Zinc in PDB 6imq: Crystal Structure of Pml B1-Box Multimers

The structure of Crystal Structure of Pml B1-Box Multimers, PDB code: 6imq was solved by Y.Li, X.Ma, Z.Chen, H.Wu, P.Wang, W.Wu, N.Cheng, L.Zeng, H.Zhang, X.Cai, S.J.Chen, Z.Chen, G.Meng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.23 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.670, 50.460, 51.430, 90.00, 101.35, 90.00
R / Rfree (%)	18.6 / 22.7

The structure of Crystal Structure of Pml B1-Box Multimers also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Pml B1-Box Multimers (pdb code 6imq). 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 B1-Box Multimers, PDB code: 6imq:
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 B1-Box Multimers


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 B1-Box Multimers within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:35.7 occ:1.00 NE2 A:HIS155 2.0 27.1 1.0 ND1 A:HIS161 2.1 38.0 1.0 SG A:CYS140 2.3 26.6 1.0 SG A:CYS143 2.3 33.1 1.0 CE1 A:HIS155 2.9 22.6 1.0 HB2 A:HIS161 2.9 45.0 1.0 CD2 A:HIS155 3.0 19.5 1.0 H A:CYS143 3.0 50.0 1.0 HE1 A:HIS155 3.1 27.2 1.0 CG A:HIS161 3.1 36.3 1.0 CE1 A:HIS161 3.1 34.8 1.0 HB2 A:CYS143 3.2 41.4 1.0 HD2 A:HIS155 3.2 23.4 1.0 HE1 A:HIS161 3.3 41.8 1.0 CB A:CYS140 3.3 26.0 1.0 CB A:HIS161 3.4 37.5 1.0 CB A:CYS143 3.4 34.5 1.0 HB2 A:CYS140 3.4 31.2 1.0 HB3 A:HIS161 3.4 45.0 1.0 HB3 A:CYS140 3.5 31.2 1.0 HD13 A:LEU159 3.5 33.5 1.0 N A:CYS143 3.7 41.6 1.0 HB2 A:GLU142 4.0 66.4 1.0 ND1 A:HIS155 4.0 22.4 1.0 CG A:HIS155 4.1 21.0 1.0 CA A:CYS143 4.1 37.3 1.0 HB3 A:CYS143 4.1 41.4 1.0 NE2 A:HIS161 4.2 34.2 1.0 CD2 A:HIS161 4.2 37.0 1.0 CD1 A:LEU159 4.4 27.9 1.0 H A:GLU142 4.4 48.9 1.0 HA A:CYS143 4.5 44.8 1.0 HD12 A:LEU159 4.6 33.5 1.0 HB2 A:LEU159 4.6 33.0 1.0 HB3 A:LEU159 4.7 33.0 1.0 C A:GLU142 4.7 44.8 1.0 CA A:CYS140 4.7 24.6 1.0 CB A:GLU142 4.8 55.3 1.0 HD1 A:HIS155 4.8 27.0 1.0 HD11 A:LEU159 4.8 33.5 1.0 CA A:HIS161 4.8 41.3 1.0 HB3 A:GLU142 4.9 66.4 1.0 HA A:CYS140 5.0 29.5 1.0 HE2 A:HIS161 5.0 41.0 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Pml B1-Box Multimers


