Zinc in PDB 8h9h: Crystal Structure of ZBTB7A in Complex with Gaccc-Containing Sequence

The structure of Crystal Structure of ZBTB7A in Complex with Gaccc-Containing Sequence, PDB code: 8h9h was solved by Y.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.30 / 2.20
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	63.542, 63.542, 201.586, 90, 90, 120
R / Rfree (%)	22.4 / 26.1

The binding sites of Zinc atom in the Crystal Structure of ZBTB7A in Complex with Gaccc-Containing Sequence (pdb code 8h9h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of ZBTB7A in Complex with Gaccc-Containing Sequence, PDB code: 8h9h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of ZBTB7A in Complex with Gaccc-Containing Sequence


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 ZBTB7A in Complex with Gaccc-Containing Sequence within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn501 b:50.5 occ:1.00 NE2 G:HIS404 2.0 42.9 1.0 NE2 G:HIS400 2.0 61.2 1.0 SG G:CYS384 2.3 52.3 1.0 SG G:CYS387 2.3 49.6 1.0 CD2 G:HIS400 2.9 39.3 1.0 CD2 G:HIS404 2.9 56.3 1.0 CB G:CYS384 3.0 51.5 1.0 CE1 G:HIS404 3.1 54.2 1.0 CE1 G:HIS400 3.1 45.8 1.0 CB G:CYS387 3.4 45.9 1.0 N G:CYS387 3.7 51.5 1.0 CG G:HIS400 4.1 42.8 1.0 CG G:HIS404 4.1 40.1 1.0 CA G:CYS387 4.1 59.3 1.0 ND1 G:HIS404 4.1 44.6 1.0 ND1 G:HIS400 4.1 45.6 1.0 CB G:ILE386 4.5 50.0 1.0 CA G:CYS384 4.5 43.6 1.0 C G:ILE386 4.7 46.1 1.0 C G:CYS387 4.7 58.6 1.0 N G:ILE386 4.9 56.3 1.0 N G:GLU388 4.9 52.8 1.0 CB G:LYS389 4.9 63.7 1.0 CA G:ILE386 5.0 45.0 1.0 C G:CYS384 5.0 49.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of ZBTB7A in Complex with Gaccc-Containing Sequence


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 ZBTB7A in Complex with Gaccc-Containing Sequence within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn502 b:80.1 occ:1.00 NE2 G:HIS432 2.0 89.7 1.0 NE2 G:HIS428 2.0 87.9 1.0 SG G:CYS415 2.3 87.6 1.0 SG G:CYS412 2.3 73.4 1.0 CD2 G:HIS432 2.9 70.8 1.0 CE1 G:HIS428 3.0 67.5 1.0 CD2 G:HIS428 3.0 65.1 1.0 CE1 G:HIS432 3.0 87.0 1.0 CB G:CYS412 3.2 63.5 1.0 CB G:CYS415 3.3 84.2 1.0 N G:CYS415 3.7 90.7 1.0 CA G:CYS415 4.1 86.1 1.0 CG G:HIS432 4.1 79.5 1.0 ND1 G:HIS432 4.1 95.6 1.0 ND1 G:HIS428 4.1 80.9 1.0 CG G:HIS428 4.2 74.0 1.0 CB G:ILE414 4.6 99.8 1.0 CA G:CYS412 4.7 76.6 1.0 C G:CYS415 4.7 98.5 1.0 C G:ILE414 4.8 90.4 1.0 SD G:MET429 4.8 93.6 1.0 CG2 G:ILE414 4.9 87.5 1.0 N G:ILE414 5.0 88.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of ZBTB7A in Complex with Gaccc-Containing Sequence


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 ZBTB7A in Complex with Gaccc-Containing Sequence within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn503 b:70.1 occ:1.00 NE2 G:HIS456 2.0 62.0 1.0 NE2 G:HIS460 2.1 73.6 1.0 SG G:CYS440 2.3 80.5 1.0 SG G:CYS443 2.3 68.0 1.0 CD2 G:HIS456 2.9 63.0 1.0 CD2 G:HIS460 3.0 93.9 1.0 CE1 G:HIS460 3.0 76.2 1.0 CE1 G:HIS456 3.1 66.8 1.0 CB G:CYS440 3.2 64.3 1.0 CB G:CYS443 3.6 70.2 1.0 N G:CYS443 3.6 80.8 1.0 CG G:HIS456 4.1 72.5 1.0 ND1 G:HIS456 4.1 69.6 1.0 ND1 G:HIS460 4.1 83.5 1.0 CA G:CYS443 4.1 71.5 1.0 CG G:HIS460 4.2 85.7 1.0 CB G:GLN442 4.2 88.6 1.0 CB G:ALA445 4.4 58.6 1.0 CA G:CYS440 4.6 74.0 1.0 C G:GLN442 4.6 86.7 1.0 N G:ALA445 4.7 63.5 1.0 C G:CYS443 4.8 71.5 1.0 N G:GLY444 4.8 65.7 1.0 CA G:GLN442 4.8 85.5 1.0 N G:GLN442 4.8 89.7 1.0 O G:CYS440 4.8 75.1 1.0 CG2 G:VAL459 4.9 84.1 1.0 C G:CYS440 4.9 73.8 1.0 SD G:MET457 4.9 77.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of ZBTB7A in Complex with Gaccc-Containing Sequence


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 ZBTB7A in Complex with Gaccc-Containing Sequence within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn501 b:153.0 occ:1.00 NE2 F:HIS456 2.1 151.2 1.0 NE2 F:HIS460 2.1 164.5 1.0 CD2 F:HIS456 2.3 144.7 1.0 SG F:CYS443 2.3 138.7 1.0 SG F:CYS440 2.3 147.0 1.0 CE1 F:HIS460 2.8 170.6 1.0 CB F:CYS440 3.2 125.9 1.0 CD2 F:HIS460 3.2 166.9 1.0 CE1 F:HIS456 3.4 154.2 1.0 CB F:CYS443 3.5 143.9 1.0 CG F:HIS456 3.6 143.7 1.0 N F:CYS443 3.8 139.5 1.0 ND1 F:HIS460 4.0 171.3 1.0 ND1 F:HIS456 4.1 149.6 1.0 CA F:CYS443 4.2 140.6 1.0 CG F:HIS460 4.3 170.8 1.0 O F:HIS456 4.4 148.7 1.0 CA F:CYS440 4.7 124.3 1.0 CB F:GLN442 4.7 146.9 1.0 C F:CYS443 4.7 136.4 1.0 CB F:HIS456 4.8 138.1 1.0 N F:GLY444 4.8 129.1 1.0 C F:GLN442 4.8 142.7 1.0 CZ F:PHE447 4.9 123.3 1.0 CB F:ALA445 4.9 126.8 1.0 C F:HIS456 5.0 137.6 1.0

Y.Yang, L.Xiao, Y.Xue, M.O.Idris, J.Liu, D.Pei, Y.Shi, B.Liao, F.Li. ZBTB7A Regulates Primed-to-Naive Transition of Pluripotent Stem Cells Via Recognition of the Pnt-Associated Sequence By Zinc Fingers 1-2 and Recognition of Gamma-Globin -200 Gene Element By Zinc Fingers 1-4. Febs J. 2023.
ISSN: ISSN 1742-464X
PubMed: 37013936
DOI: 10.1111/FEBS.16789