Zinc in PDB 5yuf: Crystal Structure of Pml Ring Tetramer

The structure of Crystal Structure of Pml Ring Tetramer, PDB code: 5yuf was solved by P.Wang, S.Benhend, H.Wu, V.Breitenbach, T.Zhen, F.Jollivet, L.Peres, Y.Li, S.Chen, Z.Chen, H.De The, G.Meng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.83 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.510, 84.690, 86.110, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 21.7

The binding sites of Zinc atom in the Crystal Structure of Pml Ring Tetramer (pdb code 5yuf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Pml Ring Tetramer, PDB code: 5yuf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Pml Ring Tetramer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Pml Ring Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:47.7 occ:1.00 SG A:CYS77 2.2 38.3 1.0 SG A:CYS80 2.3 38.2 1.0 SG A:CYS60 2.4 42.9 1.0 SG A:CYS57 2.4 33.8 1.0 HB2 A:CYS80 2.9 44.7 1.0 HB3 A:CYS57 3.1 42.9 1.0 HB3 A:CYS60 3.2 52.8 1.0 CB A:CYS57 3.2 35.7 1.0 H A:CYS77 3.2 38.3 1.0 H A:CYS60 3.2 51.6 1.0 HB2 A:CYS57 3.2 42.9 1.0 CB A:CYS80 3.2 37.3 1.0 HB3 A:CYS77 3.4 44.7 1.0 CB A:CYS60 3.4 44.0 1.0 CB A:CYS77 3.4 37.2 1.0 HB3 A:GLN59 3.5 41.8 1.0 H A:CYS80 3.6 41.1 1.0 N A:CYS60 3.8 43.0 1.0 HB3 A:CYS80 3.9 44.7 1.0 N A:CYS77 4.0 31.9 1.0 HB3 A:ALA62 4.1 49.5 1.0 HB2 A:CYS60 4.1 52.8 1.0 CA A:CYS60 4.2 44.2 1.0 HB2 A:CYS77 4.2 44.7 1.0 N A:CYS80 4.2 34.3 1.0 CA A:CYS77 4.2 33.5 1.0 H A:ALA62 4.3 49.0 1.0 CA A:CYS80 4.3 34.7 1.0 H A:GLN59 4.4 41.5 1.0 CB A:GLN59 4.4 34.8 1.0 HG3 A:GLN59 4.6 45.5 1.0 CA A:CYS57 4.7 35.4 1.0 HA A:CYS80 4.7 41.6 1.0 HG2 A:GLN59 4.7 45.5 1.0 HA A:LEU76 4.7 34.5 1.0 C A:GLN59 4.8 43.2 1.0 H A:GLN61 4.8 50.7 1.0 C A:CYS60 4.8 44.0 1.0 C A:CYS77 4.8 32.7 1.0 CG A:GLN59 4.8 37.9 1.0 O A:CYS77 4.9 33.2 1.0 CB A:ALA62 5.0 41.3 1.0 HA A:CYS60 5.0 53.1 1.0 HA A:CYS57 5.0 42.5 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Pml Ring Tetramer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Pml Ring Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:33.9 occ:1.00 ND1 A:HIS74 2.1 33.2 1.0 SG A:CYS72 2.3 25.1 1.0 SG A:CYS88 2.3 26.6 1.0 SG A:CYS91 2.3 26.1 1.0 HB2 A:CYS72 2.9 29.9 1.0 CE1 A:HIS74 2.9 27.4 1.0 HB2 A:HIS74 3.0 30.8 1.0 HE1 A:HIS74 3.1 32.9 1.0 CB A:CYS72 3.1 24.9 1.0 CG A:HIS74 3.1 26.7 1.0 H A:CYS91 3.1 30.5 1.0 CB A:CYS88 3.2 27.2 1.0 HB3 