Zinc in PDB 8djh: Ternary Complex of SUMO1 with A Phosphomimetic Sim of Pml and Zinc

The structure of Ternary Complex of SUMO1 with A Phosphomimetic Sim of Pml and Zinc, PDB code: 8djh 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)	38.04 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.776, 47.46, 63.632, 90, 90, 90
R / Rfree (%)	21.3 / 24.3

The binding sites of Zinc atom in the Ternary Complex of SUMO1 with A Phosphomimetic Sim of Pml and Zinc (pdb code 8djh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Ternary Complex of SUMO1 with A Phosphomimetic Sim of Pml and Zinc, PDB code: 8djh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Ternary Complex of SUMO1 with A Phosphomimetic 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 A Phosphomimetic Sim of Pml and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:57.5 occ:1.00 OE2 A:GLU11 2.2 61.6 1.0 OD1 A:ASP15 2.2 33.9 1.0 OD1 B:ASP17 2.3 40.8 1.0 CG B:ASP17 2.7 41.3 1.0 HG3 A:GLU11 2.7 75.5 1.0 OD2 A:ASP15 2.8 33.6 1.0 O A:HOH201 2.8 8.2 1.0 CG A:ASP15 2.8 33.7 1.0 OD2 B:ASP17 2.9 41.4 1.0 CD A:GLU11 3.1 63.0 1.0 CG A:GLU11 3.4 63.0 1.0 O A:HOH233 3.7 43.8 1.0 HB3 B:ASP17 3.7 50.4 1.0 CB B:ASP17 3.8 42.1 1.0 HG2 A:GLU11 3.8 75.5 1.0 O A:GLU11 3.8 62.2 1.0 HA B:ASP17 3.9 50.1 1.0 OE1 A:GLU11 4.3 64.5 1.0 CB A:ASP15 4.3 33.6 1.0 O B:HOH110 4.4 41.0 1.0 CA B:ASP17 4.4 41.8 1.0 HB2 B:ASP17 4.6 50.4 1.0 CB A:GLU11 4.6 64.7 1.0 C A:GLU11 4.6 63.6 1.0 HA A:GLU11 4.6 77.8 1.0 HA A:ASP15 4.6 40.5 1.0 HB2 A:ASP15 4.7 40.2 1.0 H A:ASP15 4.8 42.5 1.0 HB3 A:ASP15 4.8 40.2 1.0 HB3 A:GLU11 4.8 77.5 1.0 CA A:GLU11 4.8 64.9 1.0 N B:ASP21 4.9 53.7 1.0 CA A:ASP15 4.9 33.9 1.0

Zinc binding site 2 out of 4 in the Ternary Complex of SUMO1 with A Phosphomimetic 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 A Phosphomimetic Sim of Pml and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:14.6 occ:1.00 OE1 A:GLU85 2.0 12.2 1.0 OE2 A:GLU84 2.0 8.0 1.0 O A:HOH275 2.3 7.2 1.0 CD A:GLU85 2.9 11.8 1.0 CD A:GLU84 2.9 7.8 1.0 OE2 A:GLU85 3.0 11.6 1.0 HG2 A:GLU84 3.1 9.2 1.0 HG3 A:GLU84 3.1 9.2 1.0 CG A:GLU84 3.2 7.8 1.0 HH22 B:ARG28 3.4 11.0 1.0 HD3 A:LYS23 3.9 13.8 1.0 NH2 B:ARG28 3.9 9.2 1.0 HB3 A:LYS23 4.0 13.2 1.0 O A:HOH236 4.0 20.2 1.0 OE1 A:GLU84 4.1 7.7 1.0 HH21 B:ARG28 4.1 11.0 1.0 CG A:GLU85 4.3 11.6 1.0 HB2 A:GLU85 4.4 13.5 1.0 HG2 A:GLU85 4.5 13.8 1.0 O A:HOH230 4.5 42.6 1.0 HH12 B:ARG28 4.6 11.6 1.0 HD2 A:LYS23 4.7 13.8 1.0 CD A:LYS23 4.7 11.5 1.0 CB A:GLU84 4.8 7.7 1.0 HZ3 A:LYS23 4.8 14.8 1.0 CB A:LYS23 4.8 11.0 1.0 CB A:GLU85 4.9 11.3 1.0 CZ B:ARG28 4.9 9.8 1.0 HB2 A:LYS23 4.9 13.2 1.0 HG3 A:GLU85 4.9 13.8 1.0 H A:GLU85 4.9 13.1 1.0

