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:

Iodine (I) 1 atom

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

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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

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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

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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

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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

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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

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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: Mon Jan 25 16:48:01 2021

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