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Zinc in PDB 6dfa: Kaiso (ZBTB33) E535A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs)

Protein crystallography data

The structure of Kaiso (ZBTB33) E535A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs), PDB code: 6dfa 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) 45.48 / 1.91
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 44.372, 183.587, 104.706, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.3

Other elements in 6dfa:

The structure of Kaiso (ZBTB33) E535A 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) E535A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs) (pdb code 6dfa). 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) E535A Zinc Finger Dna Binding Domain in Complex with the Specific Kaiso Binding Sequence (Kbs), PDB code: 6dfa:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6dfa

Go back to Zinc Binding Sites List in 6dfa
Zinc binding site 1 out of 3 in the Kaiso (ZBTB33) E535A 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) E535A 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:45.9
occ:1.00
NE2 A:HIS516 2.0 47.8 1.0
NE2 A:HIS512 2.1 39.4 1.0
SG A:CYS499 2.2 50.3 1.0
SG A:CYS496 2.4 57.0 1.0
CD2 A:HIS516 2.8 52.4 1.0
CE1 A:HIS512 3.1 42.6 1.0
CD2 A:HIS512 3.1 48.3 1.0
CE1 A:HIS516 3.1 51.6 1.0
CB A:CYS496 3.2 45.6 1.0
CB A:CYS499 3.5 52.1 1.0
N A:CYS499 3.7 59.8 1.0
CG A:HIS516 4.0 51.8 1.0
ND1 A:HIS516 4.1 53.6 1.0
CA A:CYS499 4.2 58.5 1.0
ND1 A:HIS512 4.2 37.9 1.0
CG A:HIS512 4.2 42.0 1.0
CB A:VAL498 4.4 60.8 1.0
CA A:CYS496 4.6 46.7 1.0
C A:VAL498 4.7 66.8 1.0
N A:VAL498 4.8 54.7 1.0
N A:LYS500 4.8 54.1 1.0
C A:CYS499 4.8 60.0 1.0
CA A:VAL498 4.9 63.6 1.0
CD1 A:PHE513 5.0 57.5 1.0

Zinc binding site 2 out of 3 in 6dfa

Go back to Zinc Binding Sites List in 6dfa
Zinc binding site 2 out of 3 in the Kaiso (ZBTB33) E535A 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) E535A 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:44.8
occ:1.00
NE2 A:HIS544 2.1 42.3 1.0
NE2 A:HIS540 2.1 45.7 1.0
SG A:CYS524 2.1 42.4 1.0
SG A:CYS527 2.3 56.3 1.0
CD2 A:HIS544 2.9 38.9 1.0
CD2 A:HIS540 2.9 37.4 1.0
CE1 A:HIS540 3.1 44.0 1.0
CE1 A:HIS544 3.1 44.4 1.0
CB A:CYS524 3.2 53.4 1.0
CB A:CYS527 3.3 51.1 1.0
N A:CYS527 3.8 59.2 1.0
CA A:CYS527 4.0 58.8 1.0
CG A:HIS540 4.1 41.2 1.0
CG A:HIS544 4.1 45.9 1.0
ND1 A:HIS540 4.2 42.8 1.0
ND1 A:HIS544 4.2 46.2 1.0
C A:TYR526 4.4 56.9 1.0
CB A:TYR526 4.5 51.2 1.0
C A:CYS527 4.6 66.8 1.0
CA A:CYS524 4.7 51.3 1.0
CB A:LYS529 4.8 58.3 1.0
CA A:TYR526 4.8 56.4 1.0
N A:TYR526 4.8 55.7 1.0
O A:CYS527 4.9 63.6 1.0
NZ A:LYS529 4.9 95.1 1.0

Zinc binding site 3 out of 3 in 6dfa

Go back to Zinc Binding Sites List in 6dfa
Zinc binding site 3 out of 3 in the Kaiso (ZBTB33) E535A 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) E535A 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:30.8
occ:1.00
NE2 A:HIS568 2.0 30.7 1.0
NE2 A:HIS573 2.1 25.1 1.0
SG A:CYS552 2.2 30.6 1.0
SG A:CYS555 2.3 30.8 1.0
CD2 A:HIS573 2.9 22.4 1.0
CD2 A:HIS568 3.0 25.0 1.0
CE1 A:HIS568 3.0 33.8 1.0
CE1 A:HIS573 3.2 27.3 1.0
CB A:CYS552 3.2 27.0 1.0
CB A:CYS555 3.3 30.9 1.0
N A:CYS555 3.6 39.2 1.0
CA A:CYS555 4.0 36.7 1.0
CG A:HIS573 4.1 27.0 1.0
ND1 A:HIS568 4.1 30.1 1.0
CG A:HIS568 4.2 28.2 1.0
ND1 A:HIS573 4.3 28.3 1.0
CB A:ALA554 4.3 37.0 1.0
O A:HOH869 4.3 47.9 1.0
C A:ALA554 4.5 47.6 1.0
CA A:CYS552 4.7 31.8 1.0
C A:CYS555 4.7 40.9 1.0
N A:GLY556 4.8 30.6 1.0
CA A:ALA554 4.8 40.2 1.0
N A:ALA554 4.9 32.5 1.0
C A:CYS552 5.0 35.1 1.0
N A:LYS557 5.0 28.8 1.0
CB A:LYS557 5.0 32.6 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: Wed Dec 16 11:39:57 2020

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