Atomistry » Zinc » PDB 2n9o-2nwo » 2naa
Atomistry »
  Zinc »
    PDB 2n9o-2nwo »
      2naa »

Zinc in PDB 2naa: NSD1-PHD_5-C5HCH Tandem Domain Structure

Enzymatic activity of NSD1-PHD_5-C5HCH Tandem Domain Structure

All present enzymatic activity of NSD1-PHD_5-C5HCH Tandem Domain Structure:
2.1.1.43;

Zinc Binding Sites:

The binding sites of Zinc atom in the NSD1-PHD_5-C5HCH Tandem Domain Structure (pdb code 2naa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the NSD1-PHD_5-C5HCH Tandem Domain Structure, PDB code: 2naa:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2naa

Go back to Zinc Binding Sites List in 2naa
Zinc binding site 1 out of 4 in the NSD1-PHD_5-C5HCH Tandem Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of NSD1-PHD_5-C5HCH Tandem Domain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:0.3
occ:1.00
ND1 A:HIS31 2.0 0.3 1.0
SG A:CYS9 2.3 0.3 1.0
SG A:CYS12 2.3 0.5 1.0
SG A:CYS34 2.3 0.4 1.0
HB2 A:HIS31 2.8 0.3 1.0
H A:HIS31 2.9 0.3 1.0
CE1 A:HIS31 2.9 0.3 1.0
CG A:HIS31 3.0 0.3 1.0
HB2 A:SER11 3.0 1.0 1.0
HB2 A:CYS12 3.1 0.6 1.0
HE1 A:HIS31 3.2 0.3 1.0
HB3 A:CYS34 3.3 0.6 1.0
CB A:HIS31 3.3 0.3 1.0
CB A:CYS9 3.4 0.3 1.0
CB A:CYS12 3.4 0.5 1.0
CB A:CYS34 3.4 0.5 1.0
HB2 A:CYS9 3.4 0.2 1.0
HB3 A:CYS9 3.4 0.3 1.0
H A:CYS12 3.5 0.4 1.0
N A:HIS31 3.7 0.2 1.0
HB2 A:CYS34 3.7 0.7 1.0
N A:CYS12 3.9 0.5 1.0
NE2 A:HIS31 4.0 0.3 1.0
CD2 A:HIS31 4.0 0.3 1.0
CA A:HIS31 4.1 0.3 1.0
CB A:SER11 4.1 0.5 1.0
HB3 A:CYS12 4.2 0.7 1.0
HB3 A:HIS31 4.2 0.3 1.0
CA A:CYS12 4.3 0.5 1.0
H A:CYS34 4.3 0.4 1.0
HA A:TYR30 4.4 0.2 1.0
H A:SER11 4.5 0.4 1.0
HB3 A:SER11 4.5 1.0 1.0
HB3 A:TYR30 4.6 0.3 1.0
C A:SER11 4.7 0.6 1.0
O A:HIS31 4.7 0.3 1.0
OG A:SER11 4.7 1.0 1.0
CA A:CYS34 4.8 0.5 1.0
C A:TYR30 4.8 0.2 1.0
CA A:CYS9 4.8 0.2 1.0
HA A:CYS12 4.8 0.6 1.0
CA A:SER11 4.9 0.5 1.0
C A:HIS31 4.9 0.3 1.0
N A:CYS34 4.9 0.5 1.0
HE2 A:HIS31 4.9 0.3 1.0
HA A:HIS31 4.9 0.3 1.0
HD23 A:LEU18 5.0 1.0 1.0

