Zinc in PDB 6ml7: ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification)

The structure of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification), PDB code: 6ml7 was solved by J.R.Horton, X.Cheng, R.Ren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.01 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.130, 68.707, 48.448, 90.00, 92.58, 90.00
R / Rfree (%)	19.3 / 24

The binding sites of Zinc atom in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification) (pdb code 6ml7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification), PDB code: 6ml7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:36.0 occ:1.00 NE2 A:HIS399 2.0 51.7 1.0 NE2 A:HIS395 2.1 46.4 1.0 SG A:CYS382 2.3 40.1 1.0 SG A:CYS379 2.3 36.8 1.0 CD2 A:HIS399 2.9 49.0 1.0 CD2 A:HIS395 3.0 42.7 1.0 CE1 A:HIS395 3.1 44.4 1.0 CE1 A:HIS399 3.1 51.1 1.0 CB A:CYS379 3.2 33.4 1.0 CB A:CYS382 3.4 42.0 1.0 N A:CYS382 3.6 39.7 1.0 CA A:CYS382 4.0 40.4 1.0 CG A:HIS399 4.1 49.7 1.0 CG A:HIS395 4.1 40.8 1.0 ND1 A:HIS395 4.2 43.4 1.0 ND1 A:HIS399 4.2 52.0 1.0 CB A:GLN381 4.4 47.2 1.0 C A:GLN381 4.6 42.9 1.0 CA A:CYS379 4.6 32.9 1.0 C A:CYS382 4.7 38.0 1.0 N A:GLY383 4.8 34.8 1.0 CA A:GLN381 4.9 42.6 1.0 N A:GLN381 4.9 38.9 1.0 CG2 A:VAL398 5.0 41.1 1.0

Zinc binding site 2 out of 5 in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:30.1 occ:1.00 NE2 A:HIS427 2.1 41.8 1.0 NE2 A:HIS423 2.1 42.0 1.0 SG A:CYS410 2.2 34.8 1.0 SG A:CYS407 2.3 31.6 1.0 CD2 A:HIS423 2.8 37.6 1.0 CD2 A:HIS427 2.9 38.7 1.0 CB A:CYS407 3.1 29.4 1.0 CE1 A:HIS427 3.2 40.8 1.0 CB A:CYS410 3.2 34.8 1.0 CE1 A:HIS423 3.2 39.5 1.0 N A:CYS410 3.5 34.5 1.0 CA A:CYS410 3.9 37.5 1.0 CG A:HIS423 4.1 35.2 1.0 CG A:HIS427 4.1 38.0 1.0 ND1 A:HIS427 4.2 40.1 1.0 CB A:HIS409 4.2 45.1 1.0 ND1 A:HIS423 4.2 35.6 1.0 CA A:CYS407 4.6 29.9 1.0 C A:HIS409 4.6 43.4 1.0 C A:CYS410 4.6 37.3 1.0 N A:HIS411 4.7 33.0 1.0 CA A:HIS409 4.8 44.1 1.0 N A:HIS409 4.8 40.4 1.0 C A:CYS407 4.9 31.8 1.0

Zinc binding site 3 out of 5 in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:18.9 occ:1.00 NE2 A:HIS455 2.0 22.6 1.0 NE2 A:HIS451 2.0 14.9 1.0 SG A:CYS438 2.3 18.6 1.0 SG A:CYS435 2.3 17.6 1.0 CD2 A:HIS455 3.0 21.3 1.0 CD2 A:HIS451 3.0 14.0 1.0 CE1 A:HIS455 3.0 23.6 1.0 CE1 A:HIS451 3.0 15.4 1.0 CB A:CYS435 3.1 15.0 1.0 CB A:CYS438 3.3 18.6 1.0 N A:CYS438 3.7 20.8 1.0 CA A:CYS438 4.0 22.6 1.0 O A:HOH796 4.1 35.4 1.0 ND1 A:HIS455 4.1 22.4 1.0 CG A:HIS455 4.1 22.9 1.0 ND1 A:HIS451 4.1 11.8 1.0 CG A:HIS451 4.2 11.8 1.0 CB A:ILE437 4.5 23.6 1.0 CA A:CYS435 4.6 17.1 1.0 C A:ILE437 4.7 25.6 1.0 C A:CYS438 4.7 19.3 1.0 N A:GLY439 4.8 17.7 1.0 CA A:ILE437 4.9 24.0 1.0 CG2 A:ILE437 5.0 21.0 1.0 N A:ILE437 5.0 21.9 1.0 C A:CYS435 5.0 18.4 1.0

