Zinc in PDB 2rsd: Solution Structure of the Plant Homeodomain (Phd) of the E3 Sumo Ligase SIZ1 From Rice

The binding sites of Zinc atom in the Solution Structure of the Plant Homeodomain (Phd) of the E3 Sumo Ligase SIZ1 From Rice (pdb code 2rsd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Solution Structure of the Plant Homeodomain (Phd) of the E3 Sumo Ligase SIZ1 From Rice, PDB code: 2rsd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Solution Structure of the Plant Homeodomain (Phd) of the E3 Sumo Ligase SIZ1 From Rice


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Solution Structure of the Plant Homeodomain (Phd) of the E3 Sumo Ligase SIZ1 From Rice within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:0.0 occ:1.00 ND1 A:HIS141 2.1 0.0 1.0 SG A:CYS119 2.3 0.0 1.0 SG A:CYS144 2.4 0.0 1.0 SG A:CYS117 2.4 0.0 1.0 HB2 A:HIS141 2.6 0.0 1.0 CG A:HIS141 3.0 0.0 1.0 CE1 A:HIS141 3.1 0.0 1.0 HB3 A:CYS117 3.1 0.0 1.0 HB3 A:CYS119 3.2 0.0 1.0 CB A:HIS141 3.3 0.0 1.0 CB A:CYS117 3.4 0.0 1.0 HE1 A:HIS141 3.4 0.0 1.0 HB2 A:CYS144 3.4 0.0 1.0 CB A:CYS119 3.4 0.0 1.0 CB A:CYS144 3.5 0.0 1.0 H A:CYS119 3.5 0.0 1.0 HB2 A:CYS117 3.7 0.0 1.0 HB3 A:CYS144 3.7 0.0 1.0 HB3 A:HIS141 3.8 0.0 1.0 H A:HIS141 3.9 0.0 1.0 CD2 A:HIS141 4.1 0.0 1.0 NE2 A:HIS141 4.1 0.0 1.0 HB2 A:CYS119 4.1 0.0 1.0 N A:CYS119 4.3 0.0 1.0 HG13 A:ILE118 4.4 0.0 1.0 HB3 A:SER121 4.4 0.0 1.0 CA A:CYS119 4.5 0.0 1.0 CA A:HIS141 4.5 0.0 1.0 N A:HIS141 4.5 0.0 1.0 H A:SER121 4.7 0.0 1.0 CA A:CYS117 4.7 0.0 1.0 H A:ILE118 4.7 0.0 1.0 CA A:CYS144 4.9 0.0 1.0 H A:CYS144 4.9 0.0 1.0 HG12 A:ILE118 4.9 0.0 1.0 O A:SER121 4.9 0.0 1.0 N A:ILE118 5.0 0.0 1.0 HB3 A:ASN125 5.0 0.0 1.0 HE2 A:HIS141 5.0 0.0 1.0

Zinc binding site 2 out of 2 in the Solution Structure of the Plant Homeodomain (Phd) of the E3 Sumo Ligase SIZ1 From Rice


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Solution Structure of the Plant Homeodomain (Phd) of the E3 Sumo Ligase SIZ1 From Rice within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:0.0 occ:1.00 SG A:CYS166 2.4 0.0 1.0 SG A:CYS131 2.4 0.0 1.0 SG A:CYS163 2.5 0.0 1.0 SG A:CYS136 2.5 0.0 1.0 H A:CYS163 2.9 0.0 1.0 HB3 A:CYS136 2.9 0.0 1.0 CB A:CYS136 3.0 0.0 1.0 HB2 A:CYS136 3.1 0.0 1.0 HG21 A:VAL138 3.2 0.0 1.0 HB3 A:CYS163 3.2 0.0 1.0 H A:CYS166 3.2 0.0 1.0 HG23 A:VAL138 3.2 0.0 1.0 HB2 A:CYS166 3.3 0.0 1.0 HB3 A:ASP133 3.3 0.0 1.0 CB A:CYS163 3.4 0.0 1.0 HB2 A:CYS131 3.4 0.0 1.0 CB A:CYS166 3.5 0.0 1.0 CB A:CYS131 3.5 0.0 1.0 N A:CYS163 3.6 0.0 1.0 CG2 A:VAL138 3.6 0.0 1.0 HB2 A:LEU165 3.7 0.0 1.0 HD1 A:TYR162 3.8 0.0 1.0 HB3 A:CYS131 3.8 0.0 1.0 HG22 A:VAL138 4.0 0.0 1.0 CA A:CYS163 4.0 0.0 1.0 N A:CYS166 4.0 0.0 1.0 HA A:TYR162 4.1 0.0 1.0 CB A:ASP133 4.3 0.0 1.0 HB2 A:CYS163 4.3 0.0 1.0 HB3 A:CYS166 4.3 0.0 1.0 HB2 A:ASP133 4.4 0.0 1.0 CA A:CYS166 4.4 0.0 1.0 OD2 A:ASP133 4.5 0.0 1.0 HD12 A:LEU165 4.5 0.0 1.0 CA A:CYS136 4.6 0.0 1.0 C A:CYS163 4.6 0.0 1.0 C A:TYR162 4.6 0.0 1.0 H A:VAL138 4.7 0.0 1.0 H A:ASP133 4.7 0.0 1.0 O A:CYS163 4.7 0.0 1.0 CB A:LEU165 4.7 0.0 1.0 HB3 A:TYR162 4.8 0.0 1.0 CA A:TYR162 4.8 0.0 1.0 CD1 A:TYR162 4.8 0.0 1.0 HG11 A:VAL138 4.9 0.0 1.0 HA A:CYS166 4.9 0.0 1.0 CG A:ASP133 4.9 0.0 1.0 HG A:LEU165 4.9 0.0 1.0 CA A:CYS131 4.9 0.0 1.0 HA A:CYS136 4.9 0.0 1.0 H A:LEU165 4.9 0.0 1.0 HA A:CYS163 5.0 0.0 1.0

H.Shindo, R.Suzuki, W.Tsuchiya, M.Taichi, Y.Nishiuchi, T.Yamazaki. Phd Finger of the Sumo Ligase Siz/Pias Family in Rice Reveals Specific Binding For Methylated Histone H3 at Lysine 4 and Arginine 2 Febs Lett. V. 586 1783 2012.
ISSN: ISSN 0014-5793
PubMed: 22626555
DOI: 10.1016/J.FEBSLET.2012.04.063