Zinc in PDB 7sff: Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3852279B

All present enzymatic activity of Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3852279B:
2.1.1.37;

The structure of Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3852279B, PDB code: 7sff was solved by J.R.Horton, S.Pathuri, X.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.75 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.72, 78.237, 117.061, 90, 125.93, 90
R / Rfree (%)	18.2 / 21.7

The structure of Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3852279B also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Zinc atom in the Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3852279B (pdb code 7sff). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3852279B, PDB code: 7sff:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3852279B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3852279B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:72.9 occ:1.00 NE2 A:HIS1502 2.1 76.9 1.0 SG A:CYS1478 2.1 66.8 1.0 SG A:CYS1485 2.3 71.3 1.0 SG A:CYS1476 2.3 75.2 1.0 CD2 A:HIS1502 3.0 60.3 1.0 CB A:CYS1485 3.1 91.1 1.0 CE1 A:HIS1502 3.1 68.2 1.0 CB A:CYS1478 3.2 71.5 1.0 CB A:CYS1476 3.2 74.4 1.0 CA A:CYS1485 3.4 84.2 1.0 N A:CYS1478 4.1 79.4 1.0 CG A:HIS1502 4.2 65.8 1.0 ND1 A:HIS1502 4.2 67.0 1.0 CA A:CYS1478 4.3 74.3 1.0 N A:CYS1485 4.3 95.8 1.0 CA A:CYS1476 4.6 76.3 1.0 C A:CYS1485 4.6 101.5 1.0 CH2 A:TRP1498 4.8 61.0 1.0 CZ2 A:TRP1498 4.8 65.8 1.0 N A:ASP1486 4.9 97.0 1.0 N A:SER1477 4.9 85.6 1.0 C A:CYS1476 4.9 79.5 1.0

Zinc binding site 2 out of 2 in the Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3852279B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3852279B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:45.3 occ:1.00 NE2 A:HIS793 2.1 44.6 1.0 SG A:CYS820 2.2 42.1 1.0 SG A:CYS896 2.2 49.8 1.0 SG A:CYS893 2.3 51.5 1.0 CE1 A:HIS793 3.0 42.9 1.0 CB A:CYS820 3.0 35.8 1.0 CD2 A:HIS793 3.1 38.7 1.0 CB A:CYS893 3.4 57.6 1.0 CB A:CYS896 3.4 48.7 1.0 N A:CYS896 3.5 49.8 1.0 CA A:CYS896 3.8 45.6 1.0 ND1 A:HIS793 4.1 46.0 1.0 CG A:HIS793 4.2 44.6 1.0 CB A:SER895 4.3 46.1 1.0 C A:SER895 4.4 49.5 1.0 CA A:CYS820 4.4 41.9 1.0 OG A:SER895 4.5 46.7 1.0 C A:CYS820 4.7 40.9 1.0 CA A:CYS893 4.7 56.0 1.0 CA A:SER895 4.8 43.5 1.0 N A:SER895 5.0 49.4 1.0 N A:GLU821 5.0 39.2 1.0

J.R.Horton, S.Pathuri, K.Wong, R.Ren, L.Rueda, D.T.Fosbenner, D.A.Heerding, M.T.Mccabe, M.B.Pappalardi, X.Zhang, B.W.King, X.Cheng. Structural Characterization of Dicyanopyridine Containing DNMT1-Selective, Non-Nucleoside Inhibitors. Structure V. 30 793 2022.
ISSN: ISSN 0969-2126
PubMed: 35395178
DOI: 10.1016/J.STR.2022.03.009