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Sodium in PDB 6pde: Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 40

Enzymatic activity of Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 40

All present enzymatic activity of Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 40:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 40, PDB code: 6pde was solved by S.J.Hermans, M.W.Parker, T.Thomas, J.B.Baell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.14 / 2.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.081, 56.383, 122.684, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.9

Other elements in 6pde:

The structure of Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 40 also contains other interesting chemical elements:

Fluorine (F) 1 atom
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 40 (pdb code 6pde). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 40, PDB code: 6pde:

Sodium binding site 1 out of 1 in 6pde

Go back to Sodium Binding Sites List in 6pde
Sodium binding site 1 out of 1 in the Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 40


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 40 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:20.3
occ:1.00
 O A:HOH936 2.9 25.3 1.0
O A:HOH912 3.1 25.3 1.0
N A:ASP520 3.3 23.1 1.0
CA A:ILE519 3.8 22.6 1.0
OD2 A:ASP520 3.9 33.9 1.0
O A:HOH911 4.0 42.5 1.0
CB A:ASP520 4.0 23.9 1.0
CG A:ASP520 4.0 31.2 1.0
C A:ILE519 4.0 22.2 1.0
CG2 A:ILE519 4.1 19.5 1.0
O A:GLU518 4.2 28.5 1.0
CA A:ASP520 4.2 21.9 1.0
CB A:ILE519 4.6 22.2 1.0
O A:ASP520 4.6 20.1 1.0
OD1 A:ASP520 4.7 27.8 1.0
N A:ILE519 4.8 21.6 1.0
C A:GLU518 4.9 29.2 1.0
C A:ASP520 4.9 24.2 1.0
O A:HOH922 5.0 33.7 1.0

Reference:

D.L.Priebbenow, D.J.Leaver, N.Nguyen, B.Cleary, H.R.Lagiakos, J.Sanchez, L.Xue, F.Huang, Y.Sun, P.Mujumdar, R.Mudududdla, S.Varghese, S.Teguh, S.A.Charman, K.L.White, D.M.Shackleford, K.Katneni, M.Cuellar, J.M.Strasser, J.L.Dahlin, M.A.Walters, I.P.Street, B.J.Monahan, K.E.Jarman, H.Jousset Sabroux, H.Falk, M.C.Chung, S.J.Hermans, N.L.Downer, M.W.Parker, A.K.Voss, T.Thomas, J.B.Baell. Discovery of Acylsulfonohydrazide-Derived Inhibitors of the Lysine Acetyltransferase, KAT6A, As Potent Senescence-Inducing Anti-Cancer Agents. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32118427
DOI: 10.1021/ACS.JMEDCHEM.9B02071
Page generated: Tue Oct 8 12:43:02 2024

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