Zinc binding site 4 out of 5 in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:18.6 occ:1.00 NE2 A:HIS483 2.0 25.2 1.0 NE2 A:HIS479 2.0 23.2 1.0 SG A:CYS466 2.3 22.4 1.0 SG A:CYS463 2.3 18.5 1.0 CD2 A:HIS483 3.0 22.2 1.0 CE1 A:HIS479 3.0 22.1 1.0 CD2 A:HIS479 3.0 19.9 1.0 CE1 A:HIS483 3.0 23.4 1.0 CB A:CYS463 3.1 15.0 1.0 CB A:CYS466 3.3 26.0 1.0 N A:CYS466 3.6 24.5 1.0 CA A:CYS466 4.0 25.2 1.0 ND1 A:HIS479 4.1 20.1 1.0 ND1 A:HIS483 4.1 24.3 1.0 CG A:HIS483 4.1 25.7 1.0 CG A:HIS479 4.2 20.2 1.0 CB A:ILE465 4.5 22.0 1.0 CA A:CYS463 4.5 15.8 1.0 C A:ILE465 4.6 19.9 1.0 C A:CYS466 4.7 24.2 1.0 N A:GLY467 4.8 22.8 1.0 CG2 A:ILE465 4.9 20.3 1.0 CA A:ILE465 4.9 20.3 1.0 CB A:LYS468 4.9 21.1 1.0 N A:ILE465 4.9 20.6 1.0 C A:CYS463 5.0 19.0 1.0

Zinc binding site 5 out of 5 in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 4 with A Cpg 5MC Modification) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:26.4 occ:1.00 NE2 A:HIS511 2.0 36.3 1.0 NE2 A:HIS507 2.0 33.8 1.0 SG A:CYS494 2.3 31.1 1.0 SG A:CYS491 2.3 21.4 1.0 CD2 A:HIS507 3.0 28.4 1.0 CE1 A:HIS511 3.0 37.5 1.0 CD2 A:HIS511 3.0 34.7 1.0 CE1 A:HIS507 3.1 31.9 1.0 CB A:CYS491 3.2 19.6 1.0 CB A:CYS494 3.3 31.3 1.0 N A:CYS494 3.6 29.5 1.0 CA A:CYS494 4.0 31.6 1.0 ND1 A:HIS511 4.1 39.4 1.0 CG A:HIS507 4.1 29.9 1.0 ND1 A:HIS507 4.1 31.0 1.0 CG A:HIS511 4.1 38.3 1.0 CB A:GLU493 4.4 30.1 1.0 C A:GLU493 4.5 28.5 1.0 CA A:CYS491 4.6 18.4 1.0 C A:CYS494 4.6 30.7 1.0 N A:GLY495 4.7 27.9 1.0 CA A:GLU493 4.8 26.0 1.0 N A:GLU493 4.8 21.9 1.0 CB A:LEU496 4.9 37.7 1.0 N A:LEU496 5.0 21.6 1.0

R.Ren, S.Hardikar, J.R.Horton, Y.Lu, Y.Zeng, A.K.Singh, K.Lin, L.D.Coletta, J.Shen, C.S.Lin Kong, H.Hashimoto, X.Zhang, T.Chen, X.Cheng. Structural Basis of Specific Dna Binding By the Transcription Factor ZBTB24. Nucleic Acids Res. V. 47 8388 2019.
ISSN: ESSN 1362-4962
PubMed: 31226215
DOI: 10.1093/NAR/GKZ557