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Zinc in PDB 6df5: Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs)

Protein crystallography data

The structure of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs), PDB code: 6df5 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) 45.49 / 1.82
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 44.430, 184.580, 104.570, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24.1

Other elements in 6df5:

The structure of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) 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 the Specific Kaiso Binding Sequence (Kbs) (pdb code 6df5). 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 the Specific Kaiso Binding Sequence (Kbs), PDB code: 6df5:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6df5

Go back to Zinc Binding Sites List in 6df5
Zinc binding site 1 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with 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 the Specific Kaiso Binding Sequence (Kbs) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:45.8
occ:1.00
NE2 A:HIS516 2.0 51.5 1.0
NE2 A:HIS512 2.1 45.2 1.0
SG A:CYS499 2.2 49.3 1.0
SG A:CYS496 2.4 60.6 1.0
CD2 A:HIS516 2.7 57.4 1.0
CD2 A:HIS512 3.1 48.2 1.0
CE1 A:HIS512 3.1 43.3 1.0
CB A:CYS496 3.2 50.8 1.0
CE1 A:HIS516 3.2 52.6 1.0
CB A:CYS499 3.4 52.6 1.0
N A:CYS499 3.6 57.1 1.0
CG A:HIS516 4.0 55.5 1.0
CA A:CYS499 4.1 59.0 1.0
ND1 A:HIS516 4.2 56.4 1.0
ND1 A:HIS512 4.2 41.2 1.0
CG A:HIS512 4.2 42.0 1.0
CB A:VAL498 4.5 65.7 1.0
CA A:CYS496 4.7 52.7 1.0
C A:VAL498 4.7 68.6 1.0
CD1 A:PHE513 4.8 54.1 1.0
C A:CYS499 4.8 58.4 1.0
CG1 A:VAL498 4.9 63.2 1.0
N A:VAL498 4.9 60.3 1.0
N A:LYS500 4.9 55.5 1.0
CA A:VAL498 4.9 61.4 1.0

Zinc binding site 2 out of 3 in 6df5

Go back to Zinc Binding Sites List in 6df5
Zinc binding site 2 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with 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 the Specific Kaiso Binding Sequence (Kbs) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:40.9
occ:1.00
NE2 A:HIS544 2.1 40.6 1.0
NE2 A:HIS540 2.1 46.0 1.0
SG A:CYS524 2.1 41.6 1.0
SG A:CYS527 2.3 56.9 1.0
CD2 A:HIS544 2.9 38.5 1.0
CD2 A:HIS540 2.9 37.2 1.0
CB A:CYS524 3.1 43.4 1.0
CE1 A:HIS544 3.2 42.2 1.0
CE1 A:HIS540 3.2 39.8 1.0
CB A:CYS527 3.3 49.0 1.0
N A:CYS527 3.6 53.7 1.0
CA A:CYS527 4.0 61.2 1.0
CG A:HIS544 4.1 45.5 1.0
CG A:HIS540 4.1 45.6 1.0
ND1 A:HIS544 4.2 42.2 1.0
ND1 A:HIS540 4.2 45.4 1.0
C A:TYR526 4.5 49.2 1.0
C A:CYS527 4.5 61.3 1.0
CA A:CYS524 4.6 44.0 1.0
CB A:TYR526 4.6 44.8 1.0
CB A:LYS529 4.7 48.4 1.0
O A:CYS527 4.8 62.7 1.0
N A:TYR526 4.8 59.7 1.0
CA A:TYR526 4.9 54.4 1.0

Zinc binding site 3 out of 3 in 6df5

Go back to Zinc Binding Sites List in 6df5
Zinc binding site 3 out of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with 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 the Specific Kaiso Binding Sequence (Kbs) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:29.3
occ:1.00
NE2 A:HIS573 2.1 29.4 1.0
SG A:CYS552 2.1 24.3 1.0
NE2 A:HIS568 2.1 27.9 1.0
SG A:CYS555 2.3 30.7 1.0
CD2 A:HIS573 2.8 29.3 1.0
CD2 A:HIS568 3.0 25.1 1.0
CE1 A:HIS568 3.2 32.6 1.0
CE1 A:HIS573 3.2 29.8 1.0
CB A:CYS552 3.2 25.1 1.0
CB A:CYS555 3.3 35.1 1.0
N A:CYS555 3.7 44.7 1.0
CG A:HIS573 4.0 33.1 1.0
CA A:CYS555 4.1 36.0 1.0
CG A:HIS568 4.2 26.7 1.0
ND1 A:HIS573 4.2 31.8 1.0
ND1 A:HIS568 4.2 29.3 1.0
CB A:ALA554 4.4 40.8 1.0
C A:ALA554 4.4 47.1 1.0
CA A:CYS552 4.6 25.8 1.0
C A:CYS555 4.8 34.8 1.0
CA A:ALA554 4.8 45.0 1.0
N A:ALA554 4.8 41.0 1.0
N A:GLY556 4.9 27.6 1.0
CB A:LYS557 4.9 25.4 1.0
C A:CYS552 5.0 34.2 1.0

Reference:

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.
Page generated: Mon Oct 28 19:28:55 2024

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