Zinc in PDB 9b4p: Tetramer Formation of the BCL11A ZF0 Domain

The structure of Tetramer Formation of the BCL11A ZF0 Domain, PDB code: 9b4p was solved by M.Yin, K.Tenglin, S.H.Orkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.31 / 2.56
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.404, 58.311, 70.087, 90, 134.12, 90
R / Rfree (%)	27.8 / 29.4

The binding sites of Zinc atom in the Tetramer Formation of the BCL11A ZF0 Domain (pdb code 9b4p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Tetramer Formation of the BCL11A ZF0 Domain, PDB code: 9b4p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in the Tetramer Formation of the BCL11A ZF0 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tetramer Formation of the BCL11A ZF0 Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:29.5 occ:1.00 NE2 B:HIS66 2.1 52.7 1.0 SG B:CYS51 2.3 56.2 1.0 SG B:CYS48 2.4 43.8 1.0 SG B:CYS71 2.8 49.9 1.0 CE1 B:HIS66 2.9 65.6 1.0 CD2 B:HIS66 3.2 65.7 1.0 CB B:CYS51 3.5 46.5 1.0 CB B:CYS48 3.9 64.2 1.0 N B:CYS51 3.9 77.0 1.0 CB B:GLN50 4.0 82.3 1.0 ND1 B:HIS66 4.1 74.9 1.0 CB B:CYS71 4.1 59.6 1.0 CG B:HIS66 4.2 72.4 1.0 CA B:CYS51 4.3 64.0 1.0 C B:GLN50 4.5 59.9 1.0 CA B:GLN50 4.7 74.4 1.0 CD B:LYS67 4.8 77.7 1.0 N B:GLN50 4.8 74.3 1.0 CB B:MET53 4.9 67.4 1.0 CG B:MET53 5.0 71.8 1.0 C B:CYS51 5.0 58.3 1.0 N B:GLN52 5.0 60.2 1.0

Zinc binding site 2 out of 10 in the Tetramer Formation of the BCL11A ZF0 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tetramer Formation of the BCL11A ZF0 Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:36.7 occ:1.00 SG C:CYS51 2.3 46.8 1.0 NE2 C:HIS66 2.5 69.0 1.0 SG C:CYS48 2.5 55.8 1.0 CD2 C:HIS66 2.8 62.0 1.0 CB C:CYS48 3.3 66.1 1.0 CB C:CYS71 3.5 75.3 1.0 CB C:CYS51 3.5 65.6 1.0 CE1 C:HIS66 3.7 83.8 1.0 SG C:CYS71 3.8 63.0 1.0 NZ C:LYS67 3.9 84.7 1.0 CG C:HIS66 4.2 68.4 1.0 N C:CYS51 4.2 82.7 1.0 CA C:CYS51 4.4 80.0 1.0 ND1 C:HIS66 4.6 79.0 1.0 CA C:CYS48 4.8 68.3 1.0 CA C:CYS71 4.9 71.7 1.0 CB C:MET53 4.9 75.3 1.0 C C:CYS51 5.0 67.8 1.0

Zinc binding site 3 out of 10 in the Tetramer Formation of the BCL11A ZF0 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tetramer Formation of the BCL11A ZF0 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:21.6 occ:1.00 NE2 A:HIS66 2.2 79.4 1.0 SG A:CYS48 2.4 52.3 1.0 SG A:CYS71 2.5 66.4 1.0 SG A:CYS51 2.5 56.0 1.0 CB A:CYS71 2.6 50.8 1.0 CE1 A:HIS66 2.8 75.8 1.0 CD2 A:HIS66 3.4 74.0 1.0 CB A:CYS48 3.6 53.3 1.0 CB A:CYS51 3.6 62.6 1.0 ND1 A:HIS66 4.0 78.0 1.0 CA A:CYS71 4.1 81.1 1.0 N A:CYS51 4.1 76.9 1.0 O A:HOH201 4.3 30.0 1.0 CG A:HIS66 4.3 72.5 1.0 CB A:MET53 4.4 62.8 1.0 CA A:CYS51 4.4 68.9 1.0 O A:CYS71 4.6 70.9 1.0 C A:CYS71 4.7 83.9 1.0 C A:GLN50 4.7 71.1 1.0 CB A:GLN50 4.8 56.1 1.0 N A:GLN50 4.8 65.4 1.0 CG A:MET53 4.8 69.5 1.0 N A:CYS71 4.9 91.2 1.0 CA A:CYS48 5.0 63.9 1.0 CA A:GLN50 5.0 60.5 1.0

Zinc binding site 4 out of 10 in the Tetramer Formation of the BCL11A ZF0 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tetramer Formation of the BCL11A ZF0 Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn101 b:62.9 occ:1.00 NE2 D:HIS66 2.1 69.4 1.0 SG D:CYS48 2.4 71.1 1.0 SG D:CYS51 2.5 72.3 1.0 CE1 D:HIS66 2.9 79.9 1.0 CB D:CYS71 3.0 72.6 1.0 CB D:CYS51 3.1 66.0 1.0 CD2 D:HIS66 3.2 71.1 1.0 O D:CYS71 3.3 76.8 1.0 CB D:CYS48 3.3 81.2 1.0 CA D:CYS71 3.6 94.4 1.0 C D:CYS71 3.7 96.5 1.0 SG D:CYS71 3.7 80.2 1.0 N D:CYS51 3.7 90.8 1.0 CA D:CYS51 4.0 75.4 1.0 ND1 D:HIS66 4.1 75.5 1.0 CG D:HIS66 4.2 75.8 1.0 CD D:LYS67 4.3 78.4 1.0 CG D:GLN50 4.6 78.5 1.0 C D:CYS51 4.6 71.0 1.0 CA D:CYS48 4.8 85.3 1.0 N D:GLN52 4.8 78.4 1.0 CE D:LYS67 4.9 61.8 1.0 C D:GLN50 5.0 72.8 1.0 N D:CYS71 5.0 100.9 1.0

Zinc binding site 5 out of 10 in the Tetramer Formation of the BCL11A ZF0 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Tetramer Formation of the BCL11A ZF0 Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn101 b:46.9 occ:1.00 NE2 E:HIS66 2.1 95.2 1.0 SG E:CYS71 2.3 30.0 1.0 SG E:CYS48 2.4 57.0 1.0 SG E:CYS51 2.7 70.0 1.0 CD2 E:HIS66 3.0 81.3 1.0 CE1 E:HIS66 3.1 89.8 1.0 CB E:CYS71 3.3 30.0 1.0 CB E:CYS48 3.5 64.6 1.0 CB E:CYS51 3.6 71.4 1.0 ND1 E:HIS66 4.1 95.3 1.0 CG E:HIS66 4.1 80.6 1.0 N E:CYS51 4.1 81.9 1.0 CA E:CYS51 4.5 78.3 1.0 C E:GLN50 4.6 78.3 1.0 O E:HIS66 4.6 85.9 1.0 CA E:CYS71 4.7 30.0 1.0 CD E:LYS67 4.7 78.6 1.0 CB E:GLN50 4.7 67.5 1.0 N E:CYS71 4.8 30.0 1.0 CA E:CYS48 4.9 67.9 1.0

Zinc binding site 6 out of 10 in the Tetramer Formation of the BCL11A ZF0 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Tetramer Formation of the BCL11A ZF0 Domain within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:64.4 occ:1.00 CB F:CYS51 2.5 67.6 1.0 SG F:CYS48 2.5 76.1 1.0 NE2 F:HIS66 2.8 85.5 1.0 SG F:CYS51 3.2 76.2 1.0 N F:CYS51 3.4 96.6 1.0 CA F:CYS51 3.5 95.9 1.0 CD2 F:HIS66 3.5 83.5 1.0 CB F:CYS48 3.6 83.9 1.0 NZ F:LYS67 3.8 78.1 1.0 CE1 F:HIS66 3.8 82.1 1.0 C F:GLN50 4.2 86.3 1.0 O F:GLN70 4.2 73.5 1.0 CB F:GLN50 4.5 85.1 1.0 C F:CYS51 4.7 87.6 1.0 CG F:HIS66 4.7 75.2 1.0 CA F:GLN50 4.7 86.9 1.0 CE F:LYS67 4.8 92.1 1.0 O F:GLN50 4.8 71.5 1.0 ND1 F:HIS66 4.8 83.2 1.0 N F:GLN50 4.9 84.7 1.0 C F:GLN70 5.0 85.6 1.0 CA F:CYS48 5.0 85.9 1.0

Zinc binding site 7 out of 10 in the Tetramer Formation of the BCL11A ZF0 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Tetramer Formation of the BCL11A ZF0 Domain within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn101 b:54.1 occ:1.00 NE2 G:HIS66 2.3 75.8 1.0 SG G:CYS51 2.4 72.7 1.0 SG G:CYS48 2.6 81.1 1.0 SG G:CYS71 2.7 76.9 1.0 CB G:CYS71 2.8 87.4 1.0 CD2 G:HIS66 2.9 80.9 1.0 CB G:CYS51 3.1 66.7 1.0 CE1 G:HIS66 3.5 90.5 1.0 N G:CYS51 3.6 81.7 1.0 NZ G:LYS67 3.8 88.2 1.0 CA G:CYS51 3.9 86.1 1.0 CB G:CYS48 4.0 88.3 1.0 CG G:HIS66 4.1 77.2 1.0 CA G:CYS71 4.2 93.9 1.0 ND1 G:HIS66 4.4 92.2 1.0 CB G:GLN50 4.5 73.0 1.0 N G:CYS71 4.5 86.2 1.0 CD G:LYS67 4.7 85.5 1.0 C G:GLN50 4.7 77.0 1.0 C G:CYS51 4.8 75.4 1.0 CE G:LYS67 4.9 89.9 1.0 CD G:GLN50 5.0 91.1 1.0 C G:CYS71 5.0 79.5 1.0 OE1 G:GLN50 5.0 82.3 1.0

