Magnesium in PDB 6ypn: Crystal Structure of CK2ALPHA with 2 Molecules of Adp Bound

All present enzymatic activity of Crystal Structure of CK2ALPHA with 2 Molecules of Adp Bound:
2.7.11.1;

The structure of Crystal Structure of CK2ALPHA with 2 Molecules of Adp Bound, PDB code: 6ypn was solved by P.Brear, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.97 / 1.58
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.392, 45.225, 62.631, 90.00, 109.90, 90.00
R / Rfree (%)	20.5 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of CK2ALPHA with 2 Molecules of Adp Bound (pdb code 6ypn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of CK2ALPHA with 2 Molecules of Adp Bound, PDB code: 6ypn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of CK2ALPHA with 2 Molecules of Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of CK2ALPHA with 2 Molecules of Adp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:19.6 occ:1.00 O1A B:ADP401 2.2 20.9 1.0 O4 B:PO4406 2.2 19.1 1.0 OD2 B:ASP175 2.2 24.7 1.0 OD1 B:ASN161 2.2 17.7 1.0 O B:HOH525 2.2 21.3 1.0 O2B B:ADP401 2.2 21.3 1.0 CG B:ASP175 3.2 21.9 1.0 CG B:ASN161 3.2 18.9 1.0 PB B:ADP401 3.4 23.8 1.0 P B:PO4406 3.4 26.0 1.0 PA B:ADP401 3.5 21.9 1.0 ND2 B:ASN161 3.6 18.7 1.0 CB B:ASP175 3.6 19.4 1.0 O3A B:ADP401 3.7 19.2 1.0 O3 B:PO4406 3.7 24.6 1.0 O3B B:ADP401 3.8 25.7 1.0 MG B:MG405 3.9 23.2 1.0 O1 B:PO4406 3.9 27.0 1.0 OD1 B:ASP175 4.2 21.6 1.0 O3' B:ADP401 4.3 21.6 1.0 OXT B:ACT402 4.4 43.4 1.0 C5' B:ADP401 4.4 25.2 1.0 O5' B:ADP401 4.5 24.9 1.0 O2A B:ADP401 4.5 20.1 1.0 CB B:ASN161 4.6 15.7 1.0 CE B:LYS158 4.6 18.3 1.0 O B:HIS160 4.6 19.8 1.0 O2 B:PO4406 4.6 24.3 1.0 O1B B:ADP401 4.7 23.9 1.0 OD2 B:ASP156 4.8 20.4 1.0 O B:ACT402 4.8 45.0 1.0 CA B:ASN161 4.8 16.8 1.0 C3' B:ADP401 4.9 21.1 1.0 C B:HIS160 4.9 22.0 1.0 O B:HOH505 4.9 23.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of CK2ALPHA with 2 Molecules of Adp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of CK2ALPHA with 2 Molecules of Adp Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:23.2 occ:1.00 O3B B:ADP401 2.2 25.7 1.0 O3 B:PO4406 2.2 24.6 1.0 O B:HOH532 2.2 23.2 1.0 OD2 B:ASP175 2.2 24.7 1.0 OD1 B:ASP175 2.2 21.6 1.0 O B:HOH505 2.2 23.0 1.0 CG B:ASP175 2.5 21.9 1.0 PB B:ADP401 3.4 23.8 1.0 P B:PO4406 3.5 26.0 1.0 O2B B:ADP401 3.6 21.3 1.0 N1 B:ADP403 3.9 27.9 1.0 MG B:MG404 3.9 19.6 1.0 O4 B:PO4406 3.9 19.1 1.0 N6 B:ADP403 4.0 28.0 1.0 CB B:ASP175 4.0 19.4 1.0 OD2 B:ASP156 4.0 20.4 1.0 NZ B:LYS68 4.1 20.7 1.0 O B:HOH627 4.1 28.4 1.0 O1 B:PO4406 4.2 27.0 1.0 O1B B:ADP401 4.4 23.9 1.0 CA B:GLY177 4.4 21.1 1.0 C6 B:ADP403 4.4 26.9 1.0 O3A B:ADP401 4.5 19.2 1.0 N B:GLY177 4.5 20.0 1.0 O2 B:PO4406 4.6 24.3 1.0 O B:ASP175 4.7 19.4 1.0 O1A B:ADP401 4.7 20.9 1.0 N B:LEU178 4.8 19.2 1.0 CA B:ASP175 4.8 17.3 1.0 C B:ASP175 4.9 19.7 1.0 C2 B:ADP403 4.9 30.3 1.0 C B:GLY177 4.9 23.7 1.0 ND2 B:ASN161 4.9 18.7 1.0

P.Brear, D.Ball, K.Stott, S.D'arcy, M.Hyvonen. Proposed Allosteric Inhibitors Bind to the Atp Site of CK2 Alpha. J.Med.Chem. V. 63 12786 2020.
ISSN: ISSN 0022-2623
PubMed: 33119282
DOI: 10.1021/ACS.JMEDCHEM.0C01173