A:CYS88 3.2 32.6 1.0 HB2 A:CYS88 3.2 32.6 1.0 HB3 A:CYS72 3.3 29.9 1.0 HB A:ILE90 3.5 34.8 1.0 HB3 A:CYS91 3.5 30.9 1.0 CB A:HIS74 3.6 25.6 1.0 CB A:CYS91 3.6 25.7 1.0 N A:CYS91 3.8 25.4 1.0 H A:HIS74 3.9 32.6 1.0 NE2 A:HIS74 4.1 26.9 1.0 HB3 A:HIS74 4.1 30.8 1.0 HB3 A:ALA93 4.1 34.5 1.0 CD2 A:HIS74 4.2 27.4 1.0 CA A:CYS91 4.2 26.5 1.0 H A:ALA93 4.3 34.1 1.0 H A:ILE90 4.3 31.4 1.0 HA D:CYS72 4.3 32.9 1.0 HB2 A:CYS91 4.3 30.9 1.0 CB A:ILE90 4.4 29.0 1.0 HB2 A:ALA93 4.5 34.5 1.0 CA A:CYS72 4.5 26.7 1.0 HD12 A:ILE90 4.6 45.2 1.0 H A:GLN92 4.6 33.9 1.0 N A:HIS74 4.6 27.2 1.0 CA A:CYS88 4.6 26.4 1.0 HH2 A:TRP95 4.6 37.1 1.0 CA A:HIS74 4.7 24.9 1.0 H A:CYS72 4.8 31.2 1.0 CB A:ALA93 4.8 28.7 1.0 C A:ILE90 4.8 27.2 1.0 C A:CYS72 4.8 29.6 1.0 HE2 A:HIS74 4.9 32.3 1.0 C A:CYS91 4.9 28.2 1.0 HA A:CYS88 4.9 31.7 1.0 N A:GLN92 4.9 28.2 1.0 HG22 A:ILE90 4.9 36.3 1.0 O A:CYS72 4.9 31.2 1.0 N A:ILE90 5.0 26.2 1.0 CA A:ILE90 5.0 25.8 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Pml Ring Tetramer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Pml Ring Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:37.5 occ:1.00 SG B:CYS60 2.3 33.9 1.0 SG B:CYS80 2.3 35.2 1.0 SG B:CYS77 2.3 31.6 1.0 SG B:CYS57 2.4 29.6 1.0 HB2 B:CYS80 2.9 42.3 1.0 HB3 B:CYS60 3.0 43.4 1.0 HB3 B:CYS57 3.2 36.2 1.0 H B:CYS60 3.2 41.8 1.0 CB B:CYS57 3.2 30.2 1.0 H B:CYS77 3.2 37.2 1.0 CB B:CYS60 3.2 36.2 1.0 CB B:CYS80 3.2 35.3 1.0 HB2 B:CYS57 3.3 36.2 1.0 HB3 B:CYS77 3.4 37.3 1.0 CB B:CYS77 3.5 31.1 1.0 H B:CYS80 3.6 44.8 1.0 HB3 B:GLN59 3.7 32.4 1.0 N B:CYS60 3.8 34.8 1.0 HB3 B:CYS80 3.9 42.3 1.0 N B:CYS77 4.0 31.0 1.0 HB2 B:CYS60 4.0 43.4 1.0 CA B:CYS60 4.1 36.0 1.0 HB3 B:ALA62 4.2 43.8 1.0 N B:CYS80 4.2 37.3 1.0 HB2 B:CYS77 4.3 37.3 1.0 CA B:CYS77 4.3 31.7 1.0 CA B:CYS80 4.3 35.4 1.0 H B:ALA62 4.4 40.9 1.0 H B:GLN59 4.4 36.4 1.0 H B:GLN61 4.6 40.0 1.0 CB B:GLN59 4.6 27.0 1.0 CA B:CYS57 4.7 27.6 1.0 HA B:CYS80 4.7 42.5 1.0 HA B:LEU76 4.7 31.3 1.0 C B:GLN59 4.8 35.0 1.0 C B:CYS60 4.8 34.3 1.0 HG3 B:GLN59 4.8 38.4 1.0 O B:HOH258 4.8 54.9 1.0 O B:CYS77 4.9 30.2 1.0 HA B:CYS60 4.9 43.2 1.0 C B:CYS77 4.9 30.8 1.0 N B:GLN61 4.9 33.3 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Pml Ring Tetramer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Pml Ring Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:31.1 occ:1.00 ND1 B:HIS74 2.1 29.5 1.0 SG B:CYS72 