Zinc in PDB 6dfc: Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) with A T-to-U Substitution

The structure of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) with A T-to-U Substitution, PDB code: 6dfc was solved by E.N.Nikolova, R.L.Stanfield, H.J.Dyson, P.E.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.02 / 1.85
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	44.240, 184.451, 104.705, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 20.8

The structure of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) with A T-to-U Substitution also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) with A T-to-U Substitution (pdb code 6dfc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) with A T-to-U Substitution, PDB code: 6dfc:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) with A T-to-U Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) with A T-to-U Substitution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:54.6 occ:1.00 NE2 A:HIS516 2.0 58.4 1.0 NE2 A:HIS512 2.1 52.0 1.0 SG A:CYS499 2.2 62.9 1.0 SG A:CYS496 2.3 71.8 1.0 CD2 A:HIS516 2.8 68.7 1.0 CE1 A:HIS512 3.1 54.5 1.0 CD2 A:HIS512 3.1 57.2 1.0 CE1 A:HIS516 3.1 74.6 1.0 CB A:CYS496 3.1 57.7 1.0 CB A:CYS499 3.4 66.0 1.0 N A:CYS499 3.7 79.8 1.0 CG A:HIS516 4.0 62.3 1.0 CA A:CYS499 4.1 74.0 1.0 ND1 A:HIS516 4.1 69.6 1.0 ND1 A:HIS512 4.2 52.0 1.0 CG A:HIS512 4.2 48.6 1.0 CB A:VAL498 4.5 76.9 1.0 CA A:CYS496 4.6 59.8 1.0 C A:VAL498 4.7 81.8 1.0 C A:CYS499 4.8 73.0 1.0 N A:LYS500 4.8 69.1 1.0 CG1 A:VAL498 4.9 80.4 1.0 N A:VAL498 4.9 70.7 1.0 CA A:VAL498 4.9 74.6 1.0 CD A:ARG501 5.0 75.4 1.0 CD1 A:PHE513 5.0 71.1 1.0

Zinc binding site 2 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) with A T-to-U Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) with A T-to-U Substitution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:49.3 occ:1.00 NE2 A:HIS540 2.0 55.9 1.0 NE2 A:HIS544 2.1 50.3 1.0 SG A:CYS524 2.2 48.8 1.0 SG A:CYS527 2.2 63.7 1.0 CD2 A:HIS540 2.9 46.8 1.0 CD2 A:HIS544 2.9 45.9 1.0 CE1 A:HIS540 3.1 55.9 1.0 CB A:CYS524 3.2 59.4 1.0 CE1 A:HIS544 3.2 51.3 1.0 CB A:CYS527 3.3 58.4 1.0 N A:CYS527 3.6 58.4 1.0 CA A:CYS527 3.9 71.8 1.0 CG A:HIS540 4.1 53.5 1.0 CG A:HIS544 4.1 52.2 1.0 ND1 A:HIS540 4.2 55.1 1.0 ND1 A:HIS544 4.2 48.4 1.0 C A:CYS527 4.3 76.8 1.0 C A:TYR526 4.4 59.9 1.0 O A:CYS527 4.5 89.3 1.0 CD A:LYS529 4.5 76.3 1.0 CA A:CYS524 4.6 52.6 1.0 CB A:TYR526 4.6 51.5 1.0 CB A:LYS529 4.7 64.1 1.0 N A:TYR526 4.8 65.9 1.0 CG A:LYS529 4.9 69.5 1.0 CA A:TYR526 4.9 58.1 1.0 N A:LYS529 4.9 66.1 1.0

Zinc binding site 3 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) with A T-to-U Substitution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) with A T-to-U Substitution within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:35.3 occ:1.00 NE2 A:HIS568 2.0 32.5 1.0 NE2 A:HIS573 2.1 31.4 1.0 SG A:CYS555 2.3 34.3 1.0 SG A:CYS552 2.3 33.2 1.0 CD2 A:HIS573 2.9 33.0 1.0 CE1 A:HIS568 3.0 39.9 1.0 CD2 A:HIS568 3.0 30.5 1.0 CE1 A:HIS573 3.2 35.2 1.0 CB A:CYS552 3.3 33.5 1.0 CB A:CYS555 3.3 37.1 1.0 N A:CYS555 3.7 39.7 1.0 CA A:CYS555 4.1 44.6 1.0 CG A:HIS573 4.1 33.1 1.0 ND1 A:HIS568 4.1 33.0 1.0 CG A:HIS568 4.1 31.4 1.0 O A:HOH848 4.2 53.7 1.0 ND1 A:HIS573 4.2 33.2 1.0 CB A:ALA554 4.3 42.5 1.0 C A:ALA554 4.6 52.6 1.0 CA A:CYS552 4.7 36.6 1.0 C A:CYS555 4.7 47.9 1.0 CA A:ALA554 4.8 45.8 1.0 CG1 A:VAL572 4.9 43.0 1.0 N A:GLY556 4.9 33.8 1.0 N A:ALA554 4.9 39.5 1.0 CB A:LYS557 5.0 32.4 1.0 C A:CYS552 5.0 43.5 1.0

E.N.Nikolova, R.L.Stanfield, H.J.Dyson, P.E.Wright. A Conformational Switch at the Zinc Finger Protein Kaiso Directs Recognitions of Specific and Methylated Dna To Be Published.