Zinc in PDB 2mny: uc(Nmr) Structure of KDM5B PHD1 Finger

The binding sites of Zinc atom in the uc(Nmr) Structure of KDM5B PHD1 Finger (pdb code 2mny). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the uc(Nmr) Structure of KDM5B PHD1 Finger, PDB code: 2mny:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the uc(Nmr) Structure of KDM5B PHD1 Finger


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of uc(Nmr) Structure of KDM5B PHD1 Finger within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:0.0 occ:1.00 ND1 A:HIS335 2.0 0.0 1.0 SG A:CYS312 2.3 0.0 1.0 SG A:CYS338 2.3 0.0 1.0 SG A:CYS315 2.3 0.0 1.0 CE1 A:HIS335 2.7 0.0 1.0 HB2 A:LEU314 2.8 0.0 1.0 H A:HIS335 2.8 0.0 1.0 HE1 A:HIS335 2.9 0.0 1.0 CG A:HIS335 3.0 0.0 1.0 HB2 A:HIS335 3.2 0.0 1.0 CB A:CYS312 3.3 0.0 1.0 H A:CYS315 3.3 0.0 1.0 HB3 A:CYS312 3.4 0.0 1.0 CB A:CYS338 3.4 0.0 1.0 HB3 A:CYS338 3.4 0.0 1.0 HB2 A:CYS315 3.4 0.0 1.0 CB A:CYS315 3.5 0.0 1.0 HB2 A:CYS312 3.5 0.0 1.0 CB A:HIS335 3.6 0.0 1.0 HB2 A:CYS338 3.6 0.0 1.0 N A:HIS335 3.7 0.0 1.0 NE2 A:HIS335 3.7 0.0 1.0 N A:CYS315 3.8 0.0 1.0 CD2 A:HIS335 3.8 0.0 1.0 CB A:LEU314 3.8 0.0 1.0 HD13 A:LEU314 3.9 0.0 1.0 H A:GLY316 4.0 0.0 1.0 HA A:TYR334 4.0 0.0 1.0 HB3 A:LEU314 4.2 0.0 1.0 CA A:HIS335 4.3 0.0 1.0 CA A:CYS315 4.3 0.0 1.0 HB3 A:CYS315 4.4 0.0 1.0 C A:LEU314 4.4 0.0 1.0 HB3 A:HIS335 4.5 0.0 1.0 H A:LEU314 4.5 0.0 1.0 HE2 A:HIS335 4.5 0.0 1.0 CA A:LEU314 4.6 0.0 1.0 C A:TYR334 4.7 0.0 1.0 CA A:CYS312 4.7 0.0 1.0 CD1 A:LEU314 4.7 0.0 1.0 CG A:LEU314 4.7 0.0 1.0 CA A:CYS338 4.8 0.0 1.0 O A:CYS338 4.8 0.0 1.0 HD2 A:HIS335 4.8 0.0 1.0 HG A:LEU314 4.8 0.0 1.0 CA A:TYR334 4.8 0.0 1.0 HB2 A:TYR334 4.8 0.0 1.0 N A:LEU314 4.8 0.0 1.0 N A:GLY316 4.9 0.0 1.0 HA A:HIS335 5.0 0.0 1.0

Zinc binding site 2 out of 2 in the uc(Nmr) Structure of KDM5B PHD1 Finger


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of uc(Nmr) Structure of KDM5B PHD1 Finger within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:0.0 occ:1.00 SG A:CYS356 2.3 0.0 1.0 SG A:CYS327 2.3 0.0 1.0 SG A:CYS330 2.3 0.0 1.0 SG A:CYS353 2.3 0.0 1.0 H A:CYS353 2.4 0.0 1.0 HE3 A:LYS355 3.0 0.0 1.0 HB3 A:ASP332 3.2 0.0 1.0 N A:CYS353 3.2 0.0 1.0 HB3 A:CYS330 3.3 0.0 1.0 CB A:CYS327 3.3 0.0 1.0 H A:CYS330 3.3 0.0 1.0 HB3 A:CYS327 3.3 0.0 1.0 CB A:CYS330 3.4 0.0 1.0 HB2 A:CYS327 3.4 0.0 1.0 CB A:CYS353 3.5 0.0 1.0 HB2 A:CYS353 3.5 0.0 1.0 CB A:CYS356 3.6 0.0 1.0 HB3 A:CYS356 3.6 0.0 1.0 HA A:ARG352 3.7 0.0 1.0 N A:CYS330 3.7 0.0 1.0 HB2 A:ASP332 3.8 0.0 1.0 HB2 A:ARG352 3.8 0.0 1.0 CA A:CYS353 3.9 0.0 1.0 CB A:ASP332 4.0 0.0 1.0 O A:CYS330 4.0 0.0 1.0 CE A:LYS355 4.0 0.0 1.0 CA A:CYS330 4.0 0.0 1.0 HZ2 A:LYS355 4.0 0.0 1.0 HB2 A:CYS356 4.1 0.0 1.0 H A:CYS356 4.1 0.0 1.0 C A:ARG352 4.2 0.0 1.0 HZ1 A:LYS355 4.2 0.0 1.0 HG3 A:LYS355 4.2 0.0 1.0 HG2 A:LYS355 4.2 0.0 1.0 C A:CYS330 4.2 0.0 1.0 HB2 A:CYS330 4.3 0.0 1.0 O A:CYS353 4.3 0.0 1.0 NZ A:LYS355 4.3 0.0 1.0 CA A:ARG352 4.3 0.0 1.0 HE2 A:TYR334 4.4 0.0 1.0 HB3 A:CYS353 4.4 0.0 1.0 HE2 A:LYS355 4.5 0.0 1.0 C A:CYS353 4.5 0.0 1.0 CB A:ARG352 4.6 0.0 1.0 OD2 A:ASP332 4.6 0.0 1.0 HA3 A:GLY329 4.6 0.0 1.0 C A:GLY329 4.6 0.0 1.0 CG A:LYS355 4.6 0.0 1.0 CA A:CYS327 4.7 0.0 1.0 N A:CYS356 4.8 0.0 1.0 H A:ASP332 4.8 0.0 1.0 CA A:CYS356 4.8 0.0 1.0 CG A:ASP332 4.8 0.0 1.0 HA A:CYS353 4.8 0.0 1.0 CD A:LYS355 5.0 0.0 1.0 N A:ASP332 5.0 0.0 1.0 H A:GLY329 5.0 0.0 1.0

Y.Zhang, H.R.Yang, X.Guo, N.Y.Rong, Y.J.Song, Y.W.Xu, W.X.Lan, X.Zhang, M.Liu, Y.H.Xu, C.Cao. The PHD1 Finger of KDM5B Recognizes Unmodified H3K4 During the Demethylation of Histone H3K4ME2/3 By KDM5B Protein Cell 2014.
ISSN: ESSN 1674-8018
PubMed: 24952722
DOI: 10.1007/S13238-014-0078-4