Zinc in PDB 6v8u: Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs)
Protein crystallography data
The structure of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs), PDB code: 6v8u
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)
|
42.92 /
2.10
|
Space group
|
C 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.142,
183.624,
97.755,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.2 /
20.4
|
Other elements in 6v8u:
The structure of Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs) also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs)
(pdb code 6v8u). 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 A Modified Kaiso Binding Sequence (Kbs), PDB code: 6v8u:
Jump to Zinc binding site number:
1;
2;
3;
Zinc binding site 1 out
of 3 in 6v8u
Go back to
Zinc Binding Sites List in 6v8u
Zinc binding site 1 out
of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs)
![](/pictures/ZN/pdb/v8/6v8u-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/v8/6v8u-ZN-sphere_01_stereo.jpg) 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 A Modified Kaiso Binding Sequence (Kbs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn701
b:47.7
occ:1.00
|
NE2
|
A:HIS516
|
2.1
|
54.7
|
1.0
|
NE2
|
A:HIS512
|
2.1
|
49.5
|
1.0
|
SG
|
A:CYS499
|
2.2
|
48.5
|
1.0
|
SG
|
A:CYS496
|
2.3
|
56.2
|
1.0
|
CD2
|
A:HIS516
|
2.8
|
55.7
|
1.0
|
CE1
|
A:HIS512
|
3.0
|
36.4
|
1.0
|
CD2
|
A:HIS512
|
3.2
|
43.8
|
1.0
|
CE1
|
A:HIS516
|
3.2
|
56.1
|
1.0
|
CB
|
A:CYS496
|
3.3
|
40.0
|
1.0
|
CB
|
A:CYS499
|
3.4
|
56.4
|
1.0
|
N
|
A:CYS499
|
3.7
|
65.7
|
1.0
|
CG
|
A:HIS516
|
4.1
|
50.9
|
1.0
|
CA
|
A:CYS499
|
4.1
|
63.3
|
1.0
|
ND1
|
A:HIS512
|
4.1
|
44.7
|
1.0
|
ND1
|
A:HIS516
|
4.2
|
56.2
|
1.0
|
CG
|
A:HIS512
|
4.3
|
44.6
|
1.0
|
CB
|
A:VAL498
|
4.4
|
61.9
|
1.0
|
CA
|
A:CYS496
|
4.7
|
52.0
|
1.0
|
NH1
|
A:ARG501
|
4.7
|
77.2
|
1.0
|
C
|
A:VAL498
|
4.7
|
65.4
|
1.0
|
C
|
A:CYS499
|
4.8
|
56.4
|
1.0
|
N
|
A:LYS500
|
4.8
|
53.1
|
1.0
|
CG1
|
A:VAL498
|
4.8
|
58.4
|
1.0
|
N
|
A:VAL498
|
4.9
|
57.2
|
1.0
|
CA
|
A:VAL498
|
4.9
|
58.0
|
1.0
|
|
Zinc binding site 2 out
of 3 in 6v8u
Go back to
Zinc Binding Sites List in 6v8u
Zinc binding site 2 out
of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs)
![](/pictures/ZN/pdb/v8/6v8u-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/v8/6v8u-ZN-sphere_02_stereo.jpg) 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 A Modified Kaiso Binding Sequence (Kbs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn702
b:46.5
occ:1.00
|
O
|
A:HOH802
|
2.1
|
43.5
|
1.0
|
NE2
|
A:HIS540
|
2.1
|
46.5
|
1.0
|
NE2
|
A:HIS544
|
2.1
|
56.7
|
1.0
|
SG
|
A:CYS524
|
2.2
|
46.2
|
1.0
|
SG
|
A:CYS527
|
2.3
|
56.3
|
1.0
|
CD2
|
A:HIS544
|
2.9
|
42.5
|
1.0
|
CD2
|
A:HIS540
|
2.9
|
37.3
|
1.0
|
CE1
|
A:HIS540
|
3.2
|
48.5
|
1.0
|
CB
|
A:CYS524
|
3.2
|
52.5
|
1.0
|
CB
|
A:CYS527
|
3.2
|
52.8
|
1.0
|
CE1
|
A:HIS544
|
3.3
|
51.4
|
1.0
|
N
|
A:CYS527
|
3.6
|
65.3
|
1.0
|
CA
|
A:CYS527
|
3.9
|
62.5
|
1.0
|
CG
|
A:HIS540
|
4.1
|
41.9
|
1.0
|
CG
|
A:HIS544
|
4.1
|
56.9
|
1.0
|
ND1
|
A:HIS540
|
4.2
|
47.6
|
1.0
|
O
|
A:HOH850
|
4.2
|
54.4
|
1.0
|
C
|
A:TYR526
|
4.3
|
69.9
|
1.0
|
ND1
|
A:HIS544
|
4.3
|
54.1
|
1.0
|
C
|
A:CYS527
|
4.5
|
70.6
|
1.0
|
CB
|
A:TYR526
|
4.5
|
67.1
|
1.0
|
CD
|
A:LYS529
|
4.5
|
76.6
|
1.0
|
CA
|
A:CYS524
|
4.7
|
56.6
|
1.0
|
CA
|
A:TYR526
|
4.7
|
67.8
|
1.0
|
N
|
A:TYR526
|
4.8
|
60.8
|
1.0
|
O
|
A:CYS527
|
4.8
|
68.4
|
1.0
|
CB
|
A:LYS529
|
4.8
|
56.0
|
1.0
|
O
|
A:TYR526
|
4.9
|
67.8
|
1.0
|
CG
|
A:LYS529
|
5.0
|
68.7
|
1.0
|
|
Zinc binding site 3 out
of 3 in 6v8u
Go back to
Zinc Binding Sites List in 6v8u
Zinc binding site 3 out
of 3 in the Kaiso (ZBTB33) Zinc Finger Dna Binding Domain in Complex with A Modified Kaiso Binding Sequence (Kbs)
![](/pictures/ZN/pdb/v8/6v8u-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/v8/6v8u-ZN-sphere_03_stereo.jpg) 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 A Modified Kaiso Binding Sequence (Kbs) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn703
b:34.1
occ:1.00
|
NE2
|
A:HIS568
|
2.1
|
32.4
|
1.0
|
NE2
|
A:HIS573
|
2.1
|
36.7
|
1.0
|
SG
|
A:CYS552
|
2.3
|
32.4
|
1.0
|
SG
|
A:CYS555
|
2.3
|
33.9
|
1.0
|
CD2
|
A:HIS573
|
2.8
|
24.9
|
1.0
|
CD2
|
A:HIS568
|
3.0
|
27.3
|
1.0
|
CE1
|
A:HIS568
|
3.1
|
38.1
|
1.0
|
CB
|
A:CYS555
|
3.3
|
30.8
|
1.0
|
CE1
|
A:HIS573
|
3.3
|
34.8
|
1.0
|
CB
|
A:CYS552
|
3.3
|
34.1
|
1.0
|
N
|
A:CYS555
|
3.7
|
44.4
|
1.0
|
CA
|
A:CYS555
|
4.0
|
35.7
|
1.0
|
O
|
A:HOH848
|
4.1
|
59.4
|
1.0
|
CG
|
A:HIS573
|
4.1
|
40.5
|
1.0
|
ND1
|
A:HIS568
|
4.2
|
35.0
|
1.0
|
CG
|
A:HIS568
|
4.2
|
32.0
|
1.0
|
ND1
|
A:HIS573
|
4.3
|
35.6
|
1.0
|
CB
|
A:ALA554
|
4.4
|
35.6
|
1.0
|
C
|
A:ALA554
|
4.5
|
45.8
|
1.0
|
C
|
A:CYS555
|
4.7
|
47.1
|
1.0
|
N
|
A:GLY556
|
4.7
|
43.4
|
1.0
|
CA
|
A:CYS552
|
4.7
|
37.8
|
1.0
|
CA
|
A:ALA554
|
4.8
|
47.9
|
1.0
|
N
|
A:ALA554
|
4.8
|
41.6
|
1.0
|
CB
|
A:LYS557
|
5.0
|
31.1
|
1.0
|
N
|
A:LYS557
|
5.0
|
37.0
|
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 13:01:17 2020
|