Zinc in PDB 5vmw: Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Double Cpg-Methylated Dna Resembling the Specific Kaiso Binding Sequence (Kbs)

The structure of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Double Cpg-Methylated Dna Resembling the Specific Kaiso Binding Sequence (Kbs), PDB code: 5vmw was solved by E.N.Nikolova, R.L.Stanfield, M.A.Martinez-Yamout, 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)	45.67 / 2.40
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	44.341, 184.149, 105.189, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.7

The structure of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Double Cpg-Methylated Dna Resembling 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) Zinc Finger Dna Binding Domain in Complex with A Double Cpg-Methylated Dna Resembling the Specific Kaiso Binding Sequence (Kbs) (pdb code 5vmw). 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 Double Cpg-Methylated Dna Resembling the Specific Kaiso Binding Sequence (Kbs), PDB code: 5vmw:
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 Double Cpg-Methylated Dna Resembling 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) Zinc Finger Dna Binding Domain in Complex with A Double Cpg-Methylated Dna Resembling the Specific Kaiso Binding Sequence (Kbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:63.1 occ:1.00 NE2 A:HIS516 1.9 54.5 1.0 NE2 A:HIS512 2.0 74.8 1.0 SG A:CYS499 2.2 62.3 1.0 SG A:CYS496 2.3 72.3 1.0 CD2 A:HIS516 2.8 55.3 1.0 CE1 A:HIS512 2.9 53.1 1.0 CE1 A:HIS516 3.1 63.4 1.0 CD2 A:HIS512 3.1 75.5 1.0 CB A:CYS496 3.2 52.8 1.0 CB A:CYS499 3.3 70.3 1.0 N A:CYS499 3.6 70.2 1.0 CG A:HIS516 4.0 60.7 1.0 CA A:CYS499 4.0 68.4 1.0 ND1 A:HIS512 4.0 55.6 1.0 ND1 A:HIS516 4.1 68.2 1.0 CG A:HIS512 4.2 61.0 1.0 CB A:VAL498 4.4 76.2 1.0 CA A:CYS496 4.6 67.5 1.0 C A:VAL498 4.7 78.9 1.0 C A:CYS499 4.7 73.4 1.0 CD A:ARG501 4.8 70.1 1.0 N A:LYS500 4.9 78.6 1.0 CB A:ARG501 4.9 49.4 1.0 CA A:VAL498 4.9 73.0 1.0 CD1 A:PHE513 4.9 57.0 1.0 CG1 A:VAL498 5.0 82.7 1.0 N A:VAL498 5.0 81.6 1.0

Zinc binding site 2 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Double Cpg-Methylated Dna Resembling 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) Zinc Finger Dna Binding Domain in Complex with A Double Cpg-Methylated Dna Resembling the Specific Kaiso Binding Sequence (Kbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:57.5 occ:1.00 NE2 A:HIS540 2.0 51.8 1.0 NE2 A:HIS544 2.1 64.0 1.0 SG A:CYS524 2.2 48.1 1.0 SG A:CYS527 2.3 67.8 1.0 O A:HOH816 2.6 63.8 1.0 CD2 A:HIS540 2.9 41.6 1.0 CD2 A:HIS544 2.9 57.0 1.0 CE1 A:HIS540 3.1 44.4 1.0 CB A:CYS524 3.1 67.5 1.0 CE1 A:HIS544 3.2 48.8 1.0 CB A:CYS527 3.3 57.2 1.0 N A:CYS527 3.6 63.6 1.0 CA A:CYS527 4.0 64.0 1.0 CG A:HIS540 4.1 39.4 1.0 CG A:HIS544 4.1 65.0 1.0 ND1 A:HIS540 4.1 48.9 1.0 ND1 A:HIS544 4.2 61.1 1.0 C A:TYR526 4.3 57.5 1.0 CB A:TYR526 4.3 49.5 1.0 C A:CYS527 4.5 79.3 1.0 CA A:CYS524 4.6 66.5 1.0 CA A:TYR526 4.7 52.7 1.0 N A:TYR526 4.8 65.6 1.0 CB A:LYS529 4.8 57.4 1.0 CG A:LYS529 4.9 65.6 1.0 O A:CYS527 5.0 78.8 1.0 N A:GLU528 5.0 86.2 1.0 C A:CYS524 5.0 59.1 1.0

Zinc binding site 3 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Double Cpg-Methylated Dna Resembling 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) Zinc Finger Dna Binding Domain in Complex with A Double Cpg-Methylated Dna Resembling the Specific Kaiso Binding Sequence (Kbs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:46.0 occ:1.00 NE2 A:HIS568 2.0 44.0 1.0 NE2 A:HIS573 2.1 48.3 1.0 SG A:CYS552 2.2 41.2 1.0 SG A:CYS555 2.3 53.0 1.0 CD2 A:HIS573 2.9 48.4 1.0 CE1 A:HIS568 2.9 40.6 1.0 CD2 A:HIS568 3.0 38.0 1.0 CE1 A:HIS573 3.2 43.9 1.0 CB A:CYS552 3.3 37.1 1.0 CB A:CYS555 3.4 38.3 1.0 N A:CYS555 3.9 50.8 1.0 ND1 A:HIS568 4.1 42.5 1.0 CG A:HIS573 4.1 51.1 1.0 CG A:HIS568 4.2 38.3 1.0 CA A:CYS555 4.2 46.3 1.0 ND1 A:HIS573 4.2 50.7 1.0 CB A:ALA554 4.5 37.1 1.0 C A:ALA554 4.7 50.8 1.0 CA A:CYS552 4.7 33.5 1.0 C A:CYS555 4.8 45.0 1.0 N A:GLY556 4.8 47.2 1.0 N A:ALA554 4.8 45.1 1.0 CB A:LYS557 4.9 38.7 1.0 CG1 A:VAL572 4.9 40.2 1.0 CA A:ALA554 4.9 50.8 1.0 C A:CYS552 5.0 50.5 1.0 N A:LYS557 5.0 36.0 1.0

E.N.Nikolova, R.L.Stanfield, H.J.Dyson, P.E.Wright. Ch···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated Cpg Sites By the Zinc Finger Protein Kaiso. Biochemistry V. 57 2109 2018.
ISSN: ISSN 1520-4995
PubMed: 29546986
DOI: 10.1021/ACS.BIOCHEM.8B00065