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Chlorine in PDB 4xqz: Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes

Protein crystallography data

The structure of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes, PDB code: 4xqz was solved by M.Rohner, A.Medina-Molner, B.Spingler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.87 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 32.340, 35.253, 47.643, 90.00, 98.28, 90.00
R / Rfree (%) 23.1 / 30

Other elements in 4xqz:

The structure of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Copper (Cu) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes (pdb code 4xqz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes, PDB code: 4xqz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 4xqz

Go back to Chlorine Binding Sites List in 4xqz
Chlorine binding site 1 out of 7 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl103

b:23.7
occ:0.40
N4 A:DC3 2.3 30.6 1.0
CU A:CU101 2.5 34.4 1.0
CL D:CL104 2.7 25.1 0.6
N7 A:DG2 2.9 32.5 1.0
N7 D:DG2 3.0 28.3 1.0
C8 D:DG2 3.1 25.6 1.0
C4 A:DC3 3.4 29.0 1.0
O6 A:DG2 3.4 27.7 1.0
C5 A:DG2 3.4 30.1 1.0
C6 A:DG2 3.7 28.0 1.0
O3S D:MES102 3.8 27.3 1.0
C8 A:DG2 3.8 26.3 1.0
C5 A:DC3 3.8 32.4 1.0
O6 B:DG4 4.2 25.7 1.0
C5 D:DG2 4.2 25.5 1.0
N9 D:DG2 4.3 23.4 1.0
C4 A:DG2 4.5 26.6 1.0
N3 A:DC3 4.5 28.3 1.0
O B:HOH105 4.6 21.9 1.0
N9 A:DG2 4.7 30.2 1.0
O1S D:MES102 4.7 28.0 1.0
N4 B:DC3 4.8 21.3 1.0
S D:MES102 4.8 47.4 1.0
N4 D:DC3 4.8 22.2 1.0
N1 A:DG2 4.8 29.1 1.0
C5 B:DC3 4.8 25.3 1.0
C4 D:DG2 4.9 23.1 1.0

Chlorine binding site 2 out of 7 in 4xqz

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Chlorine binding site 2 out of 7 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl102

b:29.0
occ:1.00
O5' C:DC1 2.3 31.1 1.0
O B:HOH108 2.6 23.4 1.0
O5' B:DC1 2.9 24.1 1.0
CU C:CU101 3.3 27.9 1.0
C5' C:DC1 3.5 25.7 1.0
C6 B:DC1 3.6 31.1 1.0
C5' B:DC1 3.7 24.3 1.0
O6 B:DG2 3.9 25.8 1.0
N7 B:DG2 3.9 21.1 1.0
O4' B:DC1 4.0 27.4 1.0
N7 C:DG2 4.0 20.0 1.0
C6 B:DG2 4.2 27.3 1.0
C5 B:DC1 4.2 29.8 1.0
C5 B:DG2 4.3 21.9 1.0
C4' B:DC1 4.5 27.3 1.0
O6 C:DG2 4.6 22.6 1.0
N1 B:DC1 4.6 32.2 1.0
C5 C:DG2 4.7 21.7 1.0
C4' C:DC1 4.7 23.4 1.0
C1' B:DC1 4.8 29.5 1.0
C8 C:DG2 4.8 24.2 1.0
C6 C:DC1 4.8 22.6 1.0
C8 B:DG2 4.8 18.7 1.0
O4' C:DC1 4.8 19.2 1.0
C2' B:DC1 4.9 28.2 1.0
C6 C:DG2 4.9 20.6 1.0

Chlorine binding site 3 out of 7 in 4xqz

Go back to Chlorine Binding Sites List in 4xqz
Chlorine binding site 3 out of 7 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl104

b:25.1
occ:0.60
N4 D:DC3 2.6 22.2 1.0
CL A:CL103 2.7 23.7 0.4
O3S D:MES102 2.9 27.3 1.0
N7 D:DG2 3.0 28.3 1.0
CU A:CU101 3.1 34.4 1.0
O6 D:DG2 3.4 29.0 1.0
C5 D:DG2 3.5 25.5 1.0
C6 D:DG2 3.6 27.0 1.0
C4 D:DC3 3.8 23.7 1.0
C8 D:DG2 3.9 25.6 1.0
N7 A:DG2 4.1 32.5 1.0
C5 D:DC3 4.3 23.8 1.0
S D:MES102 4.3 47.4 1.0
C4 D:DG2 4.6 23.1 1.0
O6 C:DG4 4.6 20.6 1.0
C8 A:DG2 4.7 26.3 1.0
O C:HOH205 4.8 26.1 1.0
N9 D:DG2 4.8 23.4 1.0
O2S D:MES102 4.8 42.7 1.0
N1 D:DG2 4.8 28.5 1.0
O B:HOH105 4.9 21.9 1.0
N3 D:DC3 4.9 23.7 1.0
N4 A:DC3 5.0 30.6 1.0

