Bromine in PDB 7o45: Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase

All present enzymatic activity of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase:
2.1.1.37;

The structure of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase, PDB code: 7o45 was solved by K.M.Boyko, A.Y.Nikolaeva, A.N.Bonchuk, P.G.Georgiev, V.O.Popov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.38 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.282, 89.943, 92.195, 90, 90, 90
R / Rfree (%)	20 / 22.8

The structure of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase also contains other interesting chemical elements:

Zinc

(Zn)

12 atoms

The binding sites of Bromine atom in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase (pdb code 7o45). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase, PDB code: 7o45:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br604 b:107.7 occ:1.00 CE2 C:PHE550 4.2 38.7 1.0 CD2 C:PHE550 4.3 38.0 1.0 CE2 B:PHE550 4.5 39.1 1.0 CG C:GLN547 4.5 40.8 1.0 CE2 A:PHE550 4.6 36.0 1.0 CD2 B:PHE550 4.7 39.3 1.0 CG A:GLN547 4.7 40.0 1.0 CD2 A:PHE550 4.8 35.9 1.0

Bromine binding site 2 out of 3 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ A:Br605 b:78.3 occ:1.00 N A:GLN456 3.4 47.6 1.0 N A:VAL444 3.4 46.1 1.0 CA A:CYS455 3.7 44.6 1.0 CB A:CYS455 3.7 46.1 1.0 CB A:VAL444 3.8 49.4 1.0 NH1 A:ARG440 3.8 87.5 1.0 CG1 A:VAL444 3.8 50.4 1.0 CA A:PRO443 4.0 46.9 1.0 C A:CYS455 4.0 45.9 1.0 CB A:GLN456 4.1 52.1 1.0 C A:PRO443 4.1 47.1 1.0 CA A:VAL444 4.2 48.4 1.0 CZ A:ARG440 4.3 87.2 1.0 CA A:GLN456 4.4 49.4 1.0 O A:ASN442 4.5 47.1 1.0 NH2 A:ARG440 4.8 90.3 1.0 CB A:PRO443 4.9 45.8 1.0 NE A:ARG440 4.9 82.0 1.0

Bromine binding site 3 out of 3 in the Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Add Domain of the Human DNMT3B Methyltransferase within 5.0Å range: probe atom residue distance (Å) B Occ C:Br604 b:86.2 occ:1.00 N C:LYS441 3.4 55.0 1.0 N C:GLN415 3.6 62.6 1.0 CA C:ARG440 3.9 55.8 1.0 CB C:LYS441 4.0 57.4 1.0 CA C:ASP414 4.0 71.1 1.0 OD1 C:ASP414 4.0 80.1 1.0 CB C:ARG440 4.0 61.5 1.0 CG C:LYS441 4.1 61.1 1.0 C C:ARG440 4.2 55.1 1.0 CB C:GLN415 4.2 56.5 1.0 CG C:ASP414 4.3 75.4 1.0 CA C:LYS441 4.3 55.7 1.0 C C:ASP414 4.3 68.6 1.0 CA C:GLN415 4.5 58.9 1.0 CB C:ASP414 4.5 74.0 1.0 CD C:LYS441 4.7 64.7 1.0 OD2 C:ASP414 4.8 72.5 1.0 O C:LYS441 4.9 51.7 1.0

K.Boyko, O.Arkova, A.Nikolaeva, V.O.Popov, P.Georgiev, A.Bonchuk. Structure of the DNMT3B Add Domain Suggests the Absence of A DNMT3A-Like Autoinhibitory Mechanism. Biochem.Biophys.Res.Commun. V. 619 124 2022.
ISSN: ESSN 1090-2104
PubMed: 35760008
DOI: 10.1016/J.BBRC.2022.06.036