2.3 25.5 1.0 SG B:CYS88 2.3 24.5 1.0 SG B:CYS91 2.4 24.5 1.0 HB2 B:HIS74 2.9 27.4 1.0 CE1 B:HIS74 3.0 24.5 1.0 HE1 B:HIS74 3.1 29.4 1.0 CG B:HIS74 3.1 24.9 1.0 HB3 B:CYS88 3.2 29.6 1.0 CB B:CYS88 3.2 24.7 1.0 H B:CYS91 3.2 27.1 1.0 HB2 B:CYS88 3.2 29.6 1.0 HB2 B:CYS72 3.2 30.8 1.0 CB B:CYS72 3.3 25.7 1.0 HB3 B:CYS72 3.4 30.8 1.0 HB B:ILE90 3.5 28.3 1.0 HB3 B:CYS91 3.5 28.8 1.0 CB B:HIS74 3.5 22.8 1.0 CB B:CYS91 3.6 24.0 1.0 N B:CYS91 3.8 22.6 1.0 H B:HIS74 3.9 30.2 1.0 HA C:CYS72 4.0 35.0 1.0 HB3 B:HIS74 4.1 27.4 1.0 HB3 B:ALA93 4.1 30.4 1.0 NE2 B:HIS74 4.1 25.4 1.0 CD2 B:HIS74 4.2 24.3 1.0 H B:ALA93 4.3 30.8 1.0 CA B:CYS91 4.3 24.4 1.0 H B:ILE90 4.3 30.0 1.0 HB2 B:CYS91 4.3 28.8 1.0 CB B:ILE90 4.4 23.6 1.0 HD12 B:ILE90 4.4 31.4 1.0 HB2 B:ALA93 4.5 30.4 1.0 N B:HIS74 4.5 25.2 1.0 H B:GLN92 4.6 31.2 1.0 CA B:CYS88 4.6 25.2 1.0 CA B:CYS72 4.7 25.4 1.0 CA B:HIS74 4.7 23.4 1.0 CB B:ALA93 4.7 25.3 1.0 C B:ILE90 4.8 24.7 1.0 HD12 B:LEU70 4.8 36.3 1.0 H B:CYS72 4.8 31.2 1.0 HD13 B:LEU70 4.8 36.3 1.0 HG22 B:ILE90 4.9 27.5 1.0 H B:LEU73 4.9 33.0 1.0 HE2 B:HIS74 4.9 30.4 1.0 HH2 B:TRP95 4.9 37.3 1.0 C B:CYS91 4.9 23.4 1.0 CA C:CYS72 4.9 29.2 1.0 HA B:CYS88 5.0 30.2 1.0 N B:GLN92 5.0 26.0 1.0 N B:ILE90 5.0 25.0 1.0 CA B:ILE90 5.0 23.4 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Pml Ring Tetramer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Pml Ring Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:36.6 occ:1.00 SG C:CYS60 2.3 32.2 1.0 SG C:CYS57 2.3 30.7 1.0 SG C:CYS77 2.3 37.5 1.0 SG C:CYS80 2.4 38.2 1.0 HB2 C:CYS80 2.9 47.2 1.0 HB3 C:CYS57 3.1 36.5 1.0 CB C:CYS57 3.1 30.4 1.0 H C:CYS60 3.1 40.6 1.0 HB2 C:CYS57 3.1 36.5 1.0 HB3 C:CYS60 3.2 38.9 1.0 H C:CYS77 3.2 40.9 1.0 CB C:CYS80 3.3 39.4 1.0 CB C:CYS60 3.3 32.4 1.0 HB3 C:CYS77 3.5 46.1 1.0 H C:CYS80 3.5 51.0 1.0 CB C:CYS77 3.5 38.4 1.0 HB3 C:GLN59 3.6 38.2 1.0 N C:CYS60 3.8 33.8 1.0 HB3 C:CYS80 3.9 47.2 1.0 N C:CYS77 4.0 34.1 1.0 HB3 C:ALA62 4.0 51.5 1.0 CA C:CYS60 4.1 33.7 1.0 HB2 C:CYS60 4.1 38.9 1.0 H C:ALA62 4.2 45.6 1.0 N C:CYS80 4.2 42.5 1.0 HB2 C:CYS77 4.3 46.1 1.0 CA C:CYS77 4.3 37.8 1.0 CA C:CYS80 4.3 41.0 1.0 H C:GLN59 4.4 35.8 1.0 H C:GLN61 4.5 41.0 1.0 CB C:GLN59 4.5 31.9 1.0 CA C:CYS57 4.6 28.3 1.0 HA C:LEU76 4.6 35.2 1.0 C C:CYS60 4.7 36.1 1.0 HA C:CYS80 4.7 49.3 1.0 HG3 C:GLN59 4.8 45.2 1.0 C C:GLN59 4.8 32.4 1.0 N C:GLN61 4.8 34.2 1.0 O C:CYS77 4.8 