Atomistry » Zinc » PDB 7s6m-7spy » 7sff
Atomistry »
  Zinc »
    PDB 7s6m-7spy »
      7sff »

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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 7sff:

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

Zinc Binding Sites:

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 7sff

Go back to Zinc Binding Sites List in 7sff
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 7sff

Go back to Zinc Binding Sites List in 7sff
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

Reference:

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
Page generated: Sat Apr 8 03:06:59 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy