Zinc in PDB 6ryu: Nucleosome-CHD4 Complex Structure (Two CHD4 Copies)

All present enzymatic activity of Nucleosome-CHD4 Complex Structure (Two CHD4 Copies):
3.6.4.12;

The structure of Nucleosome-CHD4 Complex Structure (Two CHD4 Copies) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Nucleosome-CHD4 Complex Structure (Two CHD4 Copies) (pdb code 6ryu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Nucleosome-CHD4 Complex Structure (Two CHD4 Copies), PDB code: 6ryu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Nucleosome-CHD4 Complex Structure (Two CHD4 Copies)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Nucleosome-CHD4 Complex Structure (Two CHD4 Copies) within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn2203 b:0.8 occ:1.00 SG W:CYS455 2.5 0.1 1.0 CB W:HIS472 2.6 0.8 1.0 SG W:CYS452 2.6 0.6 1.0 SG W:CYS475 2.6 0.5 1.0 CB W:CYS452 3.0 0.6 1.0 CB W:CYS475 3.4 0.5 1.0 N W:HIS472 3.5 0.8 1.0 CA W:HIS472 3.6 0.8 1.0 CG W:HIS472 3.6 0.8 1.0 ND1 W:HIS472 3.8 0.8 1.0 CB W:CYS455 4.0 0.1 1.0 N W:CYS455 4.4 0.1 1.0 C W:HIS472 4.4 0.8 1.0 O W:HIS472 4.4 0.8 1.0 CA W:CYS452 4.6 0.6 1.0 C W:TYR471 4.7 0.8 1.0 CE1 W:HIS474 4.7 0.3 1.0 CA W:CYS475 4.8 0.5 1.0 CA W:CYS455 4.8 0.1 1.0 CD2 W:HIS472 5.0 0.8 1.0 CB W:VAL454 5.0 0.8 1.0 N W:CYS475 5.0 0.5 1.0

Zinc binding site 2 out of 4 in the Nucleosome-CHD4 Complex Structure (Two CHD4 Copies)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Nucleosome-CHD4 Complex Structure (Two CHD4 Copies) within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn2204 b:0.9 occ:1.00 SG W:CYS467 2.3 0.2 1.0 SG W:CYS493 2.3 0.3 1.0 SG W:CYS490 2.4 0.8 1.0 SG W:CYS464 2.4 0.4 1.0 CB W:CYS464 3.1 0.4 1.0 CB W:CYS490 3.1 0.8 1.0 OG W:SER469 3.5 0.3 1.0 CB W:CYS467 3.6 0.2 1.0 CB W:SER469 3.7 0.3 1.0 N W:CYS490 3.8 0.8 1.0 CB W:CYS493 3.9 0.3 1.0 CA W:CYS490 4.0 0.8 1.0 N W:CYS467 4.1 0.2 1.0 CA W:CYS467 4.3 0.2 1.0 O W:CYS467 4.3 0.2 1.0 N W:CYS493 4.3 0.3 1.0 C W:CYS467 4.5 0.2 1.0 CA W:CYS464 4.5 0.4 1.0 N W:SER469 4.6 0.3 1.0 CA W:CYS493 4.7 0.3 1.0 C W:CYS490 4.7 0.8 1.0 O W:CYS490 4.7 0.8 1.0 C W:THR466 4.7 0.9 1.0 CA W:SER469 4.8 0.3 1.0 CG2 W:THR466 4.8 0.9 1.0 N W:THR466 5.0 0.9 1.0

Zinc binding site 3 out of 4 in the Nucleosome-CHD4 Complex Structure (Two CHD4 Copies)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Nucleosome-CHD4 Complex Structure (Two CHD4 Copies) within 5.0Å range: probe atom residue distance (Å) B Occ V:Zn2203 b:0.7 occ:1.00 SG V:CYS455 2.5 0.9 1.0 SG V:CYS452 2.6 1.0 1.0 CB V:HIS472 2.6 0.5 1.0 SG V:CYS475 2.6 0.3 1.0 CB V:CYS452 3.0 1.0 1.0 CB V:CYS475 3.4 0.3 1.0 N V:HIS472 3.5 0.5 1.0 CA V:HIS472 3.6 0.5 1.0 CG V:HIS472 3.6 0.5 1.0 ND1 V:HIS472 3.8 0.5 1.0 CB V:CYS455 4.0 0.9 1.0 N V:CYS455 4.4 0.9 1.0 C V:HIS472 4.4 0.5 1.0 O V:HIS472 4.4 0.5 1.0 CA V:CYS452 4.6 1.0 1.0 C V:TYR471 4.7 1.0 1.0 CE1 V:HIS474 4.7 0.9 1.0 CA V:CYS475 4.8 0.3 1.0 CA V:CYS455 4.8 0.9 1.0 CD2 V:HIS472 5.0 0.5 1.0 CB V:VAL454 5.0 0.6 1.0 N V:CYS475 5.0 0.3 1.0

Zinc binding site 4 out of 4 in the Nucleosome-CHD4 Complex Structure (Two CHD4 Copies)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Nucleosome-CHD4 Complex Structure (Two CHD4 Copies) within 5.0Å range: probe atom residue distance (Å) B Occ V:Zn2204 b:0.6 occ:1.00 SG V:CYS467 2.3 0.2 1.0 SG V:CYS493 2.3 0.6 1.0 SG V:CYS490 2.4 0.0 1.0 SG V:CYS464 2.4 0.5 1.0 CB V:CYS464 3.1 0.5 1.0 CB V:CYS490 3.1 0.0 1.0 OG V:SER469 3.5 1.0 1.0 CB V:CYS467 3.6 0.2 1.0 CB V:SER469 3.7 1.0 1.0 N V:CYS490 3.8 0.0 1.0 CB V:CYS493 3.9 0.6 1.0 CA V:CYS490 4.0 0.0 1.0 N V:CYS467 4.1 0.2 1.0 CA V:CYS467 4.3 0.2 1.0 O V:CYS467 4.3 0.2 1.0 N V:CYS493 4.3 0.6 1.0 C V:CYS467 4.5 0.2 1.0 CA V:CYS464 4.5 0.5 1.0 N V:SER469 4.6 1.0 1.0 CA V:CYS493 4.7 0.6 1.0 C V:CYS490 4.7 0.0 1.0 O V:CYS490 4.7 0.0 1.0 C V:THR466 4.7 0.8 1.0 CA V:SER469 4.8 1.0 1.0 CG2 V:THR466 4.8 0.8 1.0 N V:THR466 5.0 0.8 1.0

L.Farnung, M.Ochmann, P.Cramer. Nucleosome-CHD4 Chromatin Remodeller Structure Maps Human Disease Mutations. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 32543371
DOI: 10.7554/ELIFE.56178