Zinc in PDB 6wi8: Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure

The structure of Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure, PDB code: 6wi8 was solved by H.J.Cho, T.Cierpicki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.72 / 3.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.081, 154.742, 49.579, 90, 92.26, 90
R / Rfree (%)	20.7 / 25.9

The binding sites of Zinc atom in the Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure (pdb code 6wi8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure, PDB code: 6wi8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1201 b:36.9 occ:1.00 SG A:CYS1021 2.3 30.6 1.0 SG A:CYS1042 2.4 33.1 1.0 SG A:CYS1039 2.5 45.7 1.0 SG A:CYS1018 2.6 33.2 1.0 CB A:CYS1018 2.9 32.6 1.0 CB A:CYS1021 3.0 32.9 1.0 CB A:CYS1039 3.0 39.9 1.0 CB A:CYS1042 3.5 34.7 1.0 N A:CYS1021 3.6 29.5 1.0 NH2 A:ARG26 3.7 37.6 1.0 N A:CYS1039 3.9 27.4 1.0 CA A:CYS1021 3.9 29.7 1.0 CA A:CYS1039 4.0 29.0 1.0 CA A:CYS1018 4.4 33.1 1.0 C A:LEU1020 4.6 43.8 1.0 O A:CYS1018 4.7 30.8 1.0 CB A:LEU1020 4.7 27.2 1.0 C A:CYS1018 4.8 32.0 1.0 C A:CYS1021 4.8 38.3 1.0 CA A:CYS1042 4.9 28.7 1.0 O A:TYR1024 4.9 42.9 1.0 CZ A:ARG26 4.9 37.2 1.0 N A:LEU1020 5.0 32.3 1.0

Zinc binding site 2 out of 8 in the Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1202 b:56.7 occ:1.00 ND1 A:HIS1036 2.1 58.2 1.0 SG A:CYS1056 2.3 49.4 1.0 SG A:CYS1034 2.3 48.1 1.0 SG A:CYS1053 2.3 41.0 1.0 CG A:HIS1036 3.1 46.3 1.0 CE1 A:HIS1036 3.1 49.2 1.0 CB A:CYS1034 3.1 44.5 1.0 CB A:CYS1053 3.2 37.0 1.0 CB A:HIS1036 3.4 24.6 1.0 CB A:CYS1056 3.7 51.3 1.0 N A:CYS1056 3.8 50.2 1.0 NE2 A:HIS1036 4.2 47.4 1.0 CD2 A:HIS1036 4.2 46.4 1.0 CA A:CYS1056 4.3 50.4 1.0 CG2 A:VAL1058 4.4 39.2 1.0 CA A:CYS1034 4.5 38.9 1.0 CB A:ILE1055 4.6 40.1 1.0 CA A:HIS1036 4.6 37.4 1.0 CA A:CYS1053 4.7 32.0 1.0 N A:HIS1036 4.7 26.3 1.0 C A:CYS1034 4.7 33.1 1.0 O A:CYS1034 4.7 35.9 1.0 N A:ASP1057 4.9 49.5 1.0 C A:CYS1056 4.9 51.4 1.0 C A:ILE1055 4.9 54.8 1.0 CD1 A:ILE1031 5.0 24.0 1.0 N A:ILE1055 5.0 40.9 1.0

Zinc binding site 3 out of 8 in the Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1203 b:49.1 occ:1.00 ND1 A:HIS69 2.1 63.5 1.0 SG A:CYS87 2.3 47.1 1.0 SG A:CYS90 2.4 85.3 1.0 SG A:CYS67 2.4 43.2 1.0 CE1 A:HIS69 2.9 59.6 1.0 CB A:CYS67 3.1 49.0 1.0 CG A:HIS69 3.2 55.1 1.0 CB A:CYS87 3.3 51.6 1.0 CB A:CYS90 3.3 84.1 1.0 CB A:HIS69 3.6 46.4 1.0 N A:CYS90 3.7 74.1 1.0 NE2 A:HIS69 4.1 60.1 1.0 CA A:CYS90 4.1 81.0 1.0 CD2 A:HIS69 4.2 57.7 1.0 OG1 A:THR64 4.4 54.3 1.0 CA A:CYS67 4.5 53.2 1.0 CB A:THR89 4.6 55.8 1.0 CA A:CYS87 4.7 60.4 1.0 C A:CYS67 4.8 52.7 1.0 C A:THR89 4.8 72.5 1.0 O A:CYS67 4.8 54.0 1.0 C A:CYS90 4.9 83.5 1.0 CA A:HIS69 4.9 43.6 1.0 N A:HIS69 5.0 41.1 1.0

Zinc binding site 4 out of 8 in the Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1204 b:77.1 occ:1.00 SG A:CYS54 2.4 88.6 1.0 SG A:CYS75 2.4 74.1 1.0 SG A:CYS72 2.4 71.8 1.0 SG A:CYS51 2.5 69.7 1.0 CB A:CYS72 2.9 65.1 1.0 CB A:CYS51 3.0 69.5 1.0 CB A:CYS75 3.3 66.1 1.0 CB A:CYS54 3.4 84.6 1.0 N A:CYS54 3.8 73.3 1.0 N A:CYS72 3.9 53.4 1.0 CA A:CYS72 4.0 58.9 1.0 CA A:CYS54 4.2 79.0 1.0 CA A:CYS51 4.5 68.1 1.0 CB A:ILE53 4.6 65.6 1.0 CA A:CYS75 4.7 69.7 1.0 C A:ILE53 4.8 77.7 1.0 CG2 A:ILE53 4.9 73.0 1.0 C A:CYS51 5.0 70.2 1.0 N A:CYS75 5.0 68.6 1.0

