Zinc in PDB 7sfc: Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3735967A

All present enzymatic activity of Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3735967A:
2.1.1.37;

The structure of Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3735967A, PDB code: 7sfc 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)	35.35 / 1.97
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.733, 78.897, 117.335, 90, 125.64, 90
R / Rfree (%)	17.6 / 20.8

The binding sites of Zinc atom in the Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3735967A (pdb code 7sfc). 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 GSK3735967A, PDB code: 7sfc:
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 GSK3735967A


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 GSK3735967A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:47.4 occ:1.00 NE2 A:HIS1502 2.1 44.9 1.0 SG A:CYS1478 2.2 44.9 1.0 SG A:CYS1476 2.3 50.8 1.0 SG A:CYS1485 2.3 58.5 1.0 CD2 A:HIS1502 3.0 42.5 1.0 CB A:CYS1478 3.1 50.8 1.0 CB A:CYS1476 3.1 50.2 1.0 CE1 A:HIS1502 3.1 45.0 1.0 CB A:CYS1485 3.2 53.4 1.0 CA A:CYS1485 3.7 60.5 1.0 N A:CYS1478 4.0 52.1 1.0 O A:HOH1870 4.0 49.2 1.0 CA A:CYS1478 4.1 56.7 1.0 CG A:HIS1502 4.2 42.0 1.0 ND1 A:HIS1502 4.2 43.6 1.0 CA A:CYS1476 4.5 45.8 1.0 N A:CYS1485 4.6 60.5 1.0 C A:CYS1476 4.7 51.3 1.0 O A:HOH1983 4.7 46.1 1.0 N A:SER1477 4.8 55.2 1.0 C A:CYS1485 4.9 63.9 1.0 CH2 A:TRP1498 4.9 45.1 1.0 CZ2 A:TRP1498 4.9 46.3 1.0 C A:CYS1478 5.0 59.2 1.0

Zinc binding site 2 out of 2 in the Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3735967A


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 GSK3735967A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:38.0 occ:1.00 NE2 A:HIS793 2.1 41.6 1.0 SG A:CYS893 2.3 40.1 1.0 SG A:CYS820 2.3 36.3 1.0 SG A:CYS896 2.3 42.7 1.0 CD2 A:HIS793 3.0 37.7 1.0 CE1 A:HIS793 3.1 40.7 1.0 CB A:CYS820 3.1 36.3 1.0 CB A:CYS893 3.2 42.2 1.0 CB A:CYS896 3.3 37.8 1.0 N A:CYS896 3.4 37.5 1.0 CA A:CYS896 3.8 40.0 1.0 ND1 A:HIS793 4.1 39.4 1.0 CG A:HIS793 4.1 41.5 1.0 O A:HOH2255 4.2 48.8 1.0 CB A:SER895 4.3 35.5 1.0 C A:SER895 4.4 40.2 1.0 O A:HOH2173 4.4 47.3 1.0 OG A:SER895 4.5 34.0 1.0 CA A:CYS820 4.5 35.1 1.0 CA A:CYS893 4.6 47.0 1.0 C A:CYS820 4.8 39.0 1.0 CA A:SER895 4.8 37.0 1.0 O A:CYS893 4.9 48.1 1.0 C A:CYS893 4.9 48.6 1.0 N A:GLU821 5.0 38.0 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