Zinc in PDB 8dtn: The Complex of Nanobody 6101 with BCL11A ZF6

The structure of The Complex of Nanobody 6101 with BCL11A ZF6, PDB code: 8dtn was solved by M.Yin, K.Tenglin, L.Zhai, L.M.Dassama, S.H.Orkin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.28 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	54.933, 54.933, 408.619, 90, 90, 120
R / Rfree (%)	19.5 / 23.2

The structure of The Complex of Nanobody 6101 with BCL11A ZF6 also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the The Complex of Nanobody 6101 with BCL11A ZF6 (pdb code 8dtn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Complex of Nanobody 6101 with BCL11A ZF6, PDB code: 8dtn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Complex of Nanobody 6101 with BCL11A ZF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Complex of Nanobody 6101 with BCL11A ZF6 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:22.9 occ:1.00 NE2 B:HIS818 2.1 24.2 1.0 NE2 B:HIS823 2.1 31.1 1.0 SG B:CYS805 2.3 24.9 1.0 SG B:CYS802 2.3 27.5 1.0 CE1 B:HIS823 3.0 26.2 1.0 CD2 B:HIS818 3.0 27.2 1.0 CE1 B:HIS818 3.1 28.3 1.0 CB B:CYS802 3.1 27.3 1.0 CD2 B:HIS823 3.1 27.6 1.0 CB B:CYS805 3.4 23.1 1.0 N B:CYS805 3.7 28.1 1.0 CA B:CYS805 4.1 24.4 1.0 ND1 B:HIS823 4.1 25.2 1.0 ND1 B:HIS818 4.2 27.1 1.0 CG B:HIS818 4.2 26.0 1.0 CG B:HIS823 4.2 27.6 1.0 CB B:ILE804 4.5 27.0 1.0 CA B:CYS802 4.5 29.8 1.0 O B:HOH1026 4.7 29.1 1.0 C B:ILE804 4.7 27.7 1.0 C B:CYS805 4.8 24.3 1.0 CA B:ILE804 4.9 28.3 1.0 CB B:MSE807 5.0 24.3 1.0 N B:ILE804 5.0 26.7 1.0

Zinc binding site 2 out of 4 in the The Complex of Nanobody 6101 with BCL11A ZF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Complex of Nanobody 6101 with BCL11A ZF6 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn901 b:26.5 occ:1.00 NE2 D:HIS818 2.0 27.7 1.0 NE2 D:HIS823 2.1 28.5 1.0 SG D:CYS802 2.3 27.1 1.0 SG D:CYS805 2.4 27.1 1.0 CE1 D:HIS823 3.0 28.0 1.0 CD2 D:HIS818 3.0 29.8 1.0 CE1 D:HIS818 3.0 28.1 1.0 CD2 D:HIS823 3.1 30.9 1.0 CB D:CYS802 3.1 27.9 1.0 CB D:CYS805 3.3 28.4 1.0 N D:CYS805 3.6 30.5 1.0 CA D:CYS805 4.0 29.4 1.0 ND1 D:HIS823 4.1 30.1 1.0 ND1 D:HIS818 4.1 27.2 1.0 CG D:HIS818 4.1 29.6 1.0 CG D:HIS823 4.2 35.5 1.0 CB D:ILE804 4.4 30.4 1.0 CA D:CYS802 4.6 25.7 1.0 C D:ILE804 4.7 32.1 1.0 C D:CYS805 4.8 27.2 1.0 CB D:TRP822 4.8 27.9 1.0 N D:ILE804 4.9 27.9 1.0 CA D:ILE804 4.9 29.1 1.0 O D:HOH1022 4.9 26.9 1.0 N D:LYS806 5.0 25.1 1.0 CB D:MSE807 5.0 24.6 1.0

Zinc binding site 3 out of 4 in the The Complex of Nanobody 6101 with BCL11A ZF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Complex of Nanobody 6101 with BCL11A ZF6 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn901 b:25.6 occ:1.00 NE2 F:HIS823 2.0 36.3 1.0 NE2 F:HIS818 2.1 28.5 1.0 SG F:CYS805 2.3 24.4 1.0 SG F:CYS802 2.4 25.5 1.0 CE1 F:HIS823 3.0 36.4 1.0 CD2 F:HIS818 3.0 26.7 1.0 CD2 F:HIS823 3.0 30.1 1.0 CE1 F:HIS818 3.1 29.5 1.0 CB F:CYS802 3.2 28.2 1.0 CB F:CYS805 3.3 27.7 1.0 N F:CYS805 3.7 27.8 1.0 CA F:CYS805 4.1 30.4 1.0 ND1 F:HIS823 4.1 38.2 1.0 CG F:HIS823 4.2 34.3 1.0 ND1 F:HIS818 4.2 29.7 1.0 CG F:HIS818 4.2 29.2 1.0 CB F:ILE804 4.5 34.4 1.0 CA F:CYS802 4.7 26.3 1.0 C F:ILE804 4.7 30.5 1.0 C F:CYS805 4.8 28.8 1.0 O F:HOH1023 4.9 34.2 1.0 CA F:ILE804 5.0 29.2 1.0 N F:LYS806 5.0 29.5 1.0 CB F:TRP822 5.0 25.8 1.0 N F:ILE804 5.0 27.8 1.0

Zinc binding site 4 out of 4 in the The Complex of Nanobody 6101 with BCL11A ZF6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Complex of Nanobody 6101 with BCL11A ZF6 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn901 b:27.1 occ:1.00 NE2 H:HIS818 2.0 32.5 1.0 NE2 H:HIS823 2.1 31.1 1.0 SG H:CYS805 2.3 28.1 1.0 SG H:CYS802 2.4 28.2 1.0 CE1 H:HIS818 2.9 33.0 1.0 CE1 H:HIS823 3.0 34.4 1.0 CD2 H:HIS818 3.0 28.6 1.0 CD2 H:HIS823 3.2 33.8 1.0 CB H:CYS802 3.2 30.9 1.0 CB H:CYS805 3.3 27.2 1.0 N H:CYS805 3.7 30.2 1.0 CA H:CYS805 4.0 31.3 1.0 ND1 H:HIS818 4.1 29.5 1.0 ND1 H:HIS823 4.1 34.4 1.0 CG H:HIS818 4.1 29.4 1.0 CG H:HIS823 4.2 37.5 1.0 CB H:ILE804 4.3 32.9 1.0 C H:ILE804 4.7 35.1 1.0 CA H:CYS802 4.7 32.1 1.0 C H:CYS805 4.7 30.8 1.0 O H:HOH1022 4.8 35.8 1.0 CA H:ILE804 4.9 34.6 1.0 N H:LYS806 4.9 26.9 1.0 N H:ILE804 4.9 35.3 1.0 CB H:TRP822 5.0 29.4 1.0

M.Yin, M.Izadi, K.Tenglin, T.Viennet, L.Zhai, G.Zheng, H.Arthanari, L.M.K.Dassama, S.H.Orkin. Evolution of Nanobodies Specific For BCL11A. Proc.Natl.Acad.Sci.Usa V. 120 59120 2023.
ISSN: ESSN 1091-6490
PubMed: 36626555
DOI: 10.1073/PNAS.2218959120