Zinc in PDB 8kd4: RPD3S in Complex with Nucleosome with H3K36MLA Modification and 187BP Dna, CLASS1

The binding sites of Zinc atom in the RPD3S in Complex with Nucleosome with H3K36MLA Modification and 187BP Dna, CLASS1 (pdb code 8kd4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the RPD3S in Complex with Nucleosome with H3K36MLA Modification and 187BP Dna, CLASS1, PDB code: 8kd4:

Zinc binding site 1 out of 1 in the RPD3S in Complex with Nucleosome with H3K36MLA Modification and 187BP Dna, CLASS1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RPD3S in Complex with Nucleosome with H3K36MLA Modification and 187BP Dna, CLASS1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:112.2 occ:1.00 CB A:HIS188 2.0 93.0 1.0 ND1 A:HIS188 2.3 93.0 1.0 CG A:HIS188 2.4 93.0 1.0 OD2 A:ASP274 2.6 87.5 1.0 O A:VAL187 3.0 82.7 1.0 CA A:HIS188 3.3 93.0 1.0 O A:HIS188 3.5 93.0 1.0 CE1 A:HIS188 3.6 93.0 1.0 OH A:TYR313 3.6 102.5 1.0 C A:VAL187 3.6 82.7 1.0 CD2 A:HIS188 3.7 93.0 1.0 N A:HIS188 3.7 93.0 1.0 CG A:ASP274 3.8 87.5 1.0 C A:HIS188 3.8 93.0 1.0 NE2 A:HIS151 4.1 80.1 1.0 CZ A:TYR313 4.1 102.5 1.0 NE2 A:HIS188 4.2 93.0 1.0 OD2 A:ASP186 4.2 78.5 1.0 CE1 A:TYR313 4.5 102.5 1.0 CB A:ASP274 4.6 87.5 1.0 OD1 A:ASP274 4.6 87.5 1.0 CD2 A:HIS151 4.7 80.1 1.0 NE2 A:HIS150 4.8 78.0 1.0 CG2 A:VAL187 4.8 82.7 1.0 CA A:VAL187 4.9 82.7 1.0 CE2 A:TYR313 4.9 102.5 1.0

S.Dong, H.Li, M.Wang, N.Rasheed, B.Zou, X.Gao, J.Guan, W.Li, J.Zhang, C.Wang, N.Zhou, X.Shi, M.Li, M.Zhou, J.Huang, H.Li, Y.Zhang, K.H.Wong, X.Zhang, W.C.H.Chao, J.He. Structural Basis of Nucleosome Deacetylation and Dna Linker Tightening By RPD3S Histone Deacetylase Complex Cell Res. 2023.
ISSN: ISSN 1001-0602
DOI: 10.1038/S41422-023-00869-1