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 B1-Box Multimers within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:38.5 occ:1.00 SG A:CYS129 2.3 21.3 1.0 SG A:CYS148 2.3 22.7 1.0 SG A:CYS151 2.4 30.1 1.0 SG A:CYS132 2.5 32.8 1.0 HB2 A:CYS151 2.9 35.2 1.0 H A:CYS148 3.1 27.5 1.0 CB A:CYS129 3.1 24.5 1.0 HB3 A:CYS129 3.1 29.4 1.0 HB2 A:CYS129 3.1 29.4 1.0 CB A:CYS151 3.3 29.3 1.0 H A:CYS132 3.3 42.5 1.0 HB3 A:CYS132 3.3 41.0 1.0 HB3 A:CYS148 3.5 32.0 1.0 CB A:CYS132 3.5 34.2 1.0 HB3 A:ARG131 3.5 34.3 1.0 CB A:CYS148 3.5 26.7 1.0 H A:CYS151 3.7 30.9 1.0 HB3 A:CYS151 3.8 35.2 1.0 N A:CYS148 3.9 22.9 1.0 HB3 A:GLU134 3.9 55.8 1.0 N A:CYS132 3.9 35.4 1.0 CA A:CYS132 4.3 35.5 1.0 CA A:CYS148 4.3 25.7 1.0 H A:GLU134 4.3 42.8 1.0 HB2 A:CYS132 4.3 41.0 1.0 HB2 A:CYS148 4.3 32.0 1.0 N A:CYS151 4.3 25.7 1.0 H A:ARG131 4.4 31.0 1.0 CA A:CYS151 4.4 24.6 1.0 HA A:LEU147 4.4 23.6 1.0 CB A:ARG131 4.5 28.5 1.0 H A:LYS133 4.6 39.5 1.0 CA A:CYS129 4.6 27.7 1.0 HH11 A:ARG131 4.6 52.6 1.0 HA A:CYS151 4.8 29.5 1.0 HG2 A:ARG131 4.8 39.6 1.0 CB A:GLU134 4.8 46.5 1.0 HD3 A:ARG131 4.9 44.5 1.0 HA A:CYS129 4.9 33.3 1.0 HD22 A:LEU147 4.9 26.7 1.0 C A:CYS132 4.9 35.9 1.0 C A:ARG131 4.9 34.5 1.0 N A:LYS133 4.9 32.9 1.0 C A:CYS148 5.0 26.4 1.0 C A:LEU147 5.0 21.8 1.0 O A:CYS148 5.0 21.4 1.0 N A:ARG131 5.0 25.8 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Pml B1-Box Multimers


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 B1-Box Multimers within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:37.7 occ:1.00 SG B:CYS148 2.3 27.2 1.0 SG B:CYS151 2.3 30.3 1.0 SG B:CYS129 2.4 21.7 1.0 SG B:CYS132 2.4 36.6 1.0 HB2 B:CYS151 2.7 32.2 1.0 CB B:CYS151 3.1 26.9 1.0 H B:CYS148 3.1 28.0 1.0 HB3 B:CYS129 3.1 30.9 1.0 CB B:CYS129 3.2 25.8 1.0 HB2 B:CYS129 3.2 30.9 1.0 H B:CYS132 3.2 47.1 1.0 HB3 B:CYS148 3.2 32.9 1.0 CB B:CYS148 3.4 27.4 1.0 HB3 B:CYS132 3.4 45.3 1.0 H B:CYS151 3.4 28.6 1.0 CB B:CYS132 3.5 37.8 1.0 HB3 B:ARG131 3.5 34.4 1.0 HB3 B:CYS151 3.7 32.2 1.0 N B:CYS132 3.9 39.2 1.0 N B:CYS148 3.9 23.3 1.0 HB2 B:GLU134 3.9 60.4 1.0 N B:CYS151 4.1 23.8 1.0 HB2 B:CYS148 4.1 32.9 1.0 HG3 B:LYS150 4.1 63.0 1.0 CA B:CYS148 4.2 23.9 1.0 CA B:CYS151 4.2 23.1 1.0 CA B:CYS132 4.3 41.0 1.0 HB2 B:CYS132 4.3 45.3 1.0 H B:ARG131 4.4 33.3 1.0 H B:GLU134 4.4 39.8 1.0 CB B:ARG131 4.5 28.6 1.0 HG2 B:ARG131 4.5 39.2 1.0 HA B:CYS151 4.6 27.8 1.0 CA B:CYS129 4.6 25.4 1.0 HA B:LEU147 4.7 26.7 1.0 HG2 B:LYS150 4.8 63.0 1.0 C B:CYS148 4.8 24.1 1.0 HZ3 B:LYS150 4.8 85.1 1.0 CB B:GLU134 4.9 50.3 1.0 C B:CYS132 4.9 43.1 1.0 O B:CYS148 4.9 19.0 1.0 C B:ARG131 4.9 38.4 1.0 HD3 B:ARG131 4.9 44.2 1.0 CG B:LYS150 4.9 52.5 1.0 HH11 B:ARG131 4.9 48.1 1.0 HA B:CYS129 5.0 30.5 1.0 HA B:CYS148 5.0 28.7 1.0 HE2 B:LYS150 5.0 79.7 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Pml B1-Box Multimers


