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: Fri Aug 2 12:56:26 2024

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