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

Protein crystallography data

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

Other elements in 5vmv:

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

Zinc Binding Sites:

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 5vmv

Go back to Zinc Binding Sites List in 5vmv
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 5vmv

Go back to Zinc Binding Sites List in 5vmv
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 5vmv

Go back to Zinc Binding Sites List in 5vmv
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

Reference:

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
Page generated: Mon Oct 28 13:10:37 2024

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