Zinc in PDB 2h0d: Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex

The structure of Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex, PDB code: 2h0d was solved by R.M.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	104.26 / 2.50
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	120.514, 120.514, 27.209, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 24.4

The binding sites of Zinc atom in the Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex (pdb code 2h0d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex, PDB code: 2h0d:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:40.6 occ:1.00 SG A:CYS18 2.3 24.5 1.0 SG A:CYS21 2.3 23.8 1.0 SG A:CYS42 2.3 27.7 1.0 SG A:CYS39 2.4 25.9 1.0 CB A:CYS18 3.1 25.6 1.0 CB A:CYS39 3.2 24.1 1.0 CB A:CYS21 3.2 24.3 1.0 CB A:CYS42 3.4 23.7 1.0 N A:CYS21 3.6 23.8 1.0 N A:CYS39 3.9 22.1 1.0 CA A:CYS21 4.0 23.6 1.0 CA A:CYS39 4.2 23.0 1.0 NH1 B:ARG26 4.3 26.6 1.0 C A:LEU20 4.4 23.9 1.0 CA A:CYS18 4.5 25.4 1.0 O A:HOH204 4.5 23.9 1.0 CB A:LEU20 4.7 24.0 1.0 CA A:CYS42 4.8 23.0 1.0 C A:CYS18 4.8 25.5 1.0 N A:LEU20 4.8 24.0 1.0 CA A:LEU20 4.8 24.1 1.0 O A:CYS18 4.9 26.0 1.0 C A:CYS21 4.9 23.1 1.0 N A:CYS42 5.0 22.8 1.0

Zinc binding site 2 out of 4 in the Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:45.0 occ:1.00 ND1 A:HIS36 2.2 32.0 1.0 SG A:CYS34 2.3 32.8 1.0 SG A:CYS53 2.3 31.6 1.0 SG A:CYS56 2.4 31.5 1.0 CE1 A:HIS36 3.0 29.4 1.0 CB A:CYS34 3.1 33.4 1.0 CG A:HIS36 3.2 27.8 1.0 CB A:CYS53 3.2 31.1 1.0 CB A:CYS56 3.5 33.4 1.0 CB A:HIS36 3.6 25.7 1.0 N A:CYS56 3.8 32.2 1.0 NE2 A:HIS36 4.2 30.6 1.0 CA A:CYS56 4.2 32.8 1.0 CD2 A:HIS36 4.3 28.1 1.0 N A:HIS36 4.5 27.1 1.0 CA A:CYS34 4.5 32.6 1.0 CB A:ILE55 4.6 30.7 1.0 CA A:HIS36 4.7 25.5 1.0 CA A:CYS53 4.7 30.5 1.0 C A:CYS34 4.8 31.8 1.0 C A:ILE55 4.9 31.5 1.0 C A:CYS56 4.9 33.3 1.0 CD1 A:ILE31 5.0 29.4 1.0 N A:ILE55 5.0 30.3 1.0

Zinc binding site 3 out of 4 in the Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:63.5 occ:1.00 SG B:CYS51 2.3 59.6 1.0 SG B:CYS54 2.3 60.2 1.0 SG B:CYS72 2.4 53.0 1.0 SG B:CYS75 2.4 51.6 1.0 CB B:CYS51 3.1 59.9 1.0 CB B:CYS72 3.3 48.9 1.0 CB B:CYS75 3.4 49.0 1.0 CB B:CYS54 3.4 60.0 1.0 N B:CYS54 3.8 59.5 1.0 N B:CYS72 4.0 46.7 1.0 CA B:CYS54 4.2 59.8 1.0 CB B:ILE53 4.2 59.0 1.0 CA B:CYS72 4.3 48.1 1.0 CA B:CYS51 4.6 59.9 1.0 CG1 B:ILE53 4.7 59.1 1.0 CA B:CYS75 4.7 48.2 1.0 C B:ILE53 4.8 59.2 1.0 CE B:LYS59 4.8 58.2 1.0 N B:CYS75 4.8 48.9 1.0 C B:CYS51 4.9 59.4 1.0 CA B:ILE53 4.9 59.0 1.0 N B:ILE53 4.9 59.1 1.0 O B:CYS72 5.0 47.6 1.0 O B:CYS51 5.0 59.4 1.0

Zinc binding site 4 out of 4 in the Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:63.1 occ:1.00 ND1 B:HIS69 2.2 52.4 1.0 SG B:CYS67 2.3 52.1 1.0 SG B:CYS87 2.3 57.3 1.0 SG B:CYS90 2.4 61.0 1.0 CE1 B:HIS69 3.0 50.0 1.0 CB B:CYS67 3.3 52.0 1.0 CG B:HIS69 3.3 48.8 1.0 CB B:CYS90 3.4 61.6 1.0 CB B:CYS87 3.4 58.0 1.0 N B:CYS90 3.7 61.2 1.0 CB B:HIS69 3.8 47.4 1.0 CA B:CYS90 4.1 61.8 1.0 NE2 B:HIS69 4.2 48.4 1.0 CB B:THR89 4.3 60.4 1.0 CD2 B:HIS69 4.4 47.9 1.0 OG1 B:THR64 4.4 50.4 1.0 CA B:CYS67 4.6 51.1 1.0 C B:THR89 4.7 60.7 1.0 C B:CYS90 4.8 62.2 1.0 CA B:CYS87 4.8 58.0 1.0 C B:CYS67 4.8 50.6 1.0 O B:CYS67 4.9 50.6 1.0 CA B:THR89 4.9 60.4 1.0 N B:HIS69 4.9 47.6 1.0 CG2 B:THR89 4.9 60.7 1.0 N B:ARG91 5.0 62.7 1.0 N B:THR89 5.0 59.9 1.0

Z.Li, R.Cao, M.Wang, M.P.Myers, Y.Zhang, R.M.Xu. Structure of A Bmi-1-RING1B Polycomb Group Ubiquitin Ligase Complex. J.Biol.Chem. V. 281 20643 2006.
ISSN: ISSN 0021-9258
PubMed: 16714294
DOI: 10.1074/JBC.M602461200