38.2 1.0 HD22 C:LEU76 4.9 39.0 1.0 HG2 C:GLN59 4.9 45.2 1.0 C C:CYS77 4.9 38.7 1.0 CB C:ALA62 4.9 42.9 1.0 HA C:CYS57 4.9 33.9 1.0 HA C:CYS60 4.9 40.4 1.0 N C:ALA62 5.0 38.0 1.0 HB3 C:LEU76 5.0 36.7 1.0 HB2 C:ALA62 5.0 51.5 1.0 CG C:GLN59 5.0 37.7 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Pml Ring Tetramer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Pml Ring Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:31.6 occ:1.00 ND1 C:HIS74 2.0 31.5 1.0 SG C:CYS88 2.3 28.6 1.0 SG C:CYS72 2.3 27.2 1.0 SG C:CYS91 2.4 27.2 1.0 CE1 C:HIS74 2.9 25.6 1.0 HE1 C:HIS74 3.0 30.8 1.0 HB2 C:CYS72 3.0 35.8 1.0 HB2 C:HIS74 3.0 31.5 1.0 HB3 C:CYS88 3.1 32.5 1.0 CB C:CYS88 3.1 27.1 1.0 CG C:HIS74 3.1 25.7 1.0 H C:CYS91 3.1 37.4 1.0 HB2 C:CYS88 3.1 32.5 1.0 CB C:CYS72 3.2 29.8 1.0 HB C:ILE90 3.4 35.9 1.0 HB3 C:CYS72 3.4 35.8 1.0 HB3 C:CYS91 3.5 31.8 1.0 CB C:CYS91 3.6 26.5 1.0 CB C:HIS74 3.6 26.3 1.0 N C:CYS91 3.8 31.1 1.0 H C:HIS74 4.0 30.6 1.0 NE2 C:HIS74 4.0 26.0 1.0 HB3 C:ALA93 4.1 33.8 1.0 HB3 C:HIS74 4.2 31.5 1.0 CD2 C:HIS74 4.2 26.4 1.0 HA B:CYS72 4.2 30.5 1.0 H C:ALA93 4.2 35.3 1.0 CA C:CYS91 4.3 28.8 1.0 H C:ILE90 4.3 36.5 1.0 HD12 C:ILE90 4.3 37.7 1.0 CB C:ILE90 4.4 29.9 1.0 HB2 C:CYS91 4.4 31.8 1.0 CA C:CYS72 4.5 29.2 1.0 HB2 C:ALA93 4.5 33.8 1.0 CA C:CYS88 4.6 29.3 1.0 H C:GLN92 4.6 34.3 1.0 HH2 C:TRP95 4.6 44.8 1.0 N C:HIS74 4.6 25.5 1.0 CA C:HIS74 4.7 26.2 1.0 H C:CYS72 4.8 33.8 1.0 HE2 C:HIS74 4.8 31.2 1.0 CB C:ALA93 4.8 28.1 1.0 C C:ILE90 4.8 34.6 1.0 C C:CYS72 4.8 29.5 1.0 HG22 C:ILE90 4.8 34.1 1.0 O C:CYS72 4.9 30.4 1.0 C C:CYS91 4.9 27.9 1.0 HA C:CYS88 4.9 35.2 1.0 HB3 B:CYS72 4.9 30.8 1.0 N C:GLN92 4.9 28.6 1.0 N C:ILE90 4.9 30.4 1.0 CA C:ILE90 5.0 31.3 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Pml Ring Tetramer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Pml Ring Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:51.5 occ:1.00 SG D:CYS80 2.3 44.7 1.0 SG D:CYS60 2.4 43.0 1.0 SG D:CYS57 2.4 37.0 1.0 SG D:CYS77 2.4 43.2 1.0 HB2 D:CYS80 2.9 50.5 1.0 HB3 D:CYS57 3.0 43.2 1.0 CB D:CYS57 3.1 36.0 1.0 HB2 D:CYS57 3.1 43.2 1.0 HB3 D:CYS60 3.1 53.0 1.0 CB D:CYS80 3.2 42.1 1.0 H D:CYS77 3.2 43.6 1.0 H D:CYS60 3.2 50.6 1.0 CB D:CYS60 3.4 44.1 1.0 HB3 D:CYS77 3.5 49.3 1.0 CB D:CYS77 3.6 41.1 1.0 H D:CYS80 3.6 51.3 1.0 HB3 D:GLN59 3.8 45.9 1.0 HB3 D:CYS80 3.8 50.5 1.0 N D:CYS60 3.9 42.2 1.0 N D:CYS77 