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 B1-Box Multimers within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:34.1 occ:1.00 NE2 B:HIS155 2.0 35.0 1.0 ND1 B:HIS161 2.1 37.9 1.0 SG B:CYS143 2.2 36.3 1.0 SG B:CYS140 2.3 27.1 1.0 CE1 B:HIS155 3.0 32.8 1.0 CD2 B:HIS155 3.0 29.8 1.0 H B:CYS143 3.0 38.3 1.0 HB2 B:HIS161 3.0 36.6 1.0 CG B:HIS161 3.1 32.5 1.0 HB2 B:CYS143 3.1 37.3 1.0 CE1 B:HIS161 3.1 32.6 1.0 HE1 B:HIS155 3.1 39.4 1.0 HD2 B:HIS155 3.2 35.7 1.0 CB B:CYS143 3.2 31.1 1.0 HE1 B:HIS161 3.3 39.1 1.0 HB3 B:HIS161 3.3 36.6 1.0 CB B:HIS161 3.3 30.5 1.0 CB B:CYS140 3.4 27.3 1.0 HB2 B:CYS140 3.5 32.7 1.0 HB3 B:CYS140 3.5 32.7 1.0 HD13 B:LEU159 3.6 34.5 1.0 N B:CYS143 3.6 31.9 1.0 CA B:CYS143 4.0 32.9 1.0 HB3 B:CYS143 4.0 37.3 1.0 ND1 B:HIS155 4.1 31.7 1.0 CG B:HIS155 4.1 29.5 1.0 HB2 B:GLU142 4.1 50.4 1.0 NE2 B:HIS161 4.2 32.7 1.0 CD2 B:HIS161 4.2 33.6 1.0 HA B:CYS143 4.4 39.4 1.0 H B:GLU142 4.4 38.7 1.0 CD1 B:LEU159 4.4 28.7 1.0 HD12 B:LEU159 4.5 34.5 1.0 HB2 B:LEU159 4.6 31.2 1.0 C B:GLU142 4.7 30.9 1.0 HB3 B:LEU159 4.7 31.2 1.0 CA B:CYS140 4.8 24.7 1.0 HD1 B:HIS155 4.8 38.1 1.0 CA B:HIS161 4.9 33.7 1.0 CB B:GLU142 4.9 42.0 1.0 HA B:CYS140 5.0 29.6 1.0 HE2 B:HIS161 5.0 39.3 1.0 HD11 B:LEU159 5.0 34.5 1.0 HB3 B:GLU142 5.0 50.4 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Pml B1-Box Multimers


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 B1-Box Multimers within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:38.4 occ:1.00 SG C:CYS148 2.2 31.3 1.0 SG C:CYS151 2.3 31.6 1.0 SG C:CYS132 2.4 34.4 1.0 SG C:CYS129 2.4 20.8 1.0 HB2 C:CYS151 2.8 34.9 1.0 H C:CYS148 3.1 22.6 1.0 CB C:CYS151 3.1 29.1 1.0 HB3 C:CYS129 3.1 24.7 1.0 CB C:CYS129 3.2 20.5 1.0 HB2 C:CYS129 3.2 24.7 1.0 HB3 C:CYS132 3.2 43.5 1.0 H C:CYS132 3.3 34.0 1.0 HB3 C:CYS148 3.4 24.7 1.0 CB C:CYS132 3.4 36.2 1.0 CB C:CYS148 3.4 20.6 1.0 H C:CYS151 3.6 31.1 1.0 HB3 C:CYS151 3.7 34.9 1.0 HB3 C:ARG131 3.7 35.6 1.0 N C:CYS148 3.9 18.8 1.0 HB3 C:GLU134 3.9 61.2 1.0 N C:CYS132 3.9 28.3 1.0 HB2 C:CYS132 4.2 43.5 1.0 HB2 C:CYS148 4.2 24.7 1.0 CA C:CYS148 4.2 21.8 1.0 CA C:CYS132 4.2 33.2 1.0 H C:GLU134 4.2 41.1 1.0 N C:CYS151 4.3 25.9 1.0 CA C:CYS151 4.3 24.4 1.0 H C:ARG131 4.5 24.4 1.0 HA C:LEU147 4.5 19.4 1.0 O C:HOH313 4.6 43.0 1.0 HE C:ARG131 4.6 48.1 1.0 H C:LYS133 4.6 43.2 1.0 CB C:ARG131 4.7 29.6 1.0 CA C:CYS129 4.7 18.6 1.0 HA C:CYS151 4.7 29.2 1.0 CB C:GLU134 4.8 51.0 1.0 C C:CYS132 4.9 35.3 1.0 C C:CYS148 4.9 24.2 1.0 C C:ARG131 4.9 28.6 1.0 N C:LYS133 5.0 36.0 1.0 HG2 C:ARG131 5.0 42.3 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Pml B1-Box Multimers