Chlorine binding site 4 out of 7 in 4xqz

Go back to Chlorine Binding Sites List in 4xqz
Chlorine binding site 4 out of 7 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl101

b:40.5
occ:1.00
CU G:CU101 2.7 32.3 1.0
N7 F:DG2 3.1 31.8 1.0
N4 F:DC3 3.3 35.2 1.0
N7 G:DG2 3.6 26.1 1.0
N4 G:DC3 3.8 20.9 1.0
C8 F:DG2 3.8 29.9 1.0
C5 F:DG2 3.8 32.5 1.0
O F:HOH206 4.1 31.3 1.0
C8 G:DG2 4.1 26.3 1.0
O6 F:DG2 4.1 34.6 1.0
C6 F:DG2 4.2 35.9 1.0
C4 F:DC3 4.3 34.1 1.0
C5 F:DC3 4.3 35.7 1.0
CL H:CL104 4.5 32.5 1.0
C5 G:DG2 4.5 24.0 1.0
N9 F:DG2 4.7 29.0 1.0
C4 F:DG2 4.7 29.9 1.0
C4 G:DC3 4.8 22.8 1.0
O6 G:DG2 4.9 20.6 1.0
C5 G:DC3 4.9 22.8 1.0

Chlorine binding site 5 out of 7 in 4xqz

Go back to Chlorine Binding Sites List in 4xqz
Chlorine binding site 5 out of 7 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl102

b:35.6
occ:0.60
CU H:CU101 2.5 37.5 1.0
CL H:CL103 2.8 31.7 0.4
N7 H:DG6 3.4 31.3 1.0
C8 H:DG6 3.7 28.1 1.0
C5 H:DG6 4.5 29.4 1.0
N9 H:DG6 4.8 27.6 1.0

Chlorine binding site 6 out of 7 in 4xqz

Go back to Chlorine Binding Sites List in 4xqz
Chlorine binding site 6 out of 7 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl103

b:31.7
occ:0.40
CL H:CL102 2.8 35.6 0.6
CU H:CU101 3.0 37.5 1.0
N7 H:DG6 3.1 31.3 1.0
C5 H:DG6 3.3 29.4 1.0
O6 H:DG6 3.3 24.7 1.0
C6 H:DG6 3.4 24.8 1.0
C8 H:DG6 3.9 28.1 1.0
C4 H:DG6 4.1 29.1 1.0
N1 H:DG6 4.3 25.7 1.0
N9 H:DG6 4.5 27.6 1.0

Chlorine binding site 7 out of 7 in 4xqz

Go back to Chlorine Binding Sites List in 4xqz
Chlorine binding site 7 out of 7 in the Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Calcium(II) and Copper(II) Bound to the Z-Dna Form of D(Cgcgcg), Complexed By Chloride and Mes within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl104

b:32.5
occ:1.00
CU E:CU101 2.6 35.4 1.0
N7 H:DG2 2.9 26.4 1.0
N4 H:DC3 3.2 28.2 1.0
C8 H:DG2 3.6 23.5 1.0
C5 H:DG2 3.6 25.9 1.0
N7 E:DG2 3.8 31.4 1.0
O6 H:DG2 3.9 24.9 1.0
C6 H:DG2 4.1 26.3 1.0
N4 E:DC3 4.2 30.0 1.0
C8 E:DG2 4.3 23.5 1.0
C4 H:DC3 4.3 26.2 1.0
O G:HOH204 4.4 29.6 1.0
CL F:CL101 4.5 40.5 1.0
N9 H:DG2 4.6 25.8 1.0
C5 H:DC3 4.6 26.5 1.0
C4 H:DG2 4.6 23.6 1.0
C5 E:DG2 4.7 31.6 1.0
O H:HOH208 4.8 28.3 1.0

Reference:

M.Rohner, A.Medina-Molner, B.Spingler. N,N,O and N,O,N Meridional Cis Coordination of Two Guanines to Copper(II) By D(Cgcgcg)2. Inorg.Chem. V. 55 6130 2016.
ISSN: ISSN 0020-1669
PubMed: 27266259
DOI: 10.1021/ACS.INORGCHEM.6B00672
Page generated: Sat Dec 12 11:21:08 2020

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