Zinc in PDB 6ml3: ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 2)

The structure of ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 2), PDB code: 6ml3 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)	38.36 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.297, 68.757, 50.010, 90.00, 93.23, 90.00
R / Rfree (%)	22.5 / 25.7

The binding sites of Zinc atom in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 2) (pdb code 6ml3). 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 2), PDB code: 6ml3:
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 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:44.7 occ:1.00 NE2 A:HIS427 2.0 65.6 1.0 NE2 A:HIS423 2.0 60.8 1.0 SG A:CYS410 2.3 49.2 1.0 SG A:CYS407 2.3 45.1 1.0 CD2 A:HIS427 2.6 59.4 1.0 CE1 A:HIS423 3.0 53.9 1.0 CD2 A:HIS423 3.0 52.5 1.0 CB A:CYS407 3.2 49.2 1.0 CE1 A:HIS427 3.2 61.1 1.0 CB A:CYS410 3.4 51.1 1.0 N A:CYS410 3.6 57.0 1.0 CG A:HIS427 3.9 57.3 1.0 CA A:CYS410 4.1 61.8 1.0 ND1 A:HIS423 4.1 49.1 1.0 CG A:HIS423 4.1 47.3 1.0 ND1 A:HIS427 4.2 60.5 1.0 CB A:HIS409 4.3 61.2 1.0 NH2 A:ARG412 4.6 74.2 1.0 C A:HIS409 4.7 60.9 1.0 CA A:CYS407 4.7 46.3 1.0 N A:HIS409 4.8 50.9 1.0 CA A:HIS409 4.8 59.3 1.0 C A:CYS410 4.8 68.6 1.0 N A:HIS411 5.0 69.8 1.0 CG A:HIS409 5.0 76.7 1.0 ND1 A:HIS409 5.0 83.6 1.0

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


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:40.2 occ:1.00 NE2 A:HIS451 2.0 40.3 1.0 NE2 A:HIS455 2.0 52.2 1.0 SG A:CYS438 2.3 36.9 1.0 SG A:CYS435 2.3 38.0 1.0 CD2 A:HIS455 2.9 49.7 1.0 CE1 A:HIS451 3.0 34.2 1.0 CD2 A:HIS451 3.0 38.4 1.0 CE1 A:HIS455 3.1 49.1 1.0 CB A:CYS435 3.2 36.8 1.0 CB A:CYS438 3.2 41.4 1.0 N A:CYS438 3.6 52.5 1.0 O A:HOH702 3.7 46.9 1.0 CA A:CYS438 4.0 48.6 1.0 CG A:HIS455 4.1 50.5 1.0 ND1 A:HIS451 4.1 36.3 1.0 CG A:HIS451 4.2 36.9 1.0 ND1 A:HIS455 4.2 47.7 1.0 CB A:ILE437 4.4 43.5 1.0 CA A:CYS435 4.6 42.0 1.0 C A:ILE437 4.7 52.1 1.0 C A:CYS438 4.7 46.4 1.0 N A:GLY439 4.8 45.1 1.0 N A:ILE437 4.9 45.1 1.0 CA A:ILE437 4.9 47.0 1.0 CG2 A:ILE437 5.0 42.4 1.0

Zinc binding site 3 out of 5 in the ZBTB24 Zinc Fingers 4-8 with 19+1MER Dna Oligonucleotide (Sequence 2)


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:41.6 occ:1.00 NE2 A:HIS483 2.0 55.6 1.0 NE2 A:HIS479 2.0 52.0 1.0 SG A:CYS466 2.3 48.7 1.0 SG A:CYS463 2.3 43.6 1.0 CD2 A:HIS483 2.9 48.1 1.0 CD2 A:HIS479 2.9 44.2 1.0 CE1 A:HIS479 3.1 46.6 1.0 CE1 A:HIS483 3.1 41.7 1.0 CB A:CYS463 3.1 44.8 1.0 CB A:CYS466 3.2 54.0 1.0 N A:CYS466 3.6 53.5 1.0 CA A:CYS466 3.9 56.1 1.0 CG A:HIS479 4.1 45.2 1.0 CG A:HIS483 4.1 50.9 1.0 ND1 A:HIS479 4.1 42.5 1.0 ND1 A:HIS483 4.1 49.1 1.0 CB A:ILE465 4.5 51.0 1.0 CA A:CYS463 4.6 44.9 1.0 C A:CYS466 4.6 54.7 1.0 C A:ILE465 4.6 55.2 1.0 N A:GLY467 4.6 61.9 1.0 CB A:LYS468 4.8 42.4 1.0 N A:LYS468 4.9 39.8 1.0 CA A:ILE465 4.9 54.8 1.0 N A:ILE465 4.9 53.7 1.0

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


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 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:45.0 occ:1.00 NE2 A:HIS511 2.0 60.8 1.0 NE2 A:HIS507 2.0 46.4 1.0 SG A:CYS491 2.3 36.3 1.0 SG A:CYS494 2.3 53.9 1.0 CD2 A:HIS511 2.5 46.3 1.0 CE1 A:HIS507 3.0 48.1 1.0 CD2 A:HIS507 3.0 41.6 1.0 CB A:CYS494 3.2 41.6 1.0 CB A:CYS491 3.2 36.1 1.0 CE1 A:HIS511 3.3 58.1 1.0 N A:CYS494 3.7 44.9 1.0 CG A:HIS511 3.8 55.5 1.0 CA A:CYS494 4.0 44.1 1.0 ND1 A:HIS507 4.1 41.7 1.0 CG A:HIS507 4.1 42.5 1.0 ND1 A:HIS511 4.1 57.6 1.0 O A:HIS507 4.5 65.8 1.0 CB A:GLU493 4.6 49.5 1.0 C A:GLU493 4.6 49.4 1.0 N A:GLY495 4.7 46.5 1.0 C A:CYS494 4.7 48.4 1.0 CA A:CYS491 4.7 38.4 1.0 CB A:LEU496 4.8 45.3 1.0 N A:LEU496 4.9 46.7 1.0 N A:GLU493 5.0 49.0 1.0 CA A:GLU493 5.0 48.8 1.0

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


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 2) within 5.0Å range:

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