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 B1-Box Multimers within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:37.3 occ:1.00 NE2 C:HIS155 2.2 34.0 1.0 ND1 C:HIS161 2.2 35.8 1.0 SG C:CYS143 2.2 35.2 1.0 SG C:CYS140 2.2 33.0 1.0 H C:CYS143 2.8 45.2 1.0 HB2 C:HIS161 2.9 47.1 1.0 HB2 C:CYS143 3.0 35.2 1.0 CG C:HIS161 3.1 38.5 1.0 CE1 C:HIS155 3.1 30.9 1.0 CD2 C:HIS155 3.2 29.3 1.0 CB C:CYS143 3.2 29.3 1.0 CE1 C:HIS161 3.2 35.1 1.0 HE1 C:HIS155 3.3 37.1 1.0 CB C:HIS161 3.3 39.2 1.0 HD2 C:HIS155 3.3 35.2 1.0 HB3 C:HIS161 3.4 47.1 1.0 HE1 C:HIS161 3.4 42.1 1.0 CB C:CYS140 3.4 23.6 1.0 HB3 C:CYS140 3.5 28.4 1.0 N C:CYS143 3.5 37.6 1.0 HB2 C:CYS140 3.6 28.4 1.0 HB3 C:GLU142 3.8 42.3 1.0 CA C:CYS143 4.0 31.8 1.0 HB3 C:CYS143 4.0 35.2 1.0 HG3 C:GLU142 4.1 52.3 1.0 ND1 C:HIS155 4.2 31.0 1.0 CD2 C:HIS161 4.3 38.0 1.0 CG C:HIS155 4.3 27.7 1.0 NE2 C:HIS161 4.3 35.5 1.0 HG C:LEU159 4.3 38.2 1.0 HA C:CYS143 4.4 38.2 1.0 H C:GLU142 4.5 37.1 1.0 CB C:GLU142 4.5 35.3 1.0 HD23 C:LEU159 4.6 40.2 1.0 C C:GLU142 4.6 40.4 1.0 HB2 C:LEU159 4.7 36.3 1.0 CG C:GLU142 4.7 43.6 1.0 HG2 C:GLU142 4.8 52.3 1.0 CA C:CYS140 4.8 21.6 1.0 CA C:HIS161 4.8 47.2 1.0 HB3 C:LEU159 4.9 36.3 1.0 N C:GLU142 4.9 30.9 1.0 CA C:GLU142 4.9 34.7 1.0 HD12 C:LEU147 4.9 34.2 1.0 HD1 C:HIS155 5.0 37.2 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Pml B1-Box Multimers


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 B1-Box Multimers within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:51.5 occ:1.00 SG D:CYS148 2.3 43.8 1.0 SG D:CYS151 2.4 46.5 1.0 SG D:CYS129 2.4 32.9 1.0 HB2 D:CYS132 2.4 86.5 1.0 HG D:CYS132 2.9 95.2 1.0 HB3 D:CYS148 3.0 49.2 1.0 HB2 D:CYS151 3.0 49.6 1.0 H D:CYS148 3.1 38.0 1.0 SG D:CYS132 3.1 79.3 1.0 CB D:CYS132 3.1 72.0 1.0 HB3 D:CYS129 3.2 44.5 1.0 CB D:CYS148 3.2 41.0 1.0 H D:CYS132 3.2 63.9 1.0 CB D:CYS129 3.3 37.1 1.0 CB D:CYS151 3.3 41.3 1.0 HB2 D:CYS129 3.4 44.5 1.0 H D:CYS151 3.6 39.8 1.0 N D:CYS132 3.8 53.3 1.0 HB3 D:CYS132 3.8 86.5 1.0 HB3 D:ARG131 3.8 43.8 1.0 N D:CYS148 3.8 31.7 1.0 HB3 D:CYS151 3.9 49.6 1.0 HB2 D:CYS148 4.0 49.2 1.0 CA D:CYS148 4.1 35.2 1.0 CA D:CYS132 4.1 63.5 1.0 HB2 D:GLU134 4.3 87.4 1.0 N D:CYS151 4.3 33.1 1.0 H D:ARG131 4.4 44.9 1.0 CA D:CYS151 4.4 33.9 1.0 H D:GLU134 4.5 79.1 1.0 HB3 D:GLU134 4.6 87.4 1.0 HG2 D:ARG131 4.6 46.9 1.0 HA D:LEU147 4.7 28.4 1.0 CB D:ARG131 4.7 36.5 1.0 C D:ARG131 4.7 49.3 1.0 HA D:CYS132 4.7 76.2 1.0 CA D:CYS129 4.8 35.2 1.0 C D:CYS148 4.8 35.8 1.0 HA D:CYS148 4.9 42.3 1.0 CB D:GLU134 4.9 72.8 1.0 HA D:CYS151 4.9 40.7 1.0 HD22 D:LEU147 5.0 31.5 1.0 HB3 D:LYS150 5.0 75.2 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Pml B1-Box Multimers