Zinc binding site 2 out of 4 in 2naa

Go back to Zinc Binding Sites List in 2naa
Zinc binding site 2 out of 4 in the NSD1-PHD_5-C5HCH Tandem Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of NSD1-PHD_5-C5HCH Tandem Domain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:0.3
occ:1.00
NE2 A:HIS50 2.0 0.3 1.0
SG A:CYS21 2.3 0.3 1.0
SG A:CYS26 2.3 0.3 1.0
SG A:CYS47 2.3 0.3 1.0
CE1 A:HIS50 2.5 0.3 1.0
HE1 A:HIS50 2.7 0.4 1.0
H A:CYS47 2.9 0.3 1.0
CD2 A:HIS50 2.9 0.3 1.0
HB3 A:CYS47 3.3 0.3 1.0
HB2 A:CYS26 3.3 0.6 1.0
HB2 A:CYS21 3.3 0.4 1.0
CB A:CYS21 3.3 0.4 1.0
CB A:CYS26 3.3 0.4 1.0
CB A:CYS47 3.4 0.3 1.0
HB3 A:CYS21 3.4 0.5 1.0
ND1 A:HIS50 3.5 0.3 1.0
HD2 A:HIS50 3.5 0.3 1.0
HB3 A:CYS26 3.5 0.5 1.0
N A:CYS47 3.7 0.3 1.0
CG A:HIS50 3.7 0.3 1.0
HB3 A:LYS23 3.9 1.1 1.0
HE3 A:TRP49 4.0 0.3 1.0
CA A:CYS47 4.1 0.3 1.0
HB3 A:TRP49 4.2 0.2 1.0
HE2 A:TYR30 4.2 0.7 1.0
HD1 A:HIS50 4.2 0.4 1.0
HB2 A:CYS47 4.3 0.3 1.0
HA A:GLU46 4.3 0.5 1.0
HH A:TYR30 4.4 1.2 1.0
O A:CYS47 4.5 0.3 1.0
HD3 A:LYS23 4.5 2.2 1.0
C A:CYS47 4.7 0.3 1.0
CA A:CYS26 4.7 0.4 1.0
CA A:CYS21 4.7 0.3 1.0
C A:GLU46 4.8 0.4 1.0
CB A:LYS23 4.8 0.8 1.0
HB2 A:LYS23 4.9 1.2 1.0
HA A:CYS26 4.9 0.4 1.0
H A:LYS23 4.9 0.6 1.0
HA A:CYS21 5.0 0.4 1.0
HB3 A:GLU46 5.0 1.1 1.0

Zinc binding site 3 out of 4 in 2naa

Go back to Zinc Binding Sites List in 2naa
Zinc binding site 3 out of 4 in the NSD1-PHD_5-C5HCH Tandem Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of NSD1-PHD_5-C5HCH Tandem Domain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:0.3
occ:1.00
ND1 A:HIS74 2.0 0.3 1.0
SG A:CYS52 2.3 0.2 1.0
SG A:CYS71 2.3 0.3 1.0
SG A:CYS55 2.3 0.3 1.0
HB2 A:HIS74 2.7 0.2 1.0
CE1 A:HIS74 2.9 0.3 1.0
CG A:HIS74 3.0 0.3 1.0
H A:CYS55 3.1 0.3 1.0
HB A:VAL54 3.2 0.3 1.0
HB3 A:CYS71 3.2 0.3 1.0
HE1 A:HIS74 3.2 0.4 1.0
H A:CYS71 3.2 0.2 1.0
HB3 A:CYS55 3.2 0.4 1.0
HB3 A:CYS52 3.3 0.2 1.0
CB A:CYS52 3.3 0.2 1.0
CB A:HIS74 3.3 0.2 1.0
CB A:CYS71 3.4 0.3 1.0
CB A:CYS55 3.4 0.4 1.0
HB2 A:CYS52 3.5 0.2 1.0
H A:HIS74 3.7 0.2 1.0
N A:CYS55 3.7 0.3 1.0
NE2 A:HIS74 4.0 0.3 1.0
N A:CYS71 4.0 0.2 1.0
HB3 A:HIS74 4.0 0.2 1.0
CD2 A:HIS74 4.0 0.3 1.0
CA A:CYS55 4.1 0.4 1.0
HB2 A:CYS71 4.2 0.3 1.0
CB A:VAL54 4.2 0.3 1.0
HB2 A:CYS55 4.3 0.4 1.0
N A:HIS74 4.3 0.2 1.0
CA A:CYS71 4.3 0.2 1.0
HB2 A:GLN73 4.3 1.0 1.0
HB2 A:LYS57 4.3 0.5 1.0
H A:VAL54 4.4 0.3 1.0
CA A:HIS74 4.4 0.2 1.0
H A:LYS57 4.4 0.3 1.0
HG12 A:VAL54 4.5 1.0 1.0
HD2 A:LYS57 4.6 0.9 1.0
C A:VAL54 4.6 0.4 1.0
H A:GLY56 4.7 0.3 1.0
CA A:CYS52 4.8 0.2 1.0
HA A:PHE70 4.8 0.2 1.0
CG1 A:VAL54 4.8 0.4 1.0
HG13 A:VAL54 4.8 1.1 1.0
CA A:VAL54 4.8 0.4 1.0
HE2 A:HIS74 4.8 0.4 1.0
H A:GLN73 4.9 0.3 1.0
C A:CYS55 4.9 0.3 1.0
N A:VAL54 5.0 0.3 1.0
HA A:CYS55 5.0 0.4 1.0

