Zinc in PDB 6ki6: Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region

The structure of Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region, PDB code: 6ki6 was solved by F.D.Li, Y.Yang, Y.Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.08 / 2.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.555, 59.555, 213.367, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 25.1

The binding sites of Zinc atom in the Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region (pdb code 6ki6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region, PDB code: 6ki6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:31.9 occ:1.00 NE2 A:HIS764 2.0 28.5 1.0 NE2 A:HIS760 2.1 36.6 1.0 SG A:CYS744 2.3 31.9 1.0 SG A:CYS747 2.3 37.9 1.0 CD2 A:HIS764 2.9 21.9 1.0 CE1 A:HIS760 2.9 30.1 1.0 CE1 A:HIS764 3.0 25.1 1.0 CB A:CYS747 3.1 25.9 1.0 CB A:CYS744 3.2 28.4 1.0 CD2 A:HIS760 3.2 33.4 1.0 N A:CYS747 3.6 26.8 1.0 CA A:CYS747 3.9 28.5 1.0 ND1 A:HIS764 4.1 29.3 1.0 CG A:HIS764 4.1 32.1 1.0 ND1 A:HIS760 4.1 30.0 1.0 CG A:HIS760 4.3 30.9 1.0 CB A:TYR746 4.4 18.5 1.0 C A:TYR746 4.5 29.2 1.0 CA A:CYS744 4.6 28.6 1.0 C A:CYS747 4.7 28.6 1.0 CA A:TYR746 4.8 27.3 1.0 N A:TYR746 4.8 26.3 1.0 CB A:LYS749 4.9 25.0 1.0 N A:GLY748 4.9 29.4 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:24.8 occ:1.00 NE2 A:HIS792 2.1 27.6 1.0 NE2 A:HIS788 2.1 29.6 1.0 SG A:CYS775 2.3 25.7 1.0 SG A:CYS772 2.4 23.7 1.0 CD2 A:HIS792 3.0 24.2 1.0 CD2 A:HIS788 3.0 23.0 1.0 CE1 A:HIS792 3.1 20.1 1.0 CE1 A:HIS788 3.1 21.5 1.0 CB A:CYS775 3.3 16.0 1.0 CB A:CYS772 3.3 13.6 1.0 N A:CYS775 3.6 16.1 1.0 CA A:CYS775 3.9 20.9 1.0 C A:LEU774 4.0 22.2 1.0 CG A:HIS792 4.2 26.8 1.0 ND1 A:HIS792 4.2 25.5 1.0 CB A:TYR777 4.2 16.4 1.0 CG A:HIS788 4.2 22.8 1.0 ND1 A:HIS788 4.2 19.4 1.0 CB A:LEU774 4.4 26.2 1.0 C A:CYS775 4.5 21.2 1.0 O A:LEU774 4.5 23.6 1.0 CA A:LEU774 4.5 25.0 1.0 N A:LEU774 4.6 27.0 1.0 O A:CYS775 4.6 27.4 1.0 CA A:CYS772 4.8 20.9 1.0 N A:TYR777 4.9 19.8 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:29.1 occ:1.00 NE2 A:HIS823 2.0 34.7 1.0 NE2 A:HIS818 2.1 29.6 1.0 SG A:CYS805 2.3 31.8 1.0 SG A:CYS802 2.4 32.8 1.0 CD2 A:HIS823 2.9 34.1 1.0 CE1 A:HIS818 3.0 30.9 1.0 CB A:CYS805 3.0 26.1 1.0 CE1 A:HIS823 3.1 32.6 1.0 CD2 A:HIS818 3.1 30.3 1.0 CB A:CYS802 3.3 32.6 1.0 N A:CYS805 3.6 33.3 1.0 CA A:CYS805 3.9 29.8 1.0 CG A:HIS823 4.1 38.1 1.0 ND1 A:HIS818 4.1 28.7 1.0 ND1 A:HIS823 4.2 32.6 1.0 CG A:HIS818 4.2 32.6 1.0 CB A:ILE804 4.6 40.3 1.0 C A:ILE804 4.6 42.8 1.0 C A:CYS805 4.6 32.9 1.0 CA A:CYS802 4.7 25.7 1.0 N A:LYS806 4.9 30.2 1.0 CA A:ILE804 5.0 46.1 1.0 CB A:MET807 5.0 22.9 1.0 N A:ILE804 5.0 47.6 1.0 SD A:MET819 5.0 54.0 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:39.8 occ:1.00 NE2 B:HIS760 2.0 42.6 1.0 NE2 B:HIS764 2.2 49.7 1.0 SG B:CYS747 2.4 54.3 1.0 SG B:CYS744 2.4 37.9 1.0 CD2 B:HIS764 2.9 42.5 1.0 CE1 B:HIS760 3.0 37.6 1.0 CD2 B:HIS760 3.0 38.5 1.0 CB B:CYS744 3.2 41.7 1.0 CE1 B:HIS764 3.3 40.2 1.0 CB B:CYS747 3.6 48.7 1.0 N B:CYS747 3.6 38.9 1.0 ND1 B:HIS760 4.1 36.9 1.0 CG B:HIS764 4.1 40.4 1.0 CA B:CYS747 4.1 45.6 1.0 CG B:HIS760 4.1 36.1 1.0 ND1 B:HIS764 4.3 38.7 1.0 CB B:TYR746 4.3 33.6 1.0 CA B:CYS744 4.7 53.2 1.0 C B:CYS747 4.7 55.3 1.0 C B:TYR746 4.7 46.0 1.0 CA B:TYR746 4.9 38.2 1.0 CB B:LYS749 4.9 54.2 1.0 N B:TYR746 4.9 38.8 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of BCL11A in Complex with Gamma-Globin -115 Hpfh Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn902 b:0.3 occ:1.00 SG B:CYS775 2.2 88.3 1.0 CD2 B:HIS792 2.7 0.7 1.0 CG B:HIS792 3.0 0.4 1.0 CB B:HIS792 3.3 0.2 1.0 O B:HIS788 3.5 0.3 1.0 NE2 B:HIS792 3.6 99.7 1.0 CB B:CYS775 3.7 0.0 1.0 CB B:TYR777 4.0 0.1 1.0 ND1 B:HIS792 4.0 0.6 1.0 SG B:CYS772 4.0 0.7 1.0 CB B:CYS772 4.2 0.3 1.0 C B:HIS788 4.2 0.1 1.0 CD1 B:TYR777 4.3 0.9 1.0 CE1 B:HIS792 4.3 98.9 1.0 CG B:TYR777 4.4 0.8 1.0 CE B:MET789 4.4 0.0 1.0 CB B:HIS788 4.5 97.5 1.0 CA B:MET789 4.7 0.7 1.0 N B:MET789 4.7 0.8 1.0 CA B:HIS792 4.8 0.3 1.0 N B:CYS775 4.8 0.0 1.0 CD1 B:LEU785 4.8 0.8 1.0 CA B:CYS775 4.9 0.7 1.0

Y.Yang, Z.Xu, C.He, B.Zhang, Y.Shi, F.Li. Structural Insights Into the Recognition of Gamma-Globin Gene Promoter By BCL11A. Cell Res. V. 29 960 2019.
ISSN: ISSN 1001-0602
PubMed: 31467406
DOI: 10.1038/S41422-019-0221-0