Zinc in PDB 6dfb: Kaiso (ZBTB33) K539A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs)

The structure of Kaiso (ZBTB33) K539A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs), PDB code: 6dfb 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)	42.20 / 1.66
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	44.467, 184.271, 105.188, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.2

The structure of Kaiso (ZBTB33) K539A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Kaiso (ZBTB33) K539A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) (pdb code 6dfb). 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) K539A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs), PDB code: 6dfb:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Kaiso (ZBTB33) K539A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Kaiso (ZBTB33) K539A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:40.1 occ:1.00 NE2 A:HIS516 2.0 47.0 1.0 NE2 A:HIS512 2.0 34.8 1.0 SG A:CYS499 2.2 45.6 1.0 SG A:CYS496 2.3 47.5 1.0 CD2 A:HIS516 2.9 49.1 1.0 CE1 A:HIS512 3.0 43.1 1.0 CD2 A:HIS512 3.1 43.0 1.0 CE1 A:HIS516 3.1 50.4 1.0 CB A:CYS496 3.2 39.3 1.0 CB A:CYS499 3.3 55.5 1.0 N A:CYS499 3.7 55.0 1.0 CA A:CYS499 4.0 56.0 1.0 CG A:HIS516 4.1 48.6 1.0 ND1 A:HIS512 4.1 39.7 1.0 ND1 A:HIS516 4.2 51.7 1.0 CG A:HIS512 4.2 39.5 1.0 CB A:VAL498 4.4 53.8 1.0 CA A:CYS496 4.6 42.3 1.0 C A:VAL498 4.7 61.2 1.0 C A:CYS499 4.7 58.2 1.0 N A:LYS500 4.8 53.3 1.0 CB A:ARG501 4.9 39.4 1.0 CG1 A:VAL498 4.9 55.2 1.0 CA A:VAL498 4.9 55.9 1.0 CD1 A:PHE513 4.9 46.0 1.0 N A:VAL498 5.0 58.9 1.0

Zinc binding site 2 out of 3 in the Kaiso (ZBTB33) K539A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Kaiso (ZBTB33) K539A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:34.7 occ:1.00 NE2 A:HIS540 2.0 35.4 1.0 NE2 A:HIS544 2.1 34.0 1.0 SG A:CYS524 2.2 33.1 1.0 SG A:CYS527 2.2 41.1 1.0 CD2 A:HIS544 2.9 33.9 1.0 CD2 A:HIS540 2.9 32.2 1.0 CE1 A:HIS540 3.1 44.5 1.0 CB A:CYS524 3.2 37.4 1.0 CE1 A:HIS544 3.2 39.0 1.0 CB A:CYS527 3.3 48.8 1.0 N A:CYS527 3.6 42.4 1.0 CA A:CYS527 3.9 43.2 1.0 CG A:HIS544 4.1 31.3 1.0 CG A:HIS540 4.1 31.7 1.0 ND1 A:HIS540 4.1 39.4 1.0 O A:HOH882 4.2 71.6 1.0 ND1 A:HIS544 4.2 36.2 1.0 C A:TYR526 4.3 45.5 1.0 C A:CYS527 4.5 45.0 1.0 CB A:TYR526 4.5 36.9 1.0 CA A:CYS524 4.6 36.1 1.0 O A:HOH876 4.7 65.6 1.0 CB A:LYS529 4.7 48.1 1.0 O A:CYS527 4.7 52.8 1.0 CA A:TYR526 4.8 45.1 1.0 N A:TYR526 4.8 42.2 1.0

Zinc binding site 3 out of 3 in the Kaiso (ZBTB33) K539A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Kaiso (ZBTB33) K539A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:26.3 occ:1.00 NE2 A:HIS573 2.0 24.5 1.0 NE2 A:HIS568 2.1 28.3 1.0 SG A:CYS555 2.2 27.0 1.0 SG A:CYS552 2.3 26.9 1.0 CD2 A:HIS573 2.9 32.6 1.0 CE1 A:HIS568 3.1 26.8 1.0 CD2 A:HIS568 3.1 22.6 1.0 CE1 A:HIS573 3.1 24.9 1.0 CB A:CYS552 3.3 23.2 1.0 CB A:CYS555 3.3 28.9 1.0 N A:CYS555 3.7 32.0 1.0 CA A:CYS555 4.0 28.1 1.0 CG A:HIS573 4.1 25.5 1.0 ND1 A:HIS568 4.2 25.6 1.0 ND1 A:HIS573 4.2 26.6 1.0 CG A:HIS568 4.2 24.0 1.0 O A:HOH899 4.4 44.9 1.0 CB A:ALA554 4.4 33.0 1.0 C A:ALA554 4.5 41.6 1.0 C A:CYS555 4.7 29.6 1.0 CA A:CYS552 4.7 22.2 1.0 N A:GLY556 4.8 26.4 1.0 CA A:ALA554 4.8 35.1 1.0 N A:ALA554 4.9 30.8 1.0 CB A:LYS557 5.0 29.1 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.