Zinc in PDB 2ckl: RING1B-BMI1 E3 Catalytic Domain Structure

The structure of RING1B-BMI1 E3 Catalytic Domain Structure, PDB code: 2ckl was solved by G.Buchwald, P.Van Der Stoop, O.Weichenrieder, A.Perrakis, M.Van Lohuizen, T.K.Sixma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.0
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	120.046, 120.046, 27.096, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 21.3

The structure of RING1B-BMI1 E3 Catalytic Domain Structure also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Zinc atom in the RING1B-BMI1 E3 Catalytic Domain Structure (pdb code 2ckl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the RING1B-BMI1 E3 Catalytic Domain Structure, PDB code: 2ckl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the RING1B-BMI1 E3 Catalytic Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of RING1B-BMI1 E3 Catalytic Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1104 b:24.0 occ:1.00 SG A:CYS42 2.3 42.1 1.0 SG A:CYS18 2.4 39.1 1.0 SG A:CYS39 2.4 39.6 1.0 SG A:CYS21 2.4 40.0 1.0 CB A:CYS18 3.0 39.4 1.0 CB A:CYS39 3.1 37.5 1.0 CB A:CYS21 3.2 38.0 1.0 CB A:CYS42 3.4 36.8 1.0 N A:CYS21 3.7 38.1 1.0 N A:CYS39 3.8 38.1 1.0 CA A:CYS39 4.1 39.0 1.0 CA A:CYS21 4.1 38.6 1.0 NH1 B:ARG26 4.2 33.3 1.0 O A:HOH2010 4.4 19.1 1.0 CA A:CYS18 4.4 38.8 1.0 C A:LEU20 4.6 38.3 1.0 CB A:LEU20 4.7 36.4 1.0 CA A:CYS42 4.7 37.7 1.0 O A:CYS18 4.7 37.7 1.0 C A:CYS18 4.8 39.0 1.0 O A:HOH2005 4.9 44.3 1.0 N A:LEU20 4.9 36.4 1.0 N A:CYS42 5.0 38.1 1.0 CA A:LEU20 5.0 38.5 1.0 C A:CYS21 5.0 37.9 1.0

Zinc binding site 2 out of 4 in the RING1B-BMI1 E3 Catalytic Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of RING1B-BMI1 E3 Catalytic Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1105 b:27.6 occ:1.00 ND1 A:HIS36 2.0 38.2 1.0 SG A:CYS53 2.2 39.2 1.0 SG A:CYS34 2.3 38.9 1.0 SG A:CYS56 2.3 38.1 1.0 CE1 A:HIS36 2.9 38.6 1.0 CG A:HIS36 3.1 38.5 1.0 CB A:CYS53 3.1 40.6 1.0 CB A:CYS34 3.2 38.7 1.0 CB A:CYS56 3.5 37.3 1.0 CB A:HIS36 3.5 37.3 1.0 N A:CYS56 3.8 37.3 1.0 NE2 A:HIS36 4.0 38.7 1.0 CD2 A:HIS36 4.1 37.6 1.0 CA A:CYS56 4.2 37.9 1.0 CG1 A:VAL58 4.2 44.1 1.0 N A:HIS36 4.5 38.1 1.0 CA A:CYS53 4.5 40.5 1.0 CA A:CYS34 4.6 38.9 1.0 CA A:HIS36 4.6 37.9 1.0 CB A:ILE55 4.6 37.3 1.0 C A:CYS34 4.8 38.9 1.0 C A:ILE55 4.8 38.4 1.0 C A:CYS56 4.9 38.0 1.0 O A:CYS34 4.9 38.7 1.0 N A:ASP57 5.0 38.9 1.0

Zinc binding site 3 out of 4 in the RING1B-BMI1 E3 Catalytic Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of RING1B-BMI1 E3 Catalytic Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1115 b:46.7 occ:1.00 ND1 B:HIS69 2.0 35.3 1.0 SG B:CYS67 2.4 40.0 1.0 SG B:CYS90 2.4 44.8 1.0 SG B:CYS87 2.4 40.5 1.0 CE1 B:HIS69 2.8 35.6 1.0 CB B:CYS67 3.0 40.3 1.0 CG B:HIS69 3.2 36.7 1.0 CB B:CYS87 3.2 42.0 1.0 CB B:CYS90 3.3 46.5 1.0 CB B:HIS69 3.7 36.2 1.0 N B:CYS90 3.8 46.3 1.0 NE2 B:HIS69 4.0 34.9 1.0 CA B:CYS90 4.1 46.4 1.0 OG1 B:THR64 4.2 37.3 1.0 CD2 B:HIS69 4.2 35.2 1.0 CA B:CYS67 4.4 40.4 1.0 CB B:THR89 4.5 45.7 1.0 C B:THR89 4.6 46.1 1.0 CA B:CYS87 4.7 42.4 1.0 C B:CYS67 4.7 40.2 1.0 C B:CYS90 4.7 46.3 1.0 O B:CYS67 4.7 40.6 1.0 CB B:LYS92 4.8 46.8 1.0 CA B:THR89 4.9 45.5 1.0 N B:HIS69 4.9 37.8 1.0 N B:ARG91 4.9 46.5 1.0 CA B:HIS69 4.9 36.8 1.0 CG2 B:THR64 5.0 35.6 1.0 N B:THR89 5.0 45.2 1.0 CB B:THR64 5.0 35.5 1.0

Zinc binding site 4 out of 4 in the RING1B-BMI1 E3 Catalytic Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of RING1B-BMI1 E3 Catalytic Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1116 b:52.2 occ:1.00 SG B:CYS54 2.3 36.1 1.0 SG B:CYS72 2.3 36.0 1.0 SG B:CYS51 2.4 39.2 1.0 SG B:CYS75 2.5 29.0 1.0 CB B:CYS51 2.8 41.0 1.0 CB B:CYS72 3.3 33.4 1.0 CB B:CYS54 3.4 38.9 1.0 CB B:CYS75 3.4 30.2 1.0 N B:CYS54 3.7 40.0 1.0 N B:CYS72 3.9 32.3 1.0 CA B:CYS54 4.2 39.5 1.0 CA B:CYS72 4.2 33.1 1.0 CA B:CYS51 4.3 41.1 1.0 CB B:ILE53 4.5 39.9 1.0 C B:CYS51 4.8 41.1 1.0 CA B:CYS75 4.8 31.0 1.0 C B:ILE53 4.8 40.2 1.0 O B:CYS51 4.9 41.6 1.0 N B:ILE53 4.9 40.4 1.0 C B:CYS54 5.0 40.5 1.0 CA B:ILE53 5.0 40.1 1.0

G.Buchwald, P.Van Der Stoop, O.Weichenrieder, A.Perrakis, M.Van Lohuizen, T.K.Sixma. Structure and E3-Ligase Activity of the Ring-Ring Complex of Polycomb Proteins BMI1 and RING1B. Embo J. V. 25 2465 2006.
ISSN: ISSN 0261-4189
PubMed: 16710298
DOI: 10.1038/SJ.EMBOJ.7601144