Fluorine in PDB 9mvy: Crystal Structure of ZMET2 in Complex with Unmethylated Ctg Dna and A Histone H3KC9ME2 Peptide

All present enzymatic activity of Crystal Structure of ZMET2 in Complex with Unmethylated Ctg Dna and A Histone H3KC9ME2 Peptide:
2.1.1.37;

The structure of Crystal Structure of ZMET2 in Complex with Unmethylated Ctg Dna and A Histone H3KC9ME2 Peptide, PDB code: 9mvy was solved by G.Herle, J.Fang, J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.40 / 2.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.515, 277.296, 64.479, 90, 97.26, 90
R / Rfree (%)	22.7 / 27.1

The binding sites of Fluorine atom in the Crystal Structure of ZMET2 in Complex with Unmethylated Ctg Dna and A Histone H3KC9ME2 Peptide (pdb code 9mvy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of ZMET2 in Complex with Unmethylated Ctg Dna and A Histone H3KC9ME2 Peptide, PDB code: 9mvy:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of ZMET2 in Complex with Unmethylated Ctg Dna and A Histone H3KC9ME2 Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of ZMET2 in Complex with Unmethylated Ctg Dna and A Histone H3KC9ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:F10 b:44.6 occ:1.00 F C:C4910 0.0 44.6 1.0 C5 C:C4910 1.4 35.3 1.0 C4 C:C4910 2.3 36.9 1.0 SG A:CYS517 2.4 45.8 1.0 CM5 C:C4910 2.4 36.9 1.0 C6 C:C4910 2.4 34.5 1.0 N A:CYS517 2.7 32.0 1.0 N4 C:C4910 2.7 36.1 1.0 O A:PRO515 2.9 29.4 1.0 CB A:CYS517 3.0 45.1 1.0 CA A:CYS517 3.4 30.5 1.0 C A:PRO516 3.4 34.2 1.0 N3 C:C4910 3.5 37.4 1.0 N1 C:C4910 3.6 33.7 1.0 CA A:PRO516 3.6 31.6 1.0 C A:PRO515 3.8 29.5 1.0 C2 C:C4910 4.0 33.7 1.0 NE2 A:GLN518 4.0 34.9 1.0 N A:PRO516 4.2 29.4 1.0 O A:GLY514 4.2 42.0 1.0 O A:PRO516 4.4 33.9 1.0 C A:CYS517 4.5 38.4 1.0 ND2 A:ASN560 4.5 43.8 1.0 OD1 A:ASN560 4.6 37.1 1.0 CG A:ASN560 4.7 39.1 1.0 C A:GLY514 4.8 34.5 1.0 N A:GLN518 4.8 34.0 1.0 C1' C:C4910 4.8 36.2 1.0 O A:HOH1150 4.9 29.6 1.0 CB A:PRO516 4.9 34.6 1.0 C2' C:C4910 5.0 33.4 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of ZMET2 in Complex with Unmethylated Ctg Dna and A Histone H3KC9ME2 Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of ZMET2 in Complex with Unmethylated Ctg Dna and A Histone H3KC9ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ F:F10 b:38.0 occ:1.00 F F:C4910 0.0 38.0 1.0 C5 F:C4910 1.4 29.9 1.0 C4 F:C4910 2.3 35.2 1.0 CM5 F:C4910 2.3 33.4 1.0 C6 F:C4910 2.4 23.3 1.0 SG D:CYS517 2.4 26.1 1.0 N D:CYS517 2.6 41.9 1.0 N4 F:C4910 2.7 26.9 1.0 O D:PRO515 2.8 31.7 1.0 CB D:CYS517 2.9 38.3 1.0 C D:PRO516 3.2 42.7 1.0 CA D:CYS517 3.3 34.2 1.0 CA D:PRO516 3.4 38.3 1.0 N3 F:C4910 3.5 30.2 1.0 N1 F:C4910 3.6 23.6 1.0 C D:PRO515 3.7 31.2 1.0 C2 F:C4910 4.0 27.6 1.0 N D:PRO516 4.1 39.4 1.0 O D:PRO516 4.1 41.4 1.0 OD1 D:ASN560 4.2 45.7 1.0 C D:CYS517 4.4 29.6 1.0 OD1 D:ASN851 4.5 39.0 1.0 O D:GLY514 4.5 32.1 1.0 NE2 D:GLN518 4.7 28.3 1.0 OE1 D:GLN518 4.7 32.8 1.0 N D:GLN518 4.8 38.5 1.0 CB D:PRO516 4.8 37.9 1.0 C1' F:C4910 4.9 23.1 1.0 C D:GLY514 4.9 24.6 1.0 CG D:ASN560 4.9 31.1 1.0 C2' F:C4910 5.0 22.6 1.0 CD D:GLN518 5.0 39.4 1.0

G.Herle, J.Fang, J.Song. Structure of An Unfavorable De Novo Dna Methylation Complex of Plant Methyltransferase ZMET2. J.Mol.Biol. 69186 2025.
ISSN: ESSN 1089-8638
PubMed: 40335018
DOI: 10.1016/J.JMB.2025.169186