Zinc binding site 3 out of 4 in the Ternary Complex of SUMO1 with A Phosphomimetic 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 A Phosphomimetic Sim of Pml and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:18.8 occ:1.00 OE2 A:GLU33 1.9 17.0 1.0 NE2 A:HIS35 2.1 6.7 1.0 O B:HOH113 2.1 19.5 1.0 OE2 B:GLU9 2.4 19.9 1.0 OE1 B:GLU9 2.4 19.7 1.0 CD B:GLU9 2.7 20.0 1.0 CD A:GLU33 2.9 16.8 1.0 CD2 A:HIS35 3.1 6.6 1.0 CE1 A:HIS35 3.1 6.3 1.0 HD2 A:HIS35 3.2 7.9 1.0 OE1 A:GLU33 3.3 16.7 1.0 HE1 A:HIS35 3.3 7.5 1.0 HE2 A:LYS25 3.6 16.2 1.0 O A:HOH247 3.9 13.1 1.0 ND1 A:HIS35 4.2 6.1 1.0 CG A:HIS35 4.2 6.2 1.0 CG B:GLU9 4.2 20.6 1.0 CG A:GLU33 4.3 16.9 1.0 HG3 A:GLU33 4.3 20.2 1.0 HA B:GLU9 4.4 25.0 1.0 HG2 B:GLU9 4.5 24.7 1.0 CE A:LYS25 4.6 13.6 1.0 HG3 A:LYS25 4.7 15.4 1.0 HG3 B:GLU9 4.7 24.7 1.0 HZ3 A:LYS25 4.8 16.8 1.0 HB2 A:GLU33 4.8 19.5 1.0 H B:ARG10 4.8 14.0 1.0 HB3 B:GLU9 4.8 25.0 1.0 HG2 A:GLU33 4.8 20.2 1.0 O A:HOH286 4.9 30.9 1.0 HE3 A:LYS25 4.9 16.2 1.0 HD1 A:HIS35 5.0 7.2 1.0 CB B:GLU9 5.0 20.9 1.0

Zinc binding site 4 out of 4 in the Ternary Complex of SUMO1 with A Phosphomimetic 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 4 of Ternary Complex of SUMO1 with A Phosphomimetic Sim of Pml and Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:28.4 occ:1.00 OD1 A:ASP86 2.1 7.3 1.0 O A:HOH205 2.2 15.4 1.0 O A:HOH283 2.3 22.1 1.0 O A:HOH265 2.3 26.0 1.0 O A:HOH239 2.5 30.4 1.0 O A:HOH217 2.5 19.0 1.0 CG A:ASP86 3.0 7.0 1.0 OD2 A:ASP86 3.2 7.2 1.0 O A:HOH243 3.8 21.9 1.0 O A:HOH269 3.8 9.6 1.0 O A:HOH203 3.9 20.2 1.0 OE2 A:GLU67 4.0 14.6 1.0 OE1 A:GLU83 4.1 16.9 1.0 HA A:ASP86 4.2 7.9 1.0 HZ A:PHE66 4.2 9.1 1.0 CB A:ASP86 4.4 6.7 1.0 HE1 A:PHE66 4.4 8.7 1.0 O A:HOH279 4.5 36.8 1.0 HB2 A:GLU83 4.5 19.4 1.0 HB3 A:ASP86 4.6 7.9 1.0 HG3 A:GLU83 4.8 19.8 1.0 CA A:ASP86 4.8 6.7 1.0 O A:HOH282 4.8 37.2 1.0 CZ A:PHE66 4.9 7.6 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