Zinc in PDB 6v8u: Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs)

The structure of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs), PDB code: 6v8u 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)	42.92 / 2.10
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	44.142, 183.624, 97.755, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.4

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

Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs) (pdb code 6v8u). 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 A Modified Kaiso Binding Sequence (Kbs), PDB code: 6v8u:
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 A Modified 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) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:47.7 occ:1.00 NE2 A:HIS516 2.1 54.7 1.0 NE2 A:HIS512 2.1 49.5 1.0 SG A:CYS499 2.2 48.5 1.0 SG A:CYS496 2.3 56.2 1.0 CD2 A:HIS516 2.8 55.7 1.0 CE1 A:HIS512 3.0 36.4 1.0 CD2 A:HIS512 3.2 43.8 1.0 CE1 A:HIS516 3.2 56.1 1.0 CB A:CYS496 3.3 40.0 1.0 CB A:CYS499 3.4 56.4 1.0 N A:CYS499 3.7 65.7 1.0 CG A:HIS516 4.1 50.9 1.0 CA A:CYS499 4.1 63.3 1.0 ND1 A:HIS512 4.1 44.7 1.0 ND1 A:HIS516 4.2 56.2 1.0 CG A:HIS512 4.3 44.6 1.0 CB A:VAL498 4.4 61.9 1.0 CA A:CYS496 4.7 52.0 1.0 NH1 A:ARG501 4.7 77.2 1.0 C A:VAL498 4.7 65.4 1.0 C A:CYS499 4.8 56.4 1.0 N A:LYS500 4.8 53.1 1.0 CG1 A:VAL498 4.8 58.4 1.0 N A:VAL498 4.9 57.2 1.0 CA A:VAL498 4.9 58.0 1.0

Zinc binding site 2 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified 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) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:46.5 occ:1.00 O A:HOH802 2.1 43.5 1.0 NE2 A:HIS540 2.1 46.5 1.0 NE2 A:HIS544 2.1 56.7 1.0 SG A:CYS524 2.2 46.2 1.0 SG A:CYS527 2.3 56.3 1.0 CD2 A:HIS544 2.9 42.5 1.0 CD2 A:HIS540 2.9 37.3 1.0 CE1 A:HIS540 3.2 48.5 1.0 CB A:CYS524 3.2 52.5 1.0 CB A:CYS527 3.2 52.8 1.0 CE1 A:HIS544 3.3 51.4 1.0 N A:CYS527 3.6 65.3 1.0 CA A:CYS527 3.9 62.5 1.0 CG A:HIS540 4.1 41.9 1.0 CG A:HIS544 4.1 56.9 1.0 ND1 A:HIS540 4.2 47.6 1.0 O A:HOH850 4.2 54.4 1.0 C A:TYR526 4.3 69.9 1.0 ND1 A:HIS544 4.3 54.1 1.0 C A:CYS527 4.5 70.6 1.0 CB A:TYR526 4.5 67.1 1.0 CD A:LYS529 4.5 76.6 1.0 CA A:CYS524 4.7 56.6 1.0 CA A:TYR526 4.7 67.8 1.0 N A:TYR526 4.8 60.8 1.0 O A:CYS527 4.8 68.4 1.0 CB A:LYS529 4.8 56.0 1.0 O A:TYR526 4.9 67.8 1.0 CG A:LYS529 5.0 68.7 1.0

Zinc binding site 3 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified 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) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:34.1 occ:1.00 NE2 A:HIS568 2.1 32.4 1.0 NE2 A:HIS573 2.1 36.7 1.0 SG A:CYS552 2.3 32.4 1.0 SG A:CYS555 2.3 33.9 1.0 CD2 A:HIS573 2.8 24.9 1.0 CD2 A:HIS568 3.0 27.3 1.0 CE1 A:HIS568 3.1 38.1 1.0 CB A:CYS555 3.3 30.8 1.0 CE1 A:HIS573 3.3 34.8 1.0 CB A:CYS552 3.3 34.1 1.0 N A:CYS555 3.7 44.4 1.0 CA A:CYS555 4.0 35.7 1.0 O A:HOH848 4.1 59.4 1.0 CG A:HIS573 4.1 40.5 1.0 ND1 A:HIS568 4.2 35.0 1.0 CG A:HIS568 4.2 32.0 1.0 ND1 A:HIS573 4.3 35.6 1.0 CB A:ALA554 4.4 35.6 1.0 C A:ALA554 4.5 45.8 1.0 C A:CYS555 4.7 47.1 1.0 N A:GLY556 4.7 43.4 1.0 CA A:CYS552 4.7 37.8 1.0 CA A:ALA554 4.8 47.9 1.0 N A:ALA554 4.8 41.6 1.0 CB A:LYS557 5.0 31.1 1.0 N A:LYS557 5.0 37.0 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.