Zinc in PDB 3rpg: BMI1/RING1B-UBCH5C Complex Structure

All present enzymatic activity of BMI1/RING1B-UBCH5C Complex Structure:
6.3.2.19;

The structure of BMI1/RING1B-UBCH5C Complex Structure, PDB code: 3rpg was solved by M.L.Bentley, K.C.Dong, A.G.Cochran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.82 / 2.65
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	107.890, 107.890, 77.572, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 24.3

The binding sites of Zinc atom in the BMI1/RING1B-UBCH5C Complex Structure (pdb code 3rpg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the BMI1/RING1B-UBCH5C Complex Structure, PDB code: 3rpg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the BMI1/RING1B-UBCH5C Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of BMI1/RING1B-UBCH5C Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1104 b:41.6 occ:1.00 SG B:CYS42 2.6 42.6 1.0 SG B:CYS21 2.6 33.9 1.0 SG B:CYS18 2.7 36.7 1.0 SG B:CYS39 2.7 38.1 1.0 CB B:CYS18 2.9 31.1 1.0 CB B:CYS39 3.0 34.0 1.0 CB B:CYS21 3.1 35.7 1.0 CB B:CYS42 3.4 39.2 1.0 N B:CYS21 3.7 37.3 1.0 N B:CYS39 3.8 33.8 1.0 CA B:CYS39 4.0 36.0 1.0 CA B:CYS21 4.0 32.2 1.0 CA B:CYS18 4.3 30.1 1.0 NH1 C:ARG26 4.6 34.7 1.0 O C:HOH126 4.6 33.0 1.0 CB B:LEU20 4.7 32.8 1.0 C B:LEU20 4.7 42.7 1.0 C B:CYS18 4.8 35.5 1.0 CA B:CYS42 4.8 37.2 1.0 O B:CYS18 4.8 40.4 1.0 C B:CYS21 4.9 42.5 1.0 C B:PHE38 5.0 33.8 1.0 N B:LEU20 5.0 38.2 1.0

Zinc binding site 2 out of 4 in the BMI1/RING1B-UBCH5C Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of BMI1/RING1B-UBCH5C Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1105 b:31.2 occ:1.00 ND1 B:HIS36 2.2 26.6 1.0 SG B:CYS53 2.5 31.2 1.0 SG B:CYS56 2.6 26.9 1.0 SG B:CYS34 2.6 29.2 1.0 CB B:CYS53 3.1 29.3 1.0 CB B:CYS34 3.1 27.5 1.0 CE1 B:HIS36 3.1 35.1 1.0 CG B:HIS36 3.2 29.6 1.0 CB B:CYS56 3.3 24.2 1.0 CB B:HIS36 3.5 26.5 1.0 N B:CYS56 3.7 32.6 1.0 CA B:CYS56 4.1 29.1 1.0 NE2 B:HIS36 4.3 32.9 1.0 CD2 B:HIS36 4.3 28.9 1.0 CG1 B:VAL58 4.4 36.9 1.0 CA B:CYS34 4.5 26.2 1.0 CA B:CYS53 4.6 30.1 1.0 CB B:ILE55 4.6 27.5 1.0 N B:HIS36 4.7 27.8 1.0 CA B:HIS36 4.7 26.2 1.0 C B:CYS56 4.7 27.2 1.0 O C:HOH144 4.8 32.7 1.0 C B:ILE55 4.8 33.3 1.0 N B:ASP57 4.8 31.6 1.0 C B:CYS34 4.9 25.6 1.0 CD1 B:ILE31 4.9 27.6 1.0 N B:ILE55 5.0 34.5 1.0

Zinc binding site 3 out of 4 in the BMI1/RING1B-UBCH5C Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of BMI1/RING1B-UBCH5C Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1115 b:34.3 occ:1.00 ND1 C:HIS69 2.1 27.5 1.0 SG C:CYS87 2.3 36.2 1.0 SG C:CYS67 2.5 31.4 1.0 SG C:CYS90 2.7 37.5 1.0 CE1 C:HIS69 3.0 28.6 1.0 CB C:CYS87 3.0 26.8 1.0 CB C:CYS67 3.0 26.1 1.0 CG C:HIS69 3.2 30.8 1.0 CB C:HIS69 3.6 27.8 1.0 OG1 C:THR64 3.9 29.1 1.0 CB C:CYS90 3.9 40.0 1.0 N C:CYS90 4.0 27.6 1.0 NE2 C:HIS69 4.2 28.1 1.0 CD2 C:HIS69 4.3 31.6 1.0 CA C:CYS67 4.3 32.1 1.0 CB C:THR89 4.4 35.0 1.0 CA C:CYS87 4.5 34.0 1.0 CA C:CYS90 4.5 36.7 1.0 O C:CYS67 4.5 31.9 1.0 C C:CYS67 4.6 35.2 1.0 CG2 C:THR64 4.7 24.0 1.0 CB C:THR64 4.7 27.8 1.0 N C:HIS69 4.7 30.5 1.0 CA C:HIS69 4.8 28.4 1.0 C C:THR89 4.8 34.8 1.0 CG2 C:THR89 4.8 24.9 1.0 CA C:THR89 4.9 31.3 1.0 N C:CYS67 4.9 31.1 1.0 N C:THR89 5.0 29.5 1.0 C C:CYS87 5.0 34.9 1.0

Zinc binding site 4 out of 4 in the BMI1/RING1B-UBCH5C Complex Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of BMI1/RING1B-UBCH5C Complex Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1116 b:29.9 occ:1.00 SG C:CYS75 2.5 29.8 1.0 SG C:CYS54 2.6 31.2 1.0 SG C:CYS51 2.6 30.2 1.0 SG C:CYS72 2.6 26.5 1.0 CB C:CYS72 2.9 23.8 1.0 CB C:CYS51 3.0 22.7 1.0 CB C:CYS54 3.2 26.9 1.0 CB C:CYS75 3.4 25.8 1.0 N C:CYS54 3.8 27.2 1.0 N C:CYS72 3.9 25.3 1.0 CA C:CYS72 4.0 26.6 1.0 CA C:CYS54 4.1 29.0 1.0 CA C:CYS51 4.5 30.7 1.0 O C:HOH125 4.6 37.7 1.0 CA C:CYS75 4.8 28.9 1.0 CB C:ILE53 4.8 28.4 1.0 C C:ILE53 4.9 31.9 1.0 C C:CYS54 4.9 28.8 1.0 C C:CYS51 5.0 31.5 1.0 C C:CYS72 5.0 31.5 1.0

M.L.Bentley, J.E.Corn, K.C.Dong, Q.Phung, T.K.Cheung, A.G.Cochran. Recognition of UBCH5C and the Nucleosome By the BMI1/RING1B Ubiquitin Ligase Complex. Embo J. V. 30 3285 2011.
ISSN: ISSN 0261-4189
PubMed: 21772249
DOI: 10.1038/EMBOJ.2011.243