Zinc in PDB 9it4: Structure of CLR4 Catalyzing Histone H3 K9 Methylation

All present enzymatic activity of Structure of CLR4 Catalyzing Histone H3 K9 Methylation:
2.1.1.355; 2.1.1.366; 2.1.1.367;

The structure of Structure of CLR4 Catalyzing Histone H3 K9 Methylation, PDB code: 9it4 was solved by Y.X.Du, L.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.88 / 2.39
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.13, 70.384, 110.466, 90, 90, 90
R / Rfree (%)	22.1 / 26.5

The binding sites of Zinc atom in the Structure of CLR4 Catalyzing Histone H3 K9 Methylation (pdb code 9it4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of CLR4 Catalyzing Histone H3 K9 Methylation, PDB code: 9it4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of CLR4 Catalyzing Histone H3 K9 Methylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of CLR4 Catalyzing Histone H3 K9 Methylation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:31.5 occ:1.00 SG B:CYS278 2.3 29.0 1.0 SG B:CYS307 2.3 31.2 1.0 SG B:CYS260 2.3 42.0 1.0 SG B:CYS311 2.3 35.9 1.0 CB B:CYS307 3.1 32.6 1.0 CB B:CYS260 3.2 44.7 1.0 CB B:CYS311 3.3 43.3 1.0 CA B:CYS307 3.6 34.3 1.0 ZN B:ZN503 3.8 38.2 1.0 N B:CYS260 3.8 49.7 1.0 ZN B:ZN504 3.8 41.5 1.0 CB B:CYS278 3.8 36.3 1.0 CA B:CYS260 4.1 53.1 1.0 SG B:CYS276 4.1 29.9 1.0 SG B:CYS313 4.3 57.6 1.0 O B:HOH602 4.5 38.0 1.0 SG B:CYS268 4.5 35.4 1.0 N B:CYS307 4.5 34.1 1.0 N B:ASN308 4.6 35.6 1.0 CA B:CYS311 4.6 46.7 1.0 C B:GLY259 4.7 47.1 1.0 C B:CYS307 4.7 35.0 1.0 CA B:GLY259 5.0 46.0 1.0 N B:CYS278 5.0 34.5 1.0 CA B:CYS278 5.0 36.4 1.0

Zinc binding site 2 out of 4 in the Structure of CLR4 Catalyzing Histone H3 K9 Methylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of CLR4 Catalyzing Histone H3 K9 Methylation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:38.2 occ:1.00 SG B:CYS268 2.3 35.4 1.0 SG B:CYS262 2.3 52.1 1.0 SG B:CYS276 2.3 29.9 1.0 SG B:CYS260 2.3 42.0 1.0 CB B:CYS260 3.0 44.7 1.0 CB B:CYS276 3.2 41.4 1.0 CB B:CYS262 3.3 56.6 1.0 CB B:CYS268 3.6 45.0 1.0 CA B:CYS276 3.8 52.5 1.0 ZN B:ZN502 3.8 31.5 1.0 ZN B:ZN504 3.9 41.5 1.0 SG B:CYS307 4.3 31.2 1.0 CA B:CYS260 4.5 53.1 1.0 CA B:CYS268 4.5 47.8 1.0 CA B:CYS262 4.5 66.0 1.0 SG B:CYS313 4.6 57.6 1.0 N B:CYS262 4.7 63.4 1.0 C B:CYS276 4.7 44.4 1.0 N B:GLU277 4.8 38.8 1.0 C B:CYS260 4.8 53.0 1.0 N B:CYS276 4.8 48.1 1.0 SG B:CYS278 4.8 29.0 1.0 CZ B:PHE288 4.9 37.6 1.0 O B:HOH601 5.0 49.8 1.0 N B:ASN261 5.0 50.9 1.0

Zinc binding site 3 out of 4 in the Structure of CLR4 Catalyzing Histone H3 K9 Methylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of CLR4 Catalyzing Histone H3 K9 Methylation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn504 b:41.5 occ:1.00 SG B:CYS268 2.3 35.4 1.0 SG B:CYS313 2.3 57.6 1.0 SG B:CYS307 2.3 31.2 1.0 SG B:CYS317 2.3 30.4 1.0 CB B:CYS307 3.5 32.6 1.0 CB B:CYS317 3.5 46.7 1.0 CB B:CYS268 3.7 45.0 1.0 CB B:CYS313 3.7 54.8 1.0 ZN B:ZN502 3.8 31.5 1.0 ZN B:ZN503 3.9 38.2 1.0 N B:CYS268 3.9 56.4 1.0 SG B:CYS260 4.0 42.0 1.0 CA B:CYS268 4.4 47.8 1.0 CB B:ASN319 4.5 30.6 1.0 CA B:CYS307 4.9 34.3 1.0 NE B:ARG320 4.9 44.6 1.0 CA B:CYS317 4.9 46.2 1.0 C B:GLY267 4.9 59.7 1.0 CA B:CYS313 5.0 50.8 1.0

Zinc binding site 4 out of 4 in the Structure of CLR4 Catalyzing Histone H3 K9 Methylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of CLR4 Catalyzing Histone H3 K9 Methylation within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn505 b:35.9 occ:1.00 SG B:CYS484 2.3 38.5 1.0 SG B:CYS479 2.3 41.9 1.0 SG B:CYS412 2.3 40.3 1.0 SG B:CYS477 2.3 34.5 1.0 CB B:CYS484 3.1 44.8 1.0 CB B:CYS477 3.2 42.1 1.0 CB B:CYS479 3.4 32.2 1.0 CB B:CYS412 3.5 45.9 1.0 CA B:CYS484 3.6 47.2 1.0 N B:CYS412 4.0 29.4 1.0 O B:HOH624 4.1 40.6 1.0 N B:CYS479 4.1 38.9 1.0 N B:ARG485 4.3 45.7 1.0 C B:CYS484 4.3 53.2 1.0 CA B:CYS479 4.3 36.3 1.0 CA B:CYS412 4.4 37.8 1.0 NE2 B:HIS410 4.4 35.6 1.0 CA B:CYS477 4.5 48.1 1.0 C B:CYS477 4.5 45.2 1.0 O B:CYS477 4.6 47.3 1.0 N B:GLY486 4.6 48.0 1.0 CD2 B:HIS410 4.6 40.6 1.0 N B:CYS484 4.9 55.2 1.0 N B:GLY480 4.9 41.1 1.0 C B:SER411 5.0 37.2 1.0

Y.X.Du, L.Liu. Mechanism of Histone H3K9 Methyltransferase CLR4 Regulation By Proximal H3K14 Ubiquitination in-Cis To Be Published.