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 B1-Box Multimers within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn202 b:37.8 occ:1.00 NE2 D:HIS155 1.9 31.9 1.0 ND1 D:HIS161 2.1 44.8 1.0 SG D:CYS143 2.1 39.9 1.0 SG D:CYS140 2.3 29.8 1.0 H D:CYS143 2.8 47.1 1.0 CE1 D:HIS155 2.9 25.9 1.0 CD2 D:HIS155 3.0 25.1 1.0 CG D:HIS161 3.0 44.8 1.0 HB2 D:CYS143 3.0 42.3 1.0 HB2 D:HIS161 3.1 56.7 1.0 HE1 D:HIS155 3.1 31.1 1.0 CE1 D:HIS161 3.1 41.5 1.0 CB D:CYS143 3.2 35.2 1.0 HD2 D:HIS155 3.2 30.2 1.0 HB3 D:HIS161 3.2 56.7 1.0 HE1 D:HIS161 3.3 49.8 1.0 CB D:HIS161 3.3 47.2 1.0 CB D:CYS140 3.4 29.0 1.0 HB2 D:CYS140 3.4 34.9 1.0 N D:CYS143 3.5 39.2 1.0 HB3 D:CYS140 3.5 34.9 1.0 HD13 D:LEU159 3.6 28.5 1.0 CA D:CYS143 3.9 37.6 1.0 HB2 D:GLU142 3.9 50.5 1.0 HB3 D:CYS143 4.0 42.3 1.0 ND1 D:HIS155 4.0 25.8 1.0 CG D:HIS155 4.1 24.1 1.0 HD12 D:LEU159 4.2 28.5 1.0 NE2 D:HIS161 4.2 44.1 1.0 CD2 D:HIS161 4.2 46.3 1.0 H D:GLU142 4.3 43.4 1.0 HA D:CYS143 4.3 45.1 1.0 CD1 D:LEU159 4.3 23.8 1.0 C D:GLU142 4.6 41.0 1.0 CB D:GLU142 4.7 42.1 1.0 HB2 D:LEU159 4.7 37.2 1.0 HB3 D:GLU142 4.7 50.5 1.0 CA D:CYS140 4.8 26.1 1.0 HB3 D:LEU159 4.8 37.2 1.0 HD1 D:HIS155 4.8 30.9 1.0 CA D:HIS161 4.8 55.3 1.0 HD11 D:LEU159 4.9 28.5 1.0 HE2 D:HIS161 5.0 52.9 1.0 N D:GLU142 5.0 36.2 1.0 CA D:GLU142 5.0 39.2 1.0 HA D:CYS140 5.0 31.4 1.0 HD11 D:LEU147 5.0 32.6 1.0

Y.Li, X.Ma, Z.Chen, H.Wu, P.Wang, W.Wu, N.Cheng, L.Zeng, H.Zhang, X.Cai, S.J.Chen, Z.Chen, G.Meng. B1 Oligomerization Regulates Pml Nuclear Body Biogenesis and Leukemogenesis. Nat Commun V. 10 3789 2019.
ISSN: ESSN 2041-1723
PubMed: 31439836
DOI: 10.1038/S41467-019-11746-0