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Sodium in PDB 6pdc: Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 42

Enzymatic activity of Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 42

All present enzymatic activity of Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 42:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 42, PDB code: 6pdc 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) 41.69 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.183, 56.837, 122.670, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.5

Other elements in 6pdc:

The structure of Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 42 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 42 (pdb code 6pdc). 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 42, PDB code: 6pdc:

Sodium binding site 1 out of 1 in 6pdc

Go back to Sodium Binding Sites List in 6pdc
Sodium binding site 1 out of 1 in the Crystal Structure of Myst Acetyltransferase Domain in Complex with Inhibitor 42


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 42 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:15.2
occ:1.00
O A:HOH923 3.1 25.0 1.0
O A:HOH975 3.1 38.3 1.0
O A:HOH932 3.1 25.0 1.0
N A:ASP520 3.2 15.5 1.0
CA A:ILE519 3.8 19.2 1.0
OD2 A:ASP520 3.9 23.2 1.0
CB A:ASP520 4.0 17.9 1.0
C A:ILE519 4.0 18.4 1.0
CG A:ASP520 4.1 21.6 1.0
CG2 A:ILE519 4.1 16.7 1.0
CA A:ASP520 4.2 17.0 1.0
O A:GLU518 4.2 20.5 1.0
O A:HOH988 4.4 30.9 1.0
CB A:ILE519 4.6 15.5 1.0
O A:ASP520 4.6 17.0 1.0
N A:ILE519 4.8 16.6 1.0
OD1 A:ASP520 4.8 22.4 1.0
C A:GLU518 4.9 22.3 1.0
C A:ASP520 4.9 18.0 1.0
O A:HOH912 4.9 26.4 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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