Sodium in PDB 7at9: Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Atp-Competitive Inhibitor MB002 and the Alphad-Pocket Ligand 3,4-Dichlorophenethylamine

Enzymatic activity of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Atp-Competitive Inhibitor MB002 and the Alphad-Pocket Ligand 3,4-Dichlorophenethylamine

All present enzymatic activity of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Atp-Competitive Inhibitor MB002 and the Alphad-Pocket Ligand 3,4-Dichlorophenethylamine:
2.7.11.1;

Protein crystallography data

The structure of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Atp-Competitive Inhibitor MB002 and the Alphad-Pocket Ligand 3,4-Dichlorophenethylamine, PDB code: 7at9 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) 43.74 / 1.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.482, 47.661, 50.733, 66.61, 89.44, 88.66
R / Rfree (%) 12.9 / 15

Other elements in 7at9:

The structure of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Atp-Competitive Inhibitor MB002 and the Alphad-Pocket Ligand 3,4-Dichlorophenethylamine also contains other interesting chemical elements:

Bromine (Br) 8 atoms
Chlorine (Cl) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Atp-Competitive Inhibitor MB002 and the Alphad-Pocket Ligand 3,4-Dichlorophenethylamine (pdb code 7at9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Atp-Competitive Inhibitor MB002 and the Alphad-Pocket Ligand 3,4-Dichlorophenethylamine, PDB code: 7at9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7at9

Go back to Sodium Binding Sites List in 7at9
Sodium binding site 1 out of 2 in the Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Atp-Competitive Inhibitor MB002 and the Alphad-Pocket Ligand 3,4-Dichlorophenethylamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Atp-Competitive Inhibitor MB002 and the Alphad-Pocket Ligand 3,4-Dichlorophenethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na513

b:44.7
occ:1.00
O A:HOH691 2.4 16.7 0.6
O A:HOH726 2.8 28.5 1.0
O A:HOH715 3.1 36.2 1.0
OD2 A:ASP206 3.2 18.5 0.4
OD2 A:ASP206 3.2 16.6 0.6
OD1 A:ASP206 3.6 14.4 0.6
O A:LEU204 3.8 12.5 1.0
HE2 A:PHE270 3.8 19.6 1.0
HE1 A:TYR240 3.8 21.7 1.0
CG A:ASP206 3.8 15.4 0.6
OD2 A:ASP267 3.9 18.1 1.0
HH A:TYR240 4.0 28.9 1.0
CE1 A:TYR240 4.0 18.1 1.0
HB2 A:ASP267 4.1 18.1 1.0
CZ A:TYR240 4.2 20.6 1.0
OH A:TYR240 4.2 24.1 1.0
HZ A:PHE270 4.4 21.4 1.0
HB3 A:ASP267 4.4 18.1 1.0
O A:HOH723 4.4 29.6 1.0
CE2 A:PHE270 4.4 16.3 1.0
CG A:ASP206 4.5 14.3 0.4
CB A:ASP267 4.6 15.1 1.0
CD1 A:TYR240 4.7 17.5 1.0
CG A:ASP267 4.7 17.2 1.0
CZ A:PHE270 4.7 17.8 1.0
C A:LEU204 4.9 11.1 1.0
O A:HOH616 4.9 43.0 1.0
CE2 A:TYR240 4.9 23.3 1.0
O A:HOH746 4.9 19.4 1.0
HD1 A:TYR240 4.9 21.0 1.0

Sodium binding site 2 out of 2 in 7at9

Go back to Sodium Binding Sites List in 7at9
Sodium binding site 2 out of 2 in the Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Atp-Competitive Inhibitor MB002 and the Alphad-Pocket Ligand 3,4-Dichlorophenethylamine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Protein Kinase CK2 Catalytic Subunit (CSNK2A2 Gene Product) in Complex with the Atp-Competitive Inhibitor MB002 and the Alphad-Pocket Ligand 3,4-Dichlorophenethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na514

b:29.5
occ:1.00
O A:HOH676 2.6 24.6 1.0
O A:HOH896 2.8 38.8 1.0
O A:ILE95 2.9 11.2 1.0
HE A:ARG173 2.9 15.0 1.0
HB2 A:LYS97 3.1 18.1 1.0
O A:HOH789 3.2 25.3 1.0
NE A:ARG173 3.3 12.5 1.0
OE2 A:GLU115 3.3 13.5 1.0
HD2 A:ARG173 3.6 13.8 1.0
HH21 A:ARG173 3.6 20.6 1.0
CZ A:ARG173 3.9 14.0 1.0
H A:LYS97 4.0 13.9 1.0
CD A:ARG173 4.0 11.5 1.0
NH2 A:ARG173 4.0 17.2 1.0
CB A:LYS97 4.0 15.1 1.0
C A:ILE95 4.0 10.3 1.0
O A:GLY92 4.1 14.5 1.0
N A:LYS97 4.1 11.6 1.0
H A:ILE95 4.1 13.2 1.0
CD A:GLU115 4.2 13.7 1.0
H A:ASN94 4.2 13.5 1.0
HD3 A:ARG173 4.3 13.8 1.0
HD3 A:LYS97 4.3 34.0 1.0
OE1 A:GLU115 4.3 17.7 1.0
HA A:ILE96 4.4 12.2 1.0
HA A:LYS97 4.4 14.8 1.0
HB3 A:LYS97 4.4 18.1 1.0
CA A:LYS97 4.4 12.4 1.0
N A:ILE95 4.5 11.0 1.0
O A:HOH891 4.6 34.2 1.0
C A:ILE96 4.6 10.5 1.0
HA A:ASN94 4.6 12.8 1.0
HH22 A:ARG173 4.6 20.6 1.0
N A:ASN94 4.8 11.3 1.0
CA A:ILE96 4.9 10.2 1.0
CA A:ILE95 4.9 11.3 1.0
NH1 A:ARG173 4.9 13.7 1.0
N A:ILE96 4.9 10.7 1.0
CG A:LYS97 4.9 21.2 1.0
HG3 A:LYS97 5.0 25.4 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: Sat Aug 21 17:20:13 2021

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