Zinc in PDB 7sfe: Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3830334A

All present enzymatic activity of Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3830334A:
2.1.1.37;

The structure of Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3830334A, PDB code: 7sfe 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)	42.13 / 2.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.969, 78.494, 117.562, 90, 125.83, 90
R / Rfree (%)	20.1 / 23.6

The binding sites of Zinc atom in the Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3830334A (pdb code 7sfe). 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 GSK3830334A, PDB code: 7sfe:
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 GSK3830334A


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 GSK3830334A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:75.5 occ:1.00 NE2 A:HIS1502 2.0 83.8 1.0 SG A:CYS1485 2.3 74.7 1.0 SG A:CYS1478 2.3 77.6 1.0 SG A:CYS1476 2.3 83.0 1.0 CB A:CYS1485 2.9 84.0 1.0 CD2 A:HIS1502 2.9 71.6 1.0 CB A:CYS1476 3.1 77.5 1.0 CB A:CYS1478 3.1 80.9 1.0 CE1 A:HIS1502 3.1 85.3 1.0 CA A:CYS1485 3.4 89.6 1.0 N A:CYS1478 3.9 88.3 1.0 CG A:HIS1502 4.1 69.9 1.0 CA A:CYS1478 4.1 87.6 1.0 ND1 A:HIS1502 4.1 73.1 1.0 N A:CYS1485 4.3 91.4 1.0 CA A:CYS1476 4.4 80.3 1.0 C A:CYS1485 4.6 97.1 1.0 C A:CYS1476 4.6 81.8 1.0 N A:SER1477 4.7 87.8 1.0 CH2 A:TRP1498 4.7 73.7 1.0 CZ2 A:TRP1498 4.7 77.8 1.0 N A:ASP1486 4.9 93.4 1.0

Zinc binding site 2 out of 2 in the Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3830334A


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 GSK3830334A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1703 b:84.4 occ:1.00 NE2 A:HIS793 2.0 80.3 1.0 SG A:CYS896 2.3 81.7 1.0 SG A:CYS820 2.3 71.3 1.0 SG A:CYS893 2.3 82.8 1.0 CE1 A:HIS793 3.0 77.9 1.0 CB A:CYS820 3.0 71.2 1.0 CD2 A:HIS793 3.0 68.8 1.0 CB A:CYS893 3.2 95.1 1.0 CB A:CYS896 3.3 77.0 1.0 N A:CYS896 3.4 80.1 1.0 CA A:CYS896 3.8 76.4 1.0 ND1 A:HIS793 4.1 77.4 1.0 CB A:SER895 4.2 73.4 1.0 CG A:HIS793 4.2 78.3 1.0 C A:SER895 4.3 87.0 1.0 CA A:CYS820 4.4 68.3 1.0 OG A:SER895 4.5 74.3 1.0 CA A:CYS893 4.6 97.2 1.0 CA A:SER895 4.7 84.8 1.0 C A:CYS820 4.7 76.1 1.0 N A:SER895 4.9 92.2 1.0 C A:CYS893 4.9 92.7 1.0 N A:GLU821 4.9 73.0 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