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Zinc in PDB 2mnz: uc(Nmr) Structure of KDM5B PHD1 Finger in Complex with H3K4ME0(1-10AA)

Zinc Binding Sites:

The binding sites of Zinc atom in the uc(Nmr) Structure of KDM5B PHD1 Finger in Complex with H3K4ME0(1-10AA) (pdb code 2mnz). 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 in Complex with H3K4ME0(1-10AA), PDB code: 2mnz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2mnz

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Zinc binding site 1 out of 2 in the uc(Nmr) Structure of KDM5B PHD1 Finger in Complex with H3K4ME0(1-10AA)


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 in Complex with H3K4ME0(1-10AA) 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:CYS315 2.3 0.0 1.0
SG A:CYS312 2.3 0.0 1.0
SG A:CYS338 2.3 0.0 1.0
HB2 A:HIS335 2.7 0.0 1.0
CG A:HIS335 3.0 0.0 1.0
CE1 A:HIS335 3.0 0.0 1.0
HB2 A:CYS315 3.1 0.0 1.0
HE1 A:PHE337 3.1 0.0 1.0
CB A:CYS312 3.2 0.0 1.0
HB3 A:CYS312 3.2 0.0 1.0
H A:CYS315 3.2 0.0 1.0
HB2 A:CYS312 3.2 0.0 1.0
HE1 A:HIS335 3.3 0.0 1.0
CB A:CYS315 3.3 0.0 1.0
HB2 A:CYS338 3.3 0.0 1.0
CB A:CYS338 3.3 0.0 1.0
CB A:HIS335 3.3 0.0 1.0
HB2 A:LEU314 3.5 0.0 1.0
HB3 A:CYS338 3.6 0.0 1.0
H A:HIS335 3.7 0.0 1.0
CE1 A:PHE337 3.8 0.0 1.0
N A:CYS315 3.8 0.0 1.0
HB3 A:HIS335 4.0 0.0 1.0
HZ A:PHE337 4.1 0.0 1.0
HB3 A:CYS315 4.1 0.0 1.0
CA A:CYS315 4.2 0.0 1.0
CD2 A:HIS335 4.2 0.0 1.0
NE2 A:HIS335 4.2 0.0 1.0
N A:HIS335 4.2 0.0 1.0
CZ A:PHE337 4.3 0.0 1.0
CA A:HIS335 4.4 0.0 1.0
CB A:LEU314 4.5 0.0 1.0
H A:GLY316 4.6 0.0 1.0
CD1 A:PHE337 4.6 0.0 1.0
H A:CYS338 4.6 0.0 1.0
CA A:CYS312 4.6 0.0 1.0
HD1 A:PHE337 4.7 0.0 1.0
CA A:CYS338 4.7 0.0 1.0
C A:LEU314 4.7 0.0 1.0
HA A:CYS315 4.7 0.0 1.0
HA A:TYR334 4.8 0.0 1.0
H A:LEU314 4.8 0.0 1.0
HB3 A:LEU314 4.9 0.0 1.0
N A:CYS338 5.0 0.0 1.0

Zinc binding site 2 out of 2 in 2mnz

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Zinc binding site 2 out of 2 in the uc(Nmr) Structure of KDM5B PHD1 Finger in Complex with H3K4ME0(1-10AA)


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 in Complex with H3K4ME0(1-10AA) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:0.0
occ:1.00
H A:ASP331 2.0 0.0 1.0
SG A:CYS356 2.3 0.0 1.0
SG A:CYS353 2.3 0.0 1.0
SG A:CYS330 2.3 0.0 1.0
SG A:CYS327 2.3 0.0 1.0
HB2 A:ASP331 2.6 0.0 1.0
H A:CYS330 2.6 0.0 1.0
H A:CYS353 2.7 0.0 1.0
H A:CYS356 2.8 0.0 1.0
N A:ASP331 2.9 0.0 1.0
HB3 A:CYS353 3.3 0.0 1.0
HB3 A:LYS355 3.3 0.0 1.0
CB A:CYS353 3.3 0.0 1.0
HB3 A:CYS356 3.3 0.0 1.0
N A:CYS330 3.3 0.0 1.0
CB A:CYS356 3.4 0.0 1.0
N A:CYS353 3.5 0.0 1.0
CB A:ASP331 3.5 0.0 1.0
N A:CYS356 3.5 0.0 1.0
CB A:CYS330 3.7 0.0 1.0
CB A:CYS327 3.7 0.0 1.0
CA A:CYS330 3.8 0.0 1.0
C A:CYS330 3.8 0.0 1.0
HB2 A:CYS327 3.8 0.0 1.0
CA A:CYS353 3.8 0.0 1.0
CA A:ASP331 3.8 0.0 1.0
O A:CYS353 3.9 0.0 1.0
HB3 A:CYS327 4.0 0.0 1.0
CG A:ASP331 4.0 0.0 1.0
C A:CYS353 4.0 0.0 1.0
CA A:CYS356 4.1 0.0 1.0
HB3 A:CYS330 4.1 0.0 1.0
HA3 A:GLY329 4.2 0.0 1.0
HB3 A:ARG352 4.3 0.0 1.0
HB2 A:CYS353 4.3 0.0 1.0
H A:LYS355 4.3 0.0 1.0
HB2 A:CYS356 4.3 0.0 1.0
CB A:LYS355 4.3 0.0 1.0
OD1 A:ASP331 4.4 0.0 1.0
HB3 A:ASP331 4.4 0.0 1.0
C A:GLY329 4.4 0.0 1.0
HB2 A:CYS330 4.5 0.0 1.0
C A:LYS355 4.5 0.0 1.0
HA A:CYS356 4.5 0.0 1.0
OD2 A:ASP331 4.5 0.0 1.0
HA A:ASP331 4.5 0.0 1.0
N A:LYS355 4.6 0.0 1.0
HA A:ARG352 4.6 0.0 1.0
C A:ARG352 4.6 0.0 1.0
HD3 A:LYS355 4.7 0.0 1.0
H A:GLY329 4.7 0.0 1.0
CA A:GLY329 4.7 0.0 1.0
CA A:LYS355 4.7 0.0 1.0
HA A:CYS353 4.8 0.0 1.0
HA A:CYS330 4.8 0.0 1.0
O A:ASP331 4.9 0.0 1.0
C A:ASP331 4.9 0.0 1.0
N A:GLY329 4.9 0.0 1.0
HB2 A:LYS355 4.9 0.0 1.0
O A:CYS330 4.9 0.0 1.0
CA A:CYS327 5.0 0.0 1.0
H A:LEU357 5.0 0.0 1.0
N A:PRO354 5.0 0.0 1.0

Reference:

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
Page generated: Wed Dec 16 03:40:41 2020

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