Zinc binding site 5 out of 8 in the Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:42.0 occ:1.00 CB B:CYS1021 2.3 60.0 1.0 SG B:CYS1042 2.4 39.3 1.0 SG B:CYS1039 2.5 43.1 1.0 SG B:CYS1018 2.8 37.3 1.0 CB B:CYS1039 2.8 36.6 1.0 CB B:CYS1018 3.0 37.8 1.0 CA B:CYS1021 3.5 57.7 1.0 SG B:CYS1021 3.5 71.3 1.0 CB B:CYS1042 3.5 37.1 1.0 N B:CYS1021 3.6 59.0 1.0 N B:CYS1039 3.8 33.7 1.0 CA B:CYS1039 3.9 26.7 1.0 NH1 B:ARG26 4.4 29.2 1.0 CA B:CYS1018 4.5 40.5 1.0 C B:LEU1020 4.7 55.6 1.0 C B:CYS1021 4.7 54.7 1.0 CA B:CYS1042 4.9 37.0 1.0 O B:TYR1024 4.9 51.2 1.0 C B:CYS1039 4.9 36.0 1.0 C B:CYS1018 5.0 43.5 1.0

Zinc binding site 6 out of 8 in the Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1202 b:59.0 occ:1.00 ND1 B:HIS1036 2.2 62.5 1.0 SG B:CYS1034 2.4 52.5 1.0 SG B:CYS1053 2.4 63.0 1.0 SG B:CYS1056 2.4 65.4 1.0 CG B:HIS1036 2.8 58.1 1.0 CE1 B:HIS1036 3.0 62.2 1.0 CB B:HIS1036 3.2 48.7 1.0 CB B:CYS1034 3.3 56.5 1.0 CB B:CYS1053 3.3 63.8 1.0 CB B:CYS1056 3.7 75.2 1.0 CD2 B:HIS1036 3.7 58.0 1.0 NE2 B:HIS1036 3.8 59.6 1.0 N B:CYS1056 3.9 71.8 1.0 CA B:CYS1056 4.4 73.9 1.0 CA B:HIS1036 4.5 43.3 1.0 N B:HIS1036 4.6 42.5 1.0 CG2 B:VAL1058 4.6 57.1 1.0 CB B:ILE1055 4.6 76.1 1.0 CA B:CYS1034 4.6 58.2 1.0 CA B:CYS1053 4.8 58.6 1.0 O B:CYS1034 4.8 55.9 1.0 C B:CYS1034 4.8 54.9 1.0 C B:ILE1055 5.0 80.7 1.0

Zinc binding site 7 out of 8 in the Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1203 b:75.2 occ:1.00 ND1 B:HIS69 2.1 110.9 1.0 SG B:CYS87 2.4 95.3 1.0 SG B:CYS90 2.4 111.5 1.0 SG B:CYS67 2.4 105.5 1.0 CE1 B:HIS69 2.7 102.9 1.0 CB B:CYS87 3.0 103.0 1.0 CB B:CYS67 3.0 98.0 1.0 CG B:HIS69 3.2 94.0 1.0 CB B:CYS90 3.5 106.6 1.0 N B:CYS90 3.6 102.8 1.0 NE2 B:HIS69 3.8 98.5 1.0 CB B:HIS69 3.9 75.9 1.0 CA B:CYS90 4.1 104.7 1.0 CD2 B:HIS69 4.1 97.7 1.0 CB B:THR89 4.2 104.0 1.0 OG1 B:THR64 4.3 72.7 1.0 CA B:CYS87 4.4 108.3 1.0 CA B:CYS67 4.5 86.5 1.0 C B:THR89 4.6 109.3 1.0 N B:THR89 4.7 103.8 1.0 C B:CYS87 4.8 101.9 1.0 CA B:THR89 4.8 106.5 1.0 O B:CYS87 4.9 105.6 1.0 C B:CYS67 4.9 73.9 1.0 C B:CYS90 4.9 112.2 1.0 OG1 B:THR89 4.9 105.6 1.0

Zinc binding site 8 out of 8 in the Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Inhibitor Compound-Induced Confrontational Change in RING1B-BMI1 Domain Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1204 b:91.5 occ:1.00 SG B:CYS51 2.5 130.6 1.0 SG B:CYS54 2.6 156.2 1.0 SG B:CYS75 2.7 113.6 1.0 CB B:CYS54 2.7 166.0 1.0 CB B:CYS51 2.9 117.1 1.0 SG B:CYS72 2.9 120.4 1.0 CB B:CYS72 3.1 113.2 1.0 CB B:CYS75 3.4 109.2 1.0 N B:CYS54 3.4 167.3 1.0 CA B:CYS54 3.7 169.6 1.0 N B:CYS72 4.2 88.7 1.0 CA B:CYS72 4.3 100.5 1.0 CA B:CYS51 4.4 112.8 1.0 C B:ILE53 4.4 176.8 1.0 CB B:ILE53 4.5 163.1 1.0 C B:CYS54 4.6 165.1 1.0 O B:CYS51 4.7 131.6 1.0 C B:CYS51 4.7 121.5 1.0 CA B:CYS75 4.8 112.1 1.0 N B:LEU55 4.8 108.2 1.0 CA B:ILE53 4.9 166.0 1.0 N B:ILE53 4.9 150.9 1.0

H.J.Cho, T.Cierpicki. RING1B-BMI1 Fusion in Open Conformation To Be Published.