Zinc in PDB 6nzo: SET2 Bound to Nucleosome

All present enzymatic activity of SET2 Bound to Nucleosome:
2.1.1.43;

The binding sites of Zinc atom in the SET2 Bound to Nucleosome (pdb code 6nzo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the SET2 Bound to Nucleosome, PDB code: 6nzo:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SET2 Bound to Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SET2 Bound to Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn1001 b:0.0 occ:1.00 SG S:CYS169 2.4 0.2 1.0 SG S:CYS143 2.4 0.2 1.0 SG S:CYS158 2.4 0.2 1.0 SG S:CYS163 2.5 0.6 1.0 ZN S:ZN1002 3.2 0.5 1.0 CB S:CYS163 3.5 0.6 1.0 CB S:CYS158 3.5 0.2 1.0 ND2 S:ASN151 3.6 83.5 1.0 CB S:CYS169 3.6 0.2 1.0 CB S:CYS143 3.7 0.2 1.0 SG S:CYS129 3.9 0.7 1.0 SG S:CYS165 4.1 0.4 1.0 CB S:CYS165 4.6 0.4 1.0 O S:ASN171 4.7 0.3 1.0 CG S:ASN151 4.8 83.5 1.0 SG S:CYS149 4.9 92.3 1.0 CA S:CYS169 4.9 0.2 1.0 ND2 S:ASN171 4.9 0.3 1.0 CA S:CYS163 4.9 0.6 1.0 CA S:CYS158 5.0 0.2 1.0 CA S:CYS143 5.0 0.2 1.0

Zinc binding site 2 out of 3 in the SET2 Bound to Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SET2 Bound to Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn1002 b:0.5 occ:1.00 SG S:CYS129 2.3 0.7 1.0 SG S:CYS149 2.3 92.3 1.0 SG S:CYS143 2.4 0.2 1.0 SG S:CYS131 2.5 0.6 1.0 ZN S:ZN1001 3.2 0.0 1.0 CB S:CYS131 3.3 0.6 1.0 ND2 S:ASN151 3.4 83.5 1.0 CB S:CYS129 3.8 0.7 1.0 CB S:CYS143 3.8 0.2 1.0 CG S:ASN151 4.0 83.5 1.0 CB S:CYS149 4.1 92.3 1.0 SG S:CYS163 4.2 0.6 1.0 CB S:ASN151 4.3 83.5 1.0 SG S:CYS158 4.4 0.2 1.0 SG S:CYS165 4.4 0.4 1.0 CA S:CYS131 4.6 0.6 1.0 N S:CYS131 4.7 0.6 1.0 N S:ASN151 4.7 83.5 1.0 CA S:CYS143 4.7 0.2 1.0 SG S:CYS169 4.8 0.2 1.0 OD1 S:ASN151 4.8 83.5 1.0 N S:ILE150 4.9 77.5 1.0 CA S:CYS129 4.9 0.7 1.0 CA S:CYS149 5.0 92.3 1.0

Zinc binding site 3 out of 3 in the SET2 Bound to Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SET2 Bound to Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ S:Zn1003 b:0.7 occ:1.00 SG S:CYS308 2.3 0.2 1.0 SG S:CYS315 2.3 0.9 1.0 SG S:CYS310 2.3 0.9 1.0 SG S:CYS261 2.3 0.7 1.0 CB S:CYS315 2.4 0.9 1.0 CB S:CYS261 2.9 0.7 1.0 CA S:CYS315 3.1 0.9 1.0 CB S:CYS308 3.4 0.2 1.0 N S:CYS261 3.7 0.7 1.0 NE2 S:HIS259 3.7 0.7 1.0 CA S:CYS261 3.9 0.7 1.0 CB S:CYS310 4.0 0.9 1.0 N S:CYS315 4.1 0.9 1.0 C S:CYS315 4.2 0.9 1.0 O S:PHE318 4.3 0.6 1.0 OE2 S:GLU312 4.3 0.0 1.0 N S:VAL316 4.4 0.7 1.0 CD2 S:HIS259 4.4 0.7 1.0 CG S:GLU312 4.6 0.0 1.0 CE1 S:HIS259 4.6 0.7 1.0 CA S:CYS308 4.7 0.2 1.0 C S:SER260 4.8 0.6 1.0 CD S:GLU312 4.8 0.0 1.0 O S:CYS308 4.8 0.2 1.0 C S:ASN314 4.8 0.8 1.0 O S:ASN314 4.9 0.8 1.0 C S:CYS308 5.0 0.2 1.0

S.Bilokapic, M.Halic. Nucleosome and Ubiquitin Position SET2 to Methylate H3K36. Nat Commun V. 10 3795 2019.
ISSN: ESSN 2041-1723
PubMed: 31439846
DOI: 10.1038/S41467-019-11726-4