Zinc in PDB 7sfg: Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Cofactor Sam

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

The structure of Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Cofactor Sam, PDB code: 7sfg 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)	41.85 / 2.43
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.776, 77.476, 116.709, 90, 125.67, 90
R / Rfree (%)	18 / 22.3

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


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 Cofactor Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1701 b:78.7 occ:1.00 NE2 A:HIS1502 2.1 82.1 1.0 SG A:CYS1476 2.3 89.2 1.0 SG A:CYS1485 2.3 84.3 1.0 SG A:CYS1478 2.4 82.4 1.0 CB A:CYS1478 2.9 92.6 1.0 CE1 A:HIS1502 3.1 71.8 1.0 CD2 A:HIS1502 3.1 73.3 1.0 CB A:CYS1485 3.4 100.9 1.0 CB A:CYS1476 3.6 82.4 1.0 CA A:CYS1485 3.8 103.6 1.0 N A:CYS1478 4.0 91.9 1.0 CA A:CYS1478 4.1 91.5 1.0 ND1 A:HIS1502 4.2 72.2 1.0 CG A:HIS1502 4.2 71.4 1.0 N A:CYS1485 4.5 101.8 1.0 CA A:CYS1476 4.9 84.6 1.0 N A:SER1477 5.0 91.2 1.0

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


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 Cofactor Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1702 b:60.9 occ:1.00 NE2 A:HIS793 2.1 70.5 1.0 SG A:CYS896 2.2 51.3 1.0 SG A:CYS820 2.3 57.8 1.0 SG A:CYS893 2.3 63.6 1.0 CE1 A:HIS793 3.0 62.3 1.0 CD2 A:HIS793 3.1 64.7 1.0 CB A:CYS820 3.2 53.4 1.0 CB A:CYS893 3.3 69.7 1.0 CB A:CYS896 3.5 58.3 1.0 N A:CYS896 3.5 59.6 1.0 CA A:CYS896 3.9 58.8 1.0 ND1 A:HIS793 4.1 64.8 1.0 CB A:SER895 4.2 57.1 1.0 CG A:HIS793 4.2 65.6 1.0 C A:SER895 4.4 62.1 1.0 OG A:SER895 4.5 55.3 1.0 CA A:CYS820 4.6 52.8 1.0 CA A:CYS893 4.7 73.5 1.0 CA A:SER895 4.8 59.2 1.0 C A:CYS820 4.8 55.9 1.0 N A:SER895 5.0 61.3 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