occ:1.00
CL22 A:3NG405 0.0 19.9 1.0
C18 A:3NG405 1.7 16.6 1.0
HG22 A:VAL54 2.4 18.3 0.3
C17 A:3NG405 2.7 15.1 1.0
C19 A:3NG405 2.7 15.9 1.0
H17 A:3NG405 2.8 18.1 1.0
H19 A:3NG405 2.8 19.1 1.0
HA3 A:GLY47 2.9 18.2 1.0
HO2 A:EDO411 3.0 41.5 1.0
HB A:VAL54 3.1 14.0 0.7
CG2 A:VAL54 3.2 15.3 0.3
H22 A:EDO411 3.2 44.2 1.0
HG23 A:VAL54 3.2 18.3 0.3
O A:HOH562 3.3 30.1 1.0
HG23 A:VAL54 3.3 15.2 0.7
HG21 A:VAL54 3.4 15.2 0.7
C A:GLY47 3.4 15.2 1.0
CA A:GLY47 3.5 15.2 1.0
HG21 A:VAL54 3.6 18.3 0.3
N A:ARG48 3.6 17.2 1.0
H21 A:EDO411 3.6 44.2 1.0
H A:ARG48 3.7 20.7 1.0
O A:HOH742 3.7 37.7 1.0
CG2 A:VAL54 3.7 12.7 0.7
C2 A:EDO411 3.7 36.8 1.0
O2 A:EDO411 3.7 34.6 1.0
O A:GLY47 3.7 15.3 1.0
CB A:VAL54 3.9 11.7 0.7
HG13 A:VAL54 3.9 17.5 0.3
C20 A:3NG405 4.0 16.1 1.0
C16 A:3NG405 4.0 13.9 1.0
N A:GLY47 4.0 14.5 1.0
H A:VAL54 4.0 15.8 0.3
H A:GLY47 4.1 17.4 1.0
H A:VAL54 4.1 14.1 0.7
HG11 A:VAL54 4.3 17.5 0.3
CB A:VAL54 4.3 14.4 0.3
CG1 A:VAL54 4.4 14.6 0.3
HA2 A:GLY47 4.4 18.2 1.0
CA A:ARG48 4.4 23.2 1.0
HA A:ARG48 4.4 27.9 1.0
C A:ARG48 4.4 24.6 1.0
O A:HOH599 4.5 19.0 1.0
C21 A:3NG405 4.5 15.0 1.0
O A:ARG48 4.6 26.4 1.0
N A:VAL54 4.6 11.7 0.7
C A:LEU46 4.6 14.9 1.0
HG22 A:VAL54 4.6 15.2 0.7
HB2 A:LEU46 4.7 17.3 1.0
O A:HOH703 4.7 32.1 1.0
H20 A:3NG405 4.7 19.3 1.0
N A:VAL54 4.8 13.1 0.3
CA A:VAL54 4.8 10.9 0.7
HA A:GLU53 4.8 17.1 0.7
HG11 A:VAL54 4.8 15.3 0.7
N A:GLY49 4.9 24.9 1.0
O A:LEU46 4.9 17.1 1.0
H A:GLY49 4.9 29.9 1.0
CG1 A:VAL54 5.0 12.7 0.7

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: Sun Jul 13 13:29:19 2025

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