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Zinc in PDB 4f6n: Crystal Structure of Kaiso Zinc Finger Dna Binding Protein in Complex with Methylated Cpg Site Dna

Protein crystallography data

The structure of Crystal Structure of Kaiso Zinc Finger Dna Binding Protein in Complex with Methylated Cpg Site Dna, PDB code: 4f6n was solved by B.A.Buck-Koehntop, R.L.Stanfield, D.C.Ekiert, M.A.Martinez-Yamout, H.J.Dyson, I.A.Wilson, P.E.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.00 / 2.80
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 44.049, 183.402, 230.138, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Kaiso Zinc Finger Dna Binding Protein in Complex with Methylated Cpg Site Dna (pdb code 4f6n). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Kaiso Zinc Finger Dna Binding Protein in Complex with Methylated Cpg Site Dna, PDB code: 4f6n:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4f6n

Go back to Zinc Binding Sites List in 4f6n
Zinc binding site 1 out of 3 in the Crystal Structure of Kaiso Zinc Finger Dna Binding Protein in Complex with Methylated Cpg Site Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Kaiso Zinc Finger Dna Binding Protein in Complex with Methylated Cpg Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:47.6
occ:1.00
NE2 A:HIS512 2.1 64.3 1.0
NE2 A:HIS516 2.1 70.9 1.0
SG A:CYS499 2.3 67.5 1.0
SG A:CYS496 2.3 69.7 1.0
CE1 A:HIS512 2.8 59.8 1.0
CD2 A:HIS516 2.9 70.2 1.0
CE1 A:HIS516 3.2 70.2 1.0
CD2 A:HIS512 3.2 61.0 1.0
CB A:CYS496 3.3 66.5 1.0
CB A:CYS499 3.5 69.1 1.0
N A:CYS499 3.7 71.9 1.0
ND1 A:HIS512 4.0 57.8 1.0
CG A:HIS516 4.1 71.2 1.0
CA A:CYS499 4.1 71.5 1.0
ND1 A:HIS516 4.2 71.6 1.0
CG A:HIS512 4.2 58.0 1.0
CB A:VAL498 4.5 74.2 1.0
N A:LYS500 4.7 70.7 1.0
C A:CYS499 4.7 70.9 1.0
CA A:CYS496 4.8 69.0 1.0
C A:VAL498 4.8 74.6 1.0
CD A:ARG501 5.0 59.2 1.0
CG1 A:VAL498 5.0 74.9 1.0

Zinc binding site 2 out of 3 in 4f6n

Go back to Zinc Binding Sites List in 4f6n
Zinc binding site 2 out of 3 in the Crystal Structure of Kaiso Zinc Finger Dna Binding Protein in Complex with Methylated Cpg Site Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Kaiso Zinc Finger Dna Binding Protein in Complex with Methylated Cpg Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:46.4
occ:1.00
NE2 A:HIS540 2.1 61.8 1.0
NE2 A:HIS544 2.1 64.2 1.0
SG A:CYS527 2.3 70.8 1.0
SG A:CYS524 2.3 63.6 1.0
CD2 A:HIS544 2.8 58.7 1.0
CD2 A:HIS540 2.9 56.9 1.0
CE1 A:HIS540 3.2 59.4 1.0
CE1 A:HIS544 3.2 64.8 1.0
CB A:CYS524 3.3 64.3 1.0
CB A:CYS527 3.6 74.7 1.0
N A:CYS527 3.7 73.3 1.0
CG A:HIS544 4.0 57.9 1.0
CG A:HIS540 4.1 53.6 1.0
ND1 A:HIS540 4.2 56.1 1.0
CA A:CYS527 4.2 76.7 1.0
ND1 A:HIS544 4.2 62.3 1.0
CB A:TYR526 4.4 66.8 1.0
C A:TYR526 4.4 73.6 1.0
O A:CYS527 4.7 76.0 1.0
CA A:CYS524 4.7 65.2 1.0
CA A:TYR526 4.7 71.0 1.0
C A:CYS527 4.8 78.1 1.0
N A:TYR526 4.8 70.1 1.0
CB A:LYS529 4.8 70.7 1.0

Zinc binding site 3 out of 3 in 4f6n

Go back to Zinc Binding Sites List in 4f6n
Zinc binding site 3 out of 3 in the Crystal Structure of Kaiso Zinc Finger Dna Binding Protein in Complex with Methylated Cpg Site Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Kaiso Zinc Finger Dna Binding Protein in Complex with Methylated Cpg Site Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:42.8
occ:1.00
NE2 A:HIS568 2.0 44.5 1.0
NE2 A:HIS573 2.1 49.5 1.0
SG A:CYS555 2.3 45.1 1.0
SG A:CYS552 2.3 43.2 1.0
CD2 A:HIS573 2.8 47.3 1.0
CE1 A:HIS568 3.0 43.8 1.0
CD2 A:HIS568 3.1 42.2 1.0
CE1 A:HIS573 3.2 49.8 1.0
CB A:CYS552 3.4 40.0 1.0
CB A:CYS555 3.5 46.3 1.0
N A:CYS555 3.8 46.6 1.0
CG A:HIS573 4.0 49.2 1.0
ND1 A:HIS568 4.1 43.0 1.0
CG A:HIS568 4.2 41.3 1.0
CA A:CYS555 4.2 46.5 1.0
ND1 A:HIS573 4.2 51.4 1.0
CB A:ALA554 4.3 50.1 1.0
C A:ALA554 4.6 48.9 1.0
CB A:LYS557 4.7 40.7 1.0
CA A:CYS552 4.8 39.9 1.0
CA A:ALA554 4.9 49.6 1.0
C A:CYS555 4.9 44.8 1.0
N A:ALA554 5.0 47.9 1.0

Reference:

B.A.Buck-Koehntop, R.L.Stanfield, D.C.Ekiert, M.A.Martinez-Yamout, H.J.Dyson, I.A.Wilson, P.E.Wright. Molecular Basis For Recognition of Methylated and Specific Dna Sequences By the Zinc Finger Protein Kaiso. Proc.Natl.Acad.Sci.Usa V. 109 15229 2012.
ISSN: ISSN 0027-8424
PubMed: 22949637
DOI: 10.1073/PNAS.1213726109
Page generated: Wed Dec 16 05:17:01 2020

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