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Sodium in PDB 6hbn: High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27

Enzymatic activity of High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27

All present enzymatic activity of High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27:
2.7.11.1;

Protein crystallography data

The structure of High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27, PDB code: 6hbn was solved by K.Niefind, J.Hochscherf, V.Dimper, B.Witulski, D.Lindenblatt, J.Jose, M.Leborgne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.02 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.550, 71.620, 128.030, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.7

Other elements in 6hbn:

The structure of High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27 also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27 (pdb code 6hbn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27, PDB code: 6hbn:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6hbn

Go back to Sodium Binding Sites List in 6hbn
Sodium binding site 1 out of 3 in the High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:37.7
occ:1.00
 O A:GLU114 2.3 31.7 1.0
O A:LYS64 2.3 30.7 1.0
O A:HOH519 2.4 41.8 1.0
O A:HOH739 2.4 54.7 1.0
O A:HOH717 2.7 67.7 1.0
C A:GLU114 3.4 30.4 1.0
C A:LYS64 3.5 30.3 1.0
CA A:GLU114 4.2 31.4 1.0
CG1 A:VAL65 4.2 30.2 1.0
OE1 A:GLU63 4.3 53.2 1.0
N A:LYS64 4.3 33.6 1.0
N A:HIS115 4.4 33.5 1.0
N A:VAL65 4.4 29.7 1.0
CB A:GLU63 4.5 42.0 1.0
CA A:VAL65 4.5 29.5 1.0
CA A:HIS115 4.5 36.8 1.0
CA A:LYS64 4.5 30.5 1.0
O A:HOH741 4.5 41.0 1.0
CB A:GLU114 4.6 35.1 1.0
C A:GLU63 4.8 32.5 1.0
N A:VAL116 4.9 38.6 1.0
CB A:VAL65 5.0 29.6 1.0

Sodium binding site 2 out of 3 in 6hbn

Go back to Sodium Binding Sites List in 6hbn
Sodium binding site 2 out of 3 in the High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na407

b:36.6
occ:1.00
 O B:LYS64 2.3 29.5 1.0
O B:GLU114 2.3 29.6 1.0
O B:HOH545 2.5 45.3 1.0
C B:GLU114 3.5 28.6 1.0
C B:LYS64 3.5 27.8 1.0
N B:LYS64 4.2 32.1 1.0
CA B:GLU114 4.3 26.7 1.0
OE1 B:GLU63 4.3 52.7 1.0
CB B:GLU63 4.4 38.5 1.0
CA B:LYS64 4.4 27.7 1.0
CG1 B:VAL65 4.4 30.8 1.0
N B:HIS115 4.4 28.5 1.0
N B:VAL65 4.5 27.1 1.0
CA B:HIS115 4.5 31.0 1.0
CA B:VAL65 4.6 27.3 1.0
O B:HOH736 4.6 37.3 1.0
CB B:GLU114 4.7 28.2 1.0
C B:GLU63 4.7 31.5 1.0
N B:VAL116 4.9 33.7 1.0
CB B:LYS64 4.9 29.4 1.0

Sodium binding site 3 out of 3 in 6hbn

Go back to Sodium Binding Sites List in 6hbn
Sodium binding site 3 out of 3 in the High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of High-Salt Structure of Protein Kinase CK2 Catalytic Subunit (Isoform CK2ALPHA/CSKN2A1 Gene Product) in Complex with the Indenoindole-Type Inhibitor THN27 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na408

b:32.4
occ:1.00
 O B:THR60 2.4 39.9 1.0
O A:HOH537 2.4 28.0 1.0
O B:HOH763 2.4 36.5 1.0
O B:HOH553 2.4 39.5 1.0
O A:HOH688 2.6 34.8 1.0
C B:THR60 3.4 37.0 1.0
OD2 A:ASP38 3.8 35.8 1.0
CA B:ASN61 4.1 36.5 1.0
CB B:ASN61 4.1 35.6 1.0
N B:ASN61 4.1 33.0 1.0
OD2 A:ASP99 4.2 33.7 1.0
O A:HOH582 4.2 35.5 1.0
CA A:GLY34 4.4 38.0 1.0
CB B:THR60 4.4 38.1 1.0
CA B:THR60 4.4 34.5 1.0
N A:ASN35 4.5 42.5 1.0
OG1 B:THR60 4.5 37.9 1.0
O B:HOH690 4.6 37.2 1.0
O A:HOH716 4.7 37.3 1.0
O B:HOH750 4.7 45.7 1.0
O B:HOH522 4.8 42.3 1.0
C A:GLY34 5.0 43.2 1.0
OD1 A:ASP99 5.0 34.5 1.0
CG A:ASP99 5.0 31.6 1.0

Reference:

D.Lindenblatt, A.Nickelsen, V.M.Applegate, J.Hochscherf, B.Witulski, Z.Bouaziz, C.Marminon, M.Bretner, M.Le Borgne, J.Jose, K.Niefind. Diacritic Binding of An Indenoindole Inhibitor By CK2 Alpha Paralogs Explored By A Reliable Path to Atomic Resolution CK2 Alpha ' Structures. Acs Omega V. 4 5471 2019.
ISSN: ESSN 2470-1343
PubMed: 31559376
DOI: 10.1021/ACSOMEGA.8B03415
Page generated: Tue Oct 8 09:16:37 2024

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