Fluorine 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:

Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human DNMT1(729-1600) Bound to Zebularine-Containing 12MER Dsdna and Inhibitor GSK3852279B, PDB code: 7sff:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7sff

Go back to Fluorine Binding Sites List in 7sff
Fluorine binding site 1 out of 3 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 Fluorine with other atoms in the F 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
C:F101

b:114.9
occ:1.00
 F24 C:C79101 0.0 114.9 1.0
C23 C:C79101 1.4 117.8 1.0
F25 C:C79101 2.2 118.4 1.0
F26 C:C79101 2.2 122.7 1.0
C22 C:C79101 2.4 114.6 1.0
C21 C:C79101 2.7 108.4 1.0
OG A:SER1230 3.0 69.6 1.0
C27 C:C79101 3.6 112.2 1.0
O2' D:PYO18 4.1 99.5 1.0
C20 C:C79101 4.1 101.0 1.0
CB A:SER1230 4.3 44.1 1.0
C28 C:C79101 4.8 110.5 1.0
C19 C:C79101 5.0 104.3 1.0
C A:SER1230 5.0 49.9 1.0

Fluorine binding site 2 out of 3 in 7sff

Go back to Fluorine Binding Sites List in 7sff
Fluorine binding site 2 out of 3 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 Fluorine with other atoms in the F 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
C:F101

b:118.4
occ:1.00
 F25 C:C79101 0.0 118.4 1.0
C23 C:C79101 1.4 117.8 1.0
F26 C:C79101 2.2 122.7 1.0
F24 C:C79101 2.2 114.9 1.0
C22 C:C79101 2.4 114.6 1.0
C27 C:C79101 3.1 112.2 1.0
C21 C:C79101 3.3 108.4 1.0
C28 C:C79101 4.3 110.5 1.0
C20 C:C79101 4.5 101.0 1.0
OG A:SER1230 4.6 69.6 1.0
C19 C:C79101 4.9 104.3 1.0

Fluorine binding site 3 out of 3 in 7sff

Go back to Fluorine Binding Sites List in 7sff
Fluorine binding site 3 out of 3 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 Fluorine with other atoms in the F binding site number 3 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
C:F101

b:122.7
occ:1.00
 F26 C:C79101 0.0 122.7 1.0
C23 C:C79101 1.4 117.8 1.0
F25 C:C79101 2.2 118.4 1.0
F24 C:C79101 2.2 114.9 1.0
C22 C:C79101 2.4 114.6 1.0
C27 C:C79101 2.8 112.2 1.0
C21 C:C79101 3.5 108.4 1.0
O2' D:PYO18 3.9 99.5 1.0
OG A:SER1230 4.1 69.6 1.0
C28 C:C79101 4.2 110.5 1.0
OP1 D:DG20 4.3 121.3 1.0
C20 C:C79101 4.7 101.0 1.0
O3' D:DG19 4.8 99.5 1.0
C19 C:C79101 4.9 104.3 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: Wed Apr 5 01:01:45 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