4.0 36.3 1.0 HB2 D:CYS60 4.1 53.0 1.0 CA D:CYS60 4.2 45.0 1.0 HB3 D:ALA62 4.2 66.2 1.0 N D:CYS80 4.2 42.8 1.0 CA D:CYS80 4.3 42.4 1.0 CA D:CYS77 4.4 38.0 1.0 HB2 D:CYS77 4.4 49.3 1.0 H D:GLN59 4.4 42.5 1.0 H D:ALA62 4.4 57.5 1.0 H D:GLN61 4.5 56.7 1.0 CA D:CYS57 4.6 35.8 1.0 HA D:LEU76 4.7 38.6 1.0 HA D:CYS80 4.7 50.8 1.0 CB D:GLN59 4.7 38.2 1.0 HG2 D:GLN59 4.8 53.7 1.0 C D:CYS60 4.8 47.7 1.0 HE21 D:GLN59 4.9 66.7 1.0 HA D:CYS57 4.9 42.9 1.0 C D:GLN59 4.9 40.5 1.0 O D:CYS77 4.9 39.2 1.0 N D:GLN61 4.9 47.2 1.0 C D:CYS77 5.0 37.0 1.0 HD22 D:LEU76 5.0 41.5 1.0 HA D:CYS60 5.0 54.1 1.0 HB3 D:LEU76 5.0 39.1 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Pml Ring Tetramer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Pml Ring Tetramer within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:36.6 occ:1.00 ND1 D:HIS74 2.1 34.0 1.0 SG D:CYS72 2.3 28.8 1.0 SG D:CYS88 2.3 32.8 1.0 SG D:CYS91 2.4 29.1 1.0 CE1 D:HIS74 3.0 29.3 1.0 HB2 D:HIS74 3.0 34.9 1.0 HB3 D:CYS88 3.1 39.9 1.0 HE1 D:HIS74 3.1 35.1 1.0 H D:CYS91 3.1 37.5 1.0 CB D:CYS88 3.1 33.3 1.0 HB2 D:CYS72 3.1 31.1 1.0 HB2 D:CYS88 3.2 39.9 1.0 CG D:HIS74 3.2 30.1 1.0 CB D:CYS72 3.2 25.9 1.0 HB3 D:CYS72 3.4 31.1 1.0 HB D:ILE90 3.5 41.1 1.0 HB3 D:CYS91 3.5 33.9 1.0 CB D:CYS91 3.6 28.2 1.0 CB D:HIS74 3.6 29.1 1.0 N D:CYS91 3.8 31.2 1.0 H D:HIS74 4.0 38.0 1.0 HB3 D:HIS74 4.1 34.9 1.0 HA A:CYS72 4.1 32.0 1.0 HB3 D:ALA93 4.1 37.1 1.0 NE2 D:HIS74 4.1 29.1 1.0 CA D:CYS91 4.2 29.3 1.0 H D:ALA93 4.2 39.0 1.0 CD2 D:HIS74 4.2 29.3 1.0 H D:ILE90 4.3 44.7 1.0 HB2 D:CYS91 4.4 33.9 1.0 CB D:ILE90 4.5 34.2 1.0 H D:GLN92 4.5 36.6 1.0 HD12 D:ILE90 4.6 42.6 1.0 HB2 D:ALA93 4.6 37.1 1.0 CA D:CYS88 4.6 34.0 1.0 CA D:CYS72 4.6 27.4 1.0 N D:HIS74 4.6 31.6 1.0 CA D:HIS74 4.8 29.7 1.0 C D:ILE90 4.8 35.1 1.0 CB D:ALA93 4.8 30.9 1.0 H D:CYS72 4.8 31.3 1.0 C D:CYS91 4.8 30.0 1.0 HH2 D:TRP95 4.8 43.6 1.0 HD12 D:LEU70 4.9 40.9 1.0 N D:GLN92 4.9 30.5 1.0 HE2 D:HIS74 4.9 35.0 1.0 HD13 D:LEU70 4.9 40.9 1.0 HA D:CYS88 4.9 40.7 1.0 N D:ILE90 4.9 37.2 1.0 HG22 D:ILE90 5.0 40.3 1.0 CA D:ILE90 5.0 36.1 1.0

P.Wang, S.Benhenda, H.Wu, V.Lallemand-Breitenbach, T.Zhen, F.Jollivet, L.Peres, Y.Li, S.J.Chen, Z.Chen, H.De The, G.Meng. Ring Tetramerization Is Required For Nuclear Body Biogenesis and Pml Sumoylation. Nat Commun V. 9 1277 2018.
ISSN: ESSN 2041-1723
PubMed: 29599493
DOI: 10.1038/S41467-018-03498-0