Zinc binding site 8 out of 10 in the Tetramer Formation of the BCL11A ZF0 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Tetramer Formation of the BCL11A ZF0 Domain within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn101 b:24.9 occ:1.00 NE2 H:HIS66 2.3 76.4 1.0 SG H:CYS51 2.3 53.9 1.0 SG H:CYS48 2.3 42.6 1.0 CB H:CYS51 3.2 47.8 1.0 CE1 H:HIS66 3.2 70.5 1.0 CD2 H:HIS66 3.2 70.0 1.0 CB H:CYS48 3.3 75.7 1.0 CB H:CYS71 3.5 68.0 1.0 SG H:CYS71 3.5 69.0 1.0 N H:CYS51 3.8 59.5 1.0 CA H:CYS51 4.0 65.4 1.0 NZ H:LYS67 4.3 57.9 1.0 ND1 H:HIS66 4.3 65.1 1.0 CG H:HIS66 4.3 65.3 1.0 CG H:GLN50 4.4 60.9 1.0 O H:GLN70 4.6 70.2 1.0 C H:CYS51 4.6 63.8 1.0 CA H:CYS48 4.7 71.7 1.0 N H:MET53 4.7 71.3 1.0 CB H:MET53 4.8 60.5 1.0 N H:GLN52 4.8 69.2 1.0 C H:GLN50 4.9 56.3 1.0 CA H:CYS71 5.0 73.2 1.0

Zinc binding site 9 out of 10 in the Tetramer Formation of the BCL11A ZF0 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Tetramer Formation of the BCL11A ZF0 Domain within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn101 b:38.8 occ:1.00 CE1 I:HIS66 2.3 74.3 1.0 SG I:CYS48 2.3 64.3 1.0 SG I:CYS71 2.5 57.0 1.0 SG I:CYS51 2.7 51.3 1.0 CB I:CYS71 2.7 71.2 1.0 CB I:CYS51 3.1 56.3 1.0 ND1 I:HIS66 3.2 72.9 1.0 NE2 I:HIS66 3.2 77.3 1.0 CB I:CYS48 3.5 77.0 1.0 N I:CYS51 3.6 65.9 1.0 CA I:CYS51 3.9 77.3 1.0 CA I:CYS71 4.1 75.5 1.0 CG I:HIS66 4.4 77.9 1.0 CD2 I:HIS66 4.4 74.5 1.0 C I:GLN50 4.4 59.0 1.0 CB I:GLN50 4.5 77.5 1.0 C I:CYS71 4.5 77.9 1.0 C I:CYS51 4.7 62.7 1.0 CB I:MET53 4.8 61.2 1.0 CA I:CYS48 4.8 70.1 1.0 CA I:GLN50 4.9 66.8 1.0 N I:GLN52 4.9 63.3 1.0 NE2 I:GLN50 5.0 72.6 1.0

Zinc binding site 10 out of 10 in the Tetramer Formation of the BCL11A ZF0 Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Tetramer Formation of the BCL11A ZF0 Domain within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:53.1 occ:1.00 SG J:CYS71 2.3 85.3 1.0 SG J:CYS51 2.4 78.1 1.0 NE2 J:HIS66 2.6 89.2 1.0 SG J:CYS48 2.7 72.8 1.0 CB J:CYS71 2.9 77.5 1.0 CB J:CYS51 3.1 88.8 1.0 CB J:CYS48 3.3 77.5 1.0 N J:CYS51 3.5 89.0 1.0 CD2 J:HIS66 3.5 81.8 1.0 CE1 J:HIS66 3.6 92.0 1.0 CA J:CYS51 3.8 89.7 1.0 CA J:CYS71 4.4 89.8 1.0 C J:CYS51 4.5 85.6 1.0 C J:GLN50 4.6 90.1 1.0 N J:GLN52 4.6 83.5 1.0 O J:CYS71 4.6 68.5 1.0 CG J:HIS66 4.7 81.3 1.0 CA J:CYS48 4.7 82.5 1.0 ND1 J:HIS66 4.7 93.6 1.0 C J:CYS71 4.8 87.7 1.0 CB J:GLN50 4.9 93.3 1.0 N J:GLN50 5.0 93.5 1.0

G.Zheng, M.Yin, S.Mehta, I.T.Chu, S.Wang, A.Alshaye, K.Drainville, A.Buyanbat, F.Bienfait, K.Tenglin, Q.Zhu, S.H.Orkin. A Tetramer of BCL11A Is Required For Stable Protein Production and Fetal Hemoglobin Silencing. Science V. 386 1010 2024.
ISSN: ESSN 1095-9203
PubMed: 39607926
DOI: 10.1126/SCIENCE.ADP3025