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

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

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 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 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 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 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

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