Zinc in PDB 8dji: Ternary Complex of SUMO1 with the Sim of Pml and Zinc

The structure of Ternary Complex of SUMO1 with the Sim of Pml and Zinc, PDB code: 8dji was solved by M.Lussier-Price, H.M.Wahba, X.H.Mascle, L.Cappadocia, V.Bourdeau, C.Gagnon, S.Igelmann, K.Sakaguchi, G.Ferbeyre, J.G.Omichinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.00 / 1.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.995, 47.156, 63.777, 90, 90, 90
R / Rfree (%)	23.1 / 25.8

The binding sites of Zinc atom in the Ternary Complex of SUMO1 with the Sim of Pml and Zinc (pdb code 8dji). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Ternary Complex of SUMO1 with the Sim of Pml and Zinc, PDB code: 8dji:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Ternary Complex of SUMO1 with the Sim of Pml and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ternary Complex of SUMO1 with the Sim of Pml and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:27.8 occ:1.00 OE1 A:GLU85 2.0 24.3 1.0 OE2 A:GLU84 2.1 23.7 1.0 O B:HOH211 2.4 16.1 1.0 CD A:GLU85 2.8 23.9 1.0 HG3 A:GLU84 2.9 28.6 1.0 CD A:GLU84 2.9 23.7 1.0 HG2 A:GLU84 3.0 28.6 1.0 OE2 A:GLU85 3.0 23.5 1.0 CG A:GLU84 3.1 24.0 1.0 HH22 B:ARG28 3.2 31.4 1.0 HD3 A:LYS23 3.8 37.4 1.0 NH2 B:ARG28 3.8 26.1 1.0 HB3 A:LYS23 3.9 37.2 1.0 HH21 B:ARG28 4.1 31.4 1.0 OE1 A:GLU84 4.1 23.5 1.0 CG A:GLU85 4.3 24.1 1.0 HD2 A:LYS23 4.3 37.4 1.0 HH12 B:ARG28 4.5 31.1 1.0 HG2 A:GLU85 4.5 28.9 1.0 CD A:LYS23 4.5 31.1 1.0 CB A:GLU84 4.6 24.0 1.0 HB2 A:GLU85 4.7 28.8 1.0 HB2 A:LYS23 4.7 37.2 1.0 CB A:LYS23 4.7 30.9 1.0 O A:HOH205 4.8 55.2 1.0 CZ B:ARG28 4.8 26.0 1.0 H A:GLU85 4.8 28.1 1.0 HG3 A:GLU85 4.9 28.9 1.0 HZ2 A:LYS23 5.0 37.9 1.0 CB A:GLU85 5.0 24.0 1.0 NH1 B:ARG28 5.0 25.9 1.0 N A:GLU85 5.0 23.4 1.0

Zinc binding site 2 out of 3 in the Ternary Complex of SUMO1 with the Sim of Pml and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ternary Complex of SUMO1 with the Sim of Pml and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:35.6 occ:1.00 OE1 A:GLU33 2.1 36.1 1.0 NE2 A:HIS35 2.3 27.6 1.0 OE1 B:GLU9 2.4 37.8 1.0 O A:HOH231 2.4 29.5 1.0 OE2 B:GLU9 2.6 37.4 1.0 CD A:GLU33 2.8 36.2 1.0 CD B:GLU9 2.8 37.6 1.0 OE2 A:GLU33 3.0 36.7 1.0 CD2 A:HIS35 3.1 27.3 1.0 HD2 A:HIS35 3.1 32.8 1.0 CE1 A:HIS35 3.4 27.5 1.0 HE1 A:HIS35 3.7 33.1 1.0 HG2 A:GLU33 4.0 43.1 1.0 CG A:GLU33 4.0 35.9 1.0 HE2 A:LYS25 4.2 39.0 1.0 O B:HOH203 4.3 30.5 1.0 CG A:HIS35 4.3 27.0 1.0 CG B:GLU9 4.3 37.5 1.0 ND1 A:HIS35 4.4 27.1 1.0 HA B:GLU9 4.5 45.6 1.0 HG3 A:LYS25 4.5 37.9 1.0 HG3 A:GLU33 4.6 43.1 1.0 O A:HOH238 4.6 57.2 1.0 HG2 B:GLU9 4.7 45.0 1.0 O B:HOH212 4.7 40.5 1.0 HB3 A:GLU33 4.7 43.3 1.0 HG3 B:GLU9 4.8 45.0 1.0 O A:HOH205 4.9 55.2 1.0 HB3 B:GLU9 4.9 45.4 1.0 H B:ARG10 5.0 35.9 1.0

Zinc binding site 3 out of 3 in the Ternary Complex of SUMO1 with the Sim of Pml and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ternary Complex of SUMO1 with the Sim of Pml and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:70.1 occ:1.00 O B:TYR29 2.1 30.1 1.0 O B:HOH208 2.6 45.6 1.0 OXT B:TYR29 2.7 30.3 1.0 C B:TYR29 2.8 30.1 1.0 HH A:TYR21 3.5 33.0 1.0 O B:HOH202 3.7 44.3 1.0 HE2 A:TYR21 3.7 32.7 1.0 HZ1 A:LYS39 4.0 37.5 1.0 HZ2 A:LYS39 4.2 37.5 1.0 CA B:TYR29 4.3 30.0 1.0 OH A:TYR21 4.3 27.4 1.0 CE2 A:TYR21 4.5 27.2 1.0 NZ A:LYS39 4.5 31.2 1.0 HE3 A:LYS39 4.6 36.3 1.0 HA B:TYR29 4.6 36.1 1.0 HB3 B:TYR29 4.7 36.1 1.0 CZ A:TYR21 4.9 27.0 1.0 HB2 B:TYR29 4.9 36.1 1.0 CB B:TYR29 4.9 30.0 1.0

M.Lussier-Price, H.M.Wahba, X.H.Mascle, L.Cappadocia, V.Bourdeau, C.Gagnon, S.Igelmann, K.Sakaguchi, G.Ferbeyre, J.G.Omichinski. Zinc Controls Pml Nuclear Body Formation Through Regulation of A Paralog Specific Auto-Inhibition in SUMO1. Nucleic Acids Res. V. 50 8331 2022.
ISSN: ESSN 1362-4962
PubMed: 35871297
DOI: 10.1093/NAR/GKAC620