Sodium in PDB 6ba4: Crystal Structure of Myst Acetyltransferase Domain in Complex with Acetyl-Coa Cofactor

All present enzymatic activity of Crystal Structure of Myst Acetyltransferase Domain in Complex with Acetyl-Coa Cofactor:
2.3.1.48;

The structure of Crystal Structure of Myst Acetyltransferase Domain in Complex with Acetyl-Coa Cofactor, PDB code: 6ba4 was solved by S.J.Hermans, M.C.Chung, T.S.Peat, J.B.Baell, T.Thomas, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.68 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.363, 57.925, 120.045, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.3

The structure of Crystal Structure of Myst Acetyltransferase Domain in Complex with Acetyl-Coa Cofactor also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Myst Acetyltransferase Domain in Complex with Acetyl-Coa Cofactor (pdb code 6ba4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Myst Acetyltransferase Domain in Complex with Acetyl-Coa Cofactor, PDB code: 6ba4:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Myst Acetyltransferase Domain in Complex with Acetyl-Coa Cofactor


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 Acetyl-Coa Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na802 b:17.6 occ:1.00 NA A:NA803 3.0 35.7 1.0 NA A:NA804 3.1 31.3 1.0 N A:ASP520 3.3 21.4 1.0 OD2 A:ASP520 3.9 27.6 1.0 CA A:ILE519 3.9 21.7 1.0 CB A:ASP520 4.0 20.0 1.0 CG A:ASP520 4.1 25.3 1.0 CG2 A:ILE519 4.1 19.4 1.0 C A:ILE519 4.1 23.7 1.0 CA A:ASP520 4.2 20.9 1.0 O A:GLU518 4.3 28.7 1.0 CB A:ILE519 4.6 20.3 1.0 O A:HOH945 4.6 47.9 1.0 O A:ASP520 4.6 22.7 1.0 OD1 A:ASP520 4.8 29.2 1.0 C A:ASP520 5.0 23.8 1.0 N A:ILE519 5.0 20.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Myst Acetyltransferase Domain in Complex with Acetyl-Coa Cofactor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Myst Acetyltransferase Domain in Complex with Acetyl-Coa Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na803 b:35.7 occ:1.00 O A:ASP520 2.7 22.7 1.0 NE1 A:TRP522 2.9 24.2 1.0 NA A:NA802 3.0 17.6 1.0 CD1 A:TRP522 3.5 25.1 1.0 C A:ASP520 3.6 23.8 1.0 N A:ASP520 3.7 21.4 1.0 CG2 A:ILE519 3.7 19.4 1.0 CB A:ASP520 3.8 20.0 1.0 NA A:NA804 3.9 31.3 1.0 CA A:ASP520 3.9 20.9 1.0 CE2 A:TRP522 4.1 21.5 1.0 CG A:PRO651 4.1 24.0 1.0 CB A:PRO651 4.3 27.1 1.0 CE1 A:PHE600 4.5 21.1 1.0 C A:ILE519 4.6 23.7 1.0 CZ2 A:TRP522 4.7 24.2 1.0 N A:ALA521 4.8 23.3 1.0 CG A:ASP520 4.8 25.3 1.0 CG A:TRP522 4.8 21.3 1.0 OD2 A:ASP520 5.0 27.6 1.0 CA A:ILE519 5.0 21.7 1.0 CB A:ILE519 5.0 20.3 1.0 O A:ALA521 5.0 24.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Myst Acetyltransferase Domain in Complex with Acetyl-Coa Cofactor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Myst Acetyltransferase Domain in Complex with Acetyl-Coa Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na804 b:31.3 occ:1.00 OD2 A:ASP520 2.5 27.6 1.0 NA A:NA802 3.1 17.6 1.0 CG A:ASP520 3.4 25.3 1.0 CB A:ASP520 3.7 20.0 1.0 NA A:NA803 3.9 35.7 1.0 OD1 A:ASP520 4.6 29.2 1.0 N A:ASP520 4.8 21.4 1.0 CA A:ASP520 4.8 20.9 1.0

J.B.Baell, D.J.Leaver, S.J.Hermans, G.L.Kelly, M.S.Brennan, N.L.Downer, N.Nguyen, J.Wichmann, H.M.Mcrae, Y.Yang, B.Cleary, H.R.Lagiakos, S.Mieruszynski, G.Pacini, H.K.Vanyai, M.I.Bergamasco, R.E.May, B.K.Davey, K.J.Morgan, A.J.Sealey, B.Wang, N.Zamudio, S.Wilcox, A.L.Garnham, B.N.Sheikh, B.J.Aubrey, K.Doggett, M.C.Chung, M.De Silva, J.Bentley, P.Pilling, M.Hattarki, O.Dolezal, M.L.Dennis, H.Falk, B.Ren, S.A.Charman, K.L.White, J.Rautela, A.Newbold, E.D.Hawkins, R.W.Johnstone, N.D.Huntington, T.S.Peat, J.K.Heath, A.Strasser, M.W.Parker, G.K.Smyth, I.P.Street, B.J.Monahan, A.K.Voss, T.Thomas. Inhibitors of Histone Acetyltransferases KAT6A/B Induce Senescence and Arrest Tumour Growth. Nature V. 560 253 2018.
ISSN: ESSN 1476-4687
PubMed: 30069049
DOI: 10.1038/S41586-018-0387-5