Zinc binding site 4 out of 4 in 2naa

Go back to Zinc Binding Sites List in 2naa
Zinc binding site 4 out of 4 in the NSD1-PHD_5-C5HCH Tandem Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of NSD1-PHD_5-C5HCH Tandem Domain Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:0.3
occ:1.00
NE2 A:HIS93 2.0 0.3 1.0
SG A:CYS66 2.3 0.3 1.0
SG A:CYS63 2.3 0.2 1.0
SG A:CYS90 2.3 0.3 1.0
CE1 A:HIS93 2.5 0.4 1.0
HE1 A:HIS93 2.7 0.4 1.0
H A:CYS90 2.8 0.2 1.0
CD2 A:HIS93 2.9 0.3 1.0
HB3 A:CYS66 3.2 0.4 1.0
HB3 A:CYS90 3.3 0.2 1.0
HB3 A:CYS63 3.3 0.2 1.0
CB A:CYS66 3.4 0.3 1.0
CB A:CYS63 3.4 0.2 1.0
CB A:CYS90 3.4 0.2 1.0
HD2 A:HIS93 3.4 0.4 1.0
ND1 A:HIS93 3.5 0.4 1.0
HB2 A:MET65 3.6 0.3 1.0
N A:CYS90 3.7 0.2 1.0
HB2 A:CYS63 3.7 0.2 1.0
CG A:HIS93 3.7 0.4 1.0
HB2 A:SER68 3.8 0.3 1.0
N A:CYS66 4.0 0.3 1.0
H A:MET65 4.0 0.3 1.0
H A:CYS66 4.0 0.3 1.0
CA A:CYS90 4.1 0.2 1.0
HA A:SER89 4.1 0.2 1.0
HB2 A:CYS66 4.2 0.4 1.0
HD1 A:HIS93 4.2 0.5 1.0
CA A:CYS66 4.2 0.3 1.0
HB2 A:CYS90 4.3 0.3 1.0
C A:MET65 4.3 0.3 1.0
CB A:MET65 4.5 0.3 1.0
HB2 A:GLU92 4.6 0.5 1.0
H A:SER68 4.7 0.3 1.0
N A:MET65 4.7 0.3 1.0
CA A:CYS63 4.7 0.2 1.0
O A:MET65 4.8 0.4 1.0
CA A:MET65 4.8 0.3 1.0
C A:SER89 4.8 0.2 1.0
O A:SER68 4.8 0.4 1.0
O A:CYS66 4.8 0.3 1.0
C A:CYS90 4.9 0.3 1.0
CB A:SER68 4.9 0.4 1.0
C A:CYS66 4.9 0.3 1.0
HE2 A:PHE70 4.9 0.3 1.0
H A:GLU92 4.9 0.4 1.0
O A:CYS90 4.9 0.3 1.0
CA A:SER89 5.0 0.2 1.0
HB3 A:MET65 5.0 0.4 1.0
HA A:CYS90 5.0 0.2 1.0

Reference:

A.Berardi, G.Quilici, D.Spiliotopoulos, M.A.Corral-Rodriguez, F.Martin-Garcia, M.Degano, G.Tonon, M.Ghitti, G.Musco. Structural Basis For PHDVC5HCHNSD1-C2HRNIZP1 Interaction: Implications For Sotos Syndrome. Nucleic Acids Res. V. 44 3448 2016.
ISSN: ISSN 0305-1048
PubMed: 26896805
DOI: 10.1093/NAR/GKW103
Page generated: Wed Dec 16 03:43:00 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy