Zinc in PDB 7kzl: Cyclopentane Peptide Nucleic Acid in Complex with Dna
Protein crystallography data
The structure of Cyclopentane Peptide Nucleic Acid in Complex with Dna, PDB code: 7kzl
was solved by
I.Botos,
D.H.Appella,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
32.09 /
1.30
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.704,
54.704,
39.633,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.2 /
18.9
|
Other elements in 7kzl:
The structure of Cyclopentane Peptide Nucleic Acid in Complex with Dna also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Cyclopentane Peptide Nucleic Acid in Complex with Dna
(pdb code 7kzl). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Cyclopentane Peptide Nucleic Acid in Complex with Dna, PDB code: 7kzl:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 7kzl
Go back to
Zinc Binding Sites List in 7kzl
Zinc binding site 1 out
of 6 in the Cyclopentane Peptide Nucleic Acid in Complex with Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Cyclopentane Peptide Nucleic Acid in Complex with Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn102
b:16.3
occ:0.27
|
O
|
A:HOH228
|
1.9
|
24.2
|
1.0
|
O
|
A:HOH232
|
2.1
|
22.6
|
1.0
|
N7
|
A:DA5
|
2.3
|
13.5
|
1.0
|
C8
|
A:DA5
|
3.2
|
13.4
|
1.0
|
C5
|
A:DA5
|
3.3
|
11.0
|
1.0
|
O
|
A:HOH239
|
3.4
|
21.0
|
1.0
|
N6
|
A:DA5
|
3.6
|
12.2
|
1.0
|
C6
|
A:DA5
|
3.9
|
11.0
|
1.0
|
C2'
|
A:DC4
|
4.0
|
12.3
|
1.0
|
O
|
A:HOH219
|
4.1
|
27.3
|
1.0
|
N9
|
A:DA5
|
4.4
|
11.1
|
1.0
|
N1
|
A:DC4
|
4.4
|
11.3
|
1.0
|
C4
|
A:DA5
|
4.4
|
10.4
|
1.0
|
N4
|
A:DC6
|
4.4
|
10.8
|
1.0
|
C1'
|
A:DC4
|
4.6
|
12.5
|
1.0
|
C6
|
A:DC4
|
4.7
|
11.9
|
1.0
|
C2
|
A:DC4
|
4.7
|
11.7
|
1.0
|
O
|
A:HOH242
|
4.8
|
32.8
|
1.0
|
O
|
A:HOH229
|
4.9
|
29.2
|
1.0
|
|
Zinc binding site 2 out
of 6 in 7kzl
Go back to
Zinc Binding Sites List in 7kzl
Zinc binding site 2 out
of 6 in the Cyclopentane Peptide Nucleic Acid in Complex with Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Cyclopentane Peptide Nucleic Acid in Complex with Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn103
b:53.2
occ:0.69
|
O
|
A:HOH238
|
2.2
|
29.1
|
1.0
|
O
|
B:HOH232
|
3.4
|
20.6
|
1.0
|
C1'
|
A:DA7
|
4.8
|
14.2
|
1.0
|
C2'
|
A:DA7
|
4.8
|
16.6
|
1.0
|
H101
|
B:XDY5
|
4.9
|
16.5
|
1.0
|
H082
|
B:XDY5
|
4.9
|
20.3
|
1.0
|
|
Zinc binding site 3 out
of 6 in 7kzl
Go back to
Zinc Binding Sites List in 7kzl
Zinc binding site 3 out
of 6 in the Cyclopentane Peptide Nucleic Acid in Complex with Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Cyclopentane Peptide Nucleic Acid in Complex with Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn105
b:12.1
occ:1.00
|
O
|
B:HOH211
|
2.1
|
12.9
|
1.0
|
N15
|
B:XDJ6
|
2.1
|
10.8
|
1.0
|
C14
|
B:XDJ6
|
3.0
|
10.6
|
1.0
|
C17
|
B:XDJ6
|
3.0
|
10.7
|
1.0
|
H141
|
B:XDJ6
|
3.2
|
12.7
|
1.0
|
H193
|
B:XDY5
|
3.3
|
13.7
|
1.0
|
O23
|
B:XDJ6
|
3.4
|
11.3
|
1.0
|
C18
|
B:XDJ6
|
3.6
|
10.1
|
1.0
|
O
|
B:HOH201
|
3.8
|
15.7
|
1.0
|
N15
|
B:XDD7
|
4.0
|
10.6
|
1.0
|
O20
|
B:XDY5
|
4.1
|
11.9
|
1.0
|
C19
|
B:XDY5
|
4.1
|
11.4
|
1.0
|
O
|
B:HOH233
|
4.1
|
18.4
|
1.0
|
N13
|
B:XDJ6
|
4.1
|
10.6
|
1.0
|
C16
|
B:XDJ6
|
4.2
|
9.8
|
1.0
|
C16
|
B:XDY5
|
4.2
|
11.7
|
1.0
|
C17
|
B:XDY5
|
4.2
|
10.9
|
1.0
|
H191
|
B:XDD7
|
4.4
|
14.9
|
1.0
|
H191
|
B:XDY5
|
4.4
|
13.7
|
1.0
|
H141
|
B:XDD7
|
4.6
|
13.1
|
1.0
|
C14
|
B:XDD7
|
4.7
|
10.9
|
1.0
|
H192
|
B:XDY5
|
4.9
|
13.7
|
1.0
|
C17
|
B:XDD7
|
4.9
|
9.9
|
1.0
|
N19
|
B:XDJ6
|
4.9
|
10.3
|
1.0
|
C18
|
B:XDY5
|
4.9
|
10.7
|
1.0
|
N15
|
B:XDY5
|
5.0
|
11.0
|
1.0
|
|
Zinc binding site 4 out
of 6 in 7kzl
Go back to
Zinc Binding Sites List in 7kzl
Zinc binding site 4 out
of 6 in the Cyclopentane Peptide Nucleic Acid in Complex with Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Cyclopentane Peptide Nucleic Acid in Complex with Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn106
b:17.5
occ:0.69
|
ZN
|
B:ZN108
|
1.2
|
16.3
|
0.4
|
O
|
B:HOH229
|
2.0
|
30.1
|
1.0
|
O
|
B:HOH202
|
2.1
|
20.8
|
1.0
|
O
|
B:HOH247
|
2.1
|
27.5
|
1.0
|
O
|
B:HOH204
|
2.1
|
25.3
|
1.0
|
N15
|
B:XDJ1
|
2.1
|
13.9
|
1.0
|
C14
|
B:XDJ1
|
3.0
|
12.7
|
1.0
|
H141
|
B:XDJ1
|
3.0
|
15.2
|
1.0
|
C17
|
B:XDJ1
|
3.2
|
11.8
|
1.0
|
O23
|
B:XDJ1
|
3.8
|
12.6
|
1.0
|
O
|
B:HOH234
|
3.9
|
32.8
|
1.0
|
C18
|
B:XDJ1
|
3.9
|
12.4
|
1.0
|
N15
|
B:XDD2
|
4.2
|
12.5
|
1.0
|
N13
|
B:XDJ1
|
4.2
|
12.4
|
1.0
|
H191
|
B:XDD2
|
4.2
|
15.2
|
1.0
|
C16
|
B:XDJ1
|
4.3
|
12.5
|
1.0
|
H141
|
B:XDD2
|
4.8
|
14.4
|
1.0
|
C14
|
B:XDD2
|
4.8
|
12.0
|
1.0
|
O
|
B:HOH217
|
4.9
|
26.8
|
1.0
|
N19
|
B:XDD2
|
5.0
|
12.6
|
1.0
|
C17
|
B:XDD2
|
5.0
|
11.1
|
1.0
|
|
Zinc binding site 5 out
of 6 in 7kzl
Go back to
Zinc Binding Sites List in 7kzl
Zinc binding site 5 out
of 6 in the Cyclopentane Peptide Nucleic Acid in Complex with Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Cyclopentane Peptide Nucleic Acid in Complex with Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn107
b:24.9
occ:0.81
|
O
|
B:MOH102
|
2.1
|
18.2
|
1.0
|
O
|
B:MOH103
|
2.1
|
12.6
|
1.0
|
O2
|
B:EDO104
|
2.2
|
24.7
|
1.0
|
O
|
B:MOH101
|
2.4
|
40.6
|
1.0
|
C
|
B:MOH102
|
2.8
|
13.6
|
1.0
|
C
|
B:MOH103
|
2.9
|
22.4
|
1.0
|
O1
|
B:EDO104
|
2.9
|
42.4
|
1.0
|
C2
|
B:EDO104
|
2.9
|
31.4
|
1.0
|
C
|
B:MOH101
|
3.2
|
32.4
|
1.0
|
C1
|
B:EDO104
|
3.6
|
36.9
|
1.0
|
H082
|
B:XDD9
|
3.9
|
25.1
|
1.0
|
H081
|
B:XDD9
|
4.0
|
25.1
|
1.0
|
H091
|
B:XDD9
|
4.1
|
27.5
|
1.0
|
C08
|
B:XDD9
|
4.3
|
20.9
|
1.0
|
C09
|
B:XDD9
|
4.6
|
22.9
|
1.0
|
H092
|
B:XDD9
|
4.7
|
27.5
|
1.0
|
|
Zinc binding site 6 out
of 6 in 7kzl
Go back to
Zinc Binding Sites List in 7kzl
Zinc binding site 6 out
of 6 in the Cyclopentane Peptide Nucleic Acid in Complex with Dna
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Cyclopentane Peptide Nucleic Acid in Complex with Dna within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn108
b:16.3
occ:0.43
|
ZN
|
B:ZN106
|
1.2
|
17.5
|
0.7
|
O
|
B:HOH202
|
1.9
|
20.8
|
1.0
|
N15
|
B:XDJ1
|
2.3
|
13.9
|
1.0
|
O
|
B:HOH247
|
2.4
|
27.5
|
1.0
|
O
|
B:HOH229
|
2.7
|
30.1
|
1.0
|
O
|
B:HOH204
|
3.1
|
25.3
|
1.0
|
C14
|
B:XDJ1
|
3.2
|
12.7
|
1.0
|
C17
|
B:XDJ1
|
3.3
|
11.8
|
1.0
|
H141
|
B:XDJ1
|
3.3
|
15.2
|
1.0
|
O23
|
B:XDJ1
|
3.6
|
12.6
|
1.0
|
C18
|
B:XDJ1
|
3.9
|
12.4
|
1.0
|
N13
|
B:XDJ1
|
4.3
|
12.4
|
1.0
|
C16
|
B:XDJ1
|
4.4
|
12.5
|
1.0
|
O
|
B:HOH234
|
4.4
|
32.8
|
1.0
|
H191
|
B:XDD2
|
4.8
|
15.2
|
1.0
|
N15
|
B:XDD2
|
5.0
|
12.5
|
1.0
|
|
Reference:
H.Zheng,
I.Botos,
H.Nikolayevskiy,
E.E.Rastede,
M.Fouz,
D.H.Appella.
Conformational Constraints of Cyclopentane Peptide Nucleic Acids Facilitate Tunable Binding to Dna To Be Published.
Page generated: Tue Oct 29 22:35:43 2024
|