Zinc in PDB 5vmv: Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with Its Double Cpg-Methylated Dna Consensus Binding Site

The structure of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with Its Double Cpg-Methylated Dna Consensus Binding Site, PDB code: 5vmv 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)	45.44 / 2.31
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	44.219, 183.792, 104.566, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.7

The structure of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with Its Double Cpg-Methylated Dna Consensus Binding Site 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 Its Double Cpg-Methylated Dna Consensus Binding Site (pdb code 5vmv). 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 Its Double Cpg-Methylated Dna Consensus Binding Site, PDB code: 5vmv:
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 Its Double Cpg-Methylated Dna Consensus Binding Site


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 Its Double Cpg-Methylated Dna Consensus Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:57.6 occ:1.00 NE2 A:HIS516 1.9 59.8 1.0 NE2 A:HIS512 2.0 77.5 1.0 SG A:CYS499 2.2 52.0 1.0 SG A:CYS496 2.3 69.9 1.0 CD2 A:HIS516 2.7 61.5 1.0 CE1 A:HIS512 2.9 52.8 1.0 CD2 A:HIS512 3.0 65.4 1.0 CE1 A:HIS516 3.1 64.0 1.0 CB A:CYS496 3.3 58.0 1.0 CB A:CYS499 3.3 64.0 1.0 N A:CYS499 3.7 62.7 1.0 CG A:HIS516 4.0 62.7 1.0 ND1 A:HIS512 4.0 61.3 1.0 CA A:CYS499 4.0 53.9 1.0 CG A:HIS512 4.1 54.5 1.0 ND1 A:HIS516 4.1 66.2 1.0 CB A:VAL498 4.4 67.4 1.0 CA A:CYS496 4.7 67.0 1.0 C A:VAL498 4.7 64.6 1.0 C A:CYS499 4.7 56.1 1.0 CG1 A:VAL498 4.8 65.0 1.0 CD1 A:PHE513 4.8 73.8 1.0 CB A:ARG501 4.9 60.8 1.0 CA A:VAL498 4.9 57.7 1.0

Zinc binding site 2 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with Its Double Cpg-Methylated Dna Consensus Binding Site


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 Its Double Cpg-Methylated Dna Consensus Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:40.6 occ:1.00 NE2 A:HIS540 2.0 37.4 1.0 NE2 A:HIS544 2.1 54.3 1.0 O A:HOH803 2.2 33.2 1.0 SG A:CYS524 2.2 45.3 1.0 SG A:CYS527 2.3 53.4 1.0 CD2 A:HIS540 2.8 36.8 1.0 CD2 A:HIS544 2.8 36.1 1.0 CB A:CYS524 3.0 55.9 1.0 CE1 A:HIS540 3.2 36.7 1.0 CE1 A:HIS544 3.3 50.4 1.0 CB A:CYS527 3.4 51.0 1.0 N A:CYS527 3.6 50.1 1.0 CG A:HIS540 4.0 36.3 1.0 CA A:CYS527 4.0 56.6 1.0 CG A:HIS544 4.1 46.8 1.0 ND1 A:HIS540 4.2 37.8 1.0 C A:TYR526 4.2 64.9 1.0 ND1 A:HIS544 4.2 42.6 1.0 CB A:TYR526 4.3 50.1 1.0 C A:CYS527 4.5 65.5 1.0 CA A:CYS524 4.5 60.3 1.0 N A:TYR526 4.6 53.7 1.0 CA A:TYR526 4.6 56.4 1.0 O A:CYS527 4.7 54.5 1.0 CB A:LYS529 4.8 53.6 1.0 C A:CYS524 5.0 50.9 1.0 O A:TYR526 5.0 70.7 1.0

Zinc binding site 3 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with Its Double Cpg-Methylated Dna Consensus Binding Site


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 Its Double Cpg-Methylated Dna Consensus Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn703 b:30.6 occ:1.00 NE2 A:HIS568 1.9 27.0 1.0 NE2 A:HIS573 2.0 34.6 1.0 SG A:CYS552 2.3 29.2 1.0 SG A:CYS555 2.3 35.5 1.0 CD2 A:HIS573 2.8 37.6 1.0 CD2 A:HIS568 2.9 20.4 1.0 CE1 A:HIS568 2.9 30.7 1.0 CE1 A:HIS573 3.2 31.8 1.0 CB A:CYS552 3.2 28.0 1.0 CB A:CYS555 3.5 29.6 1.0 N A:CYS555 3.8 41.3 1.0 ND1 A:HIS568 4.0 29.0 1.0 CG A:HIS573 4.0 40.4 1.0 CG A:HIS568 4.1 29.2 1.0 CA A:CYS555 4.2 37.8 1.0 ND1 A:HIS573 4.2 40.3 1.0 CB A:ALA554 4.3 35.6 1.0 C A:ALA554 4.5 45.0 1.0 CA A:CYS552 4.6 31.1 1.0 N A:GLY556 4.7 31.2 1.0 C A:CYS555 4.8 38.8 1.0 CA A:ALA554 4.8 38.0 1.0 N A:ALA554 4.8 40.2 1.0 C A:CYS552 4.9 35.6 1.0 CB A:LYS557 5.0 35.4 1.0 CG1 A:VAL572 5.0 23.8 1.0 CG1 A:ILE569 5.0 18.9 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