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Copper 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
Chlorine (Cl) 7 atoms

Copper Binding Sites:

The binding sites of Copper 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 Copper atom.
In total 6 binding sites of Copper 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 Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 4xqz

Go back to Copper Binding Sites List in 4xqz
Copper binding site 1 out of 6 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 Copper with other atoms in the Cu 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:Cu101

b:34.4
occ:1.00
O3S D:MES102 1.9 27.3 1.0
N7 D:DG2 2.0 28.3 1.0
N7 A:DG2 2.0 32.5 1.0
O1S D:MES102 2.3 28.0 1.0
S D:MES102 2.4 47.4 1.0
CL A:CL103 2.5 23.7 0.4
C8 D:DG2 2.8 25.6 1.0
O6 A:DG2 2.8 27.7 1.0
C5 A:DG2 2.8 30.1 1.0
CL D:CL104 3.1 25.1 0.6
C6 A:DG2 3.1 28.0 1.0
C8 A:DG2 3.2 26.3 1.0
C5 D:DG2 3.2 25.5 1.0
O2S D:MES102 3.2 42.7 1.0
O6 D:DG2 3.8 29.0 1.0
C8 D:MES102 3.9 30.4 1.0
C6 D:DG2 3.9 27.0 1.0
N4 A:DC3 4.0 30.6 1.0
N9 D:DG2 4.0 23.4 1.0
C4 A:DG2 4.1 26.6 1.0
C4 D:DG2 4.2 23.1 1.0
N9 A:DG2 4.3 30.2 1.0
C5' D:DC1 4.4 24.4 1.0
N1 A:DG2 4.5 29.1 1.0
O5' D:DC1 4.9 28.2 1.0
C4 A:DC3 5.0 29.0 1.0

Copper binding site 2 out of 6 in 4xqz

Go back to Copper Binding Sites List in 4xqz
Copper binding site 2 out of 6 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 Copper with other atoms in the Cu 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:Cu101

b:27.9
occ:1.00
N7 B:DG2 1.9 21.1 1.0
N7 C:DG2 2.0 20.0 1.0
O B:HOH108 2.3 23.4 1.0
O B:HOH105 2.8 21.9 1.0
C8 B:DG2 2.8 18.7 1.0
C5 C:DG2 2.9 21.7 1.0
C8 C:DG2 3.0 24.2 1.0
O6 C:DG2 3.0 22.6 1.0
C5 B:DG2 3.1 21.9 1.0
C6 C:DG2 3.3 20.6 1.0
CL C:CL102 3.3 29.0 1.0
O6 B:DG2 3.6 25.8 1.0
C6 B:DG2 3.7 27.3 1.0
N4 C:DC3 3.8 19.0 1.0
O5' C:DC1 3.9 31.1 1.0
N9 B:DG2 4.0 20.2 1.0
C4 C:DG2 4.2 21.5 1.0
C4 B:DG2 4.2 20.6 1.0
N9 C:DG2 4.2 20.7 1.0
C5' B:DC1 4.4 24.3 1.0
O5' B:DC1 4.6 24.1 1.0
N1 C:DG2 4.7 20.0 1.0
N4 B:DC3 4.9 21.3 1.0
C4 C:DC3 4.9 23.0 1.0

Copper binding site 3 out of 6 in 4xqz

Go back to Copper Binding Sites List in 4xqz
Copper binding site 3 out of 6 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 Copper with other atoms in the Cu 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:Cu101

b:33.1
occ:1.00
N7 D:DG6 1.9 28.6 1.0
O D:HOH203 2.1 31.4 1.0
C8 D:DG6 2.9 25.7 1.0
C5 D:DG6 3.1 25.9 1.0
O6 D:DG6 3.5 24.9 1.0
C6 D:DG6 3.6 25.1 1.0
OP1 D:DC5 3.8 21.8 0.4
N9 D:DG6 4.1 24.6 1.0
C4 D:DG6 4.2 28.4 1.0
P D:DC5 4.9 20.7 0.4
N1 D:DG6 5.0 24.8 1.0

Copper binding site 4 out of 6 in 4xqz

Go back to Copper Binding Sites List in 4xqz
Copper binding site 4 out of 6 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 Copper with other atoms in the Cu 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
E:Cu101

b:35.4
occ:1.00
N7 H:DG2 2.1 26.4 1.0
N7 E:DG2 2.2 31.4 1.0
O H:HOH208 2.3 28.3 1.0
CL H:CL104 2.6 32.5 1.0
C8 H:DG2 3.1 23.5 1.0
C5 H:DG2 3.1 25.9 1.0
C8 E:DG2 3.1 23.5 1.0
C5 E:DG2 3.2 31.6 1.0
O6 H:DG2 3.3 24.9 1.0
O6 E:DG2 3.4 35.6 1.0
C6 H:DG2 3.5 26.3 1.0
C6 E:DG2 3.7 30.2 1.0
N9 H:DG2 4.2 25.8 1.0
C4 H:DG2 4.3 23.6 1.0
N4 E:DC3 4.3 30.0 1.0
N9 E:DG2 4.3 29.9 1.0
C4 E:DG2 4.4 31.4 1.0
C5' H:DC1 4.6 27.6 1.0
O5' H:DC1 4.7 30.3 1.0
N4 H:DC3 4.8 28.2 1.0
O G:HOH204 4.9 29.6 1.0
N1 H:DG2 4.9 29.9 1.0

Copper binding site 5 out of 6 in 4xqz

Go back to Copper Binding Sites List in 4xqz
Copper binding site 5 out of 6 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 Copper with other atoms in the Cu 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
G:Cu101

b:32.3
occ:1.00
N7 G:DG2 1.8 26.1 1.0
N7 F:DG2 2.0 31.8 1.0
O F:HOH206 2.6 31.3 1.0
CL F:CL101 2.7 40.5 1.0
C5 G:DG2 2.8 24.0 1.0
C8 G:DG2 2.9 26.3 1.0
C8 F:DG2 2.9 29.9 1.0
O6 G:DG2 3.0 20.6 1.0
C5 F:DG2 3.2 32.5 1.0
C6 G:DG2 3.2 22.4 1.0
O5' F:DC1 3.3 38.2 1.0
O6 F:DG2 3.6 34.6 1.0
C6 F:DG2 3.7 35.9 1.0
N4 G:DC3 3.9 20.9 1.0
C4 G:DG2 4.0 22.4 1.0
N9 G:DG2 4.1 24.6 1.0
N9 F:DG2 4.2 29.0 1.0
C4 F:DG2 4.3 29.9 1.0
C5' G:DC1 4.6 25.7 1.0
N1 G:DG2 4.6 20.5 1.0
C5' F:DC1 4.6 30.7 1.0
O G:HOH201 4.8 30.7 1.0
C4 G:DC3 4.9 22.8 1.0
N4 F:DC3 4.9 35.2 1.0

Copper binding site 6 out of 6 in 4xqz

Go back to Copper Binding Sites List in 4xqz
Copper binding site 6 out of 6 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 Copper with other atoms in the Cu 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:Cu101

b:37.5
occ:1.00
N7 H:DG6 2.0 31.3 1.0
CL H:CL102 2.5 35.6 0.6
C8 H:DG6 2.9 28.1 1.0
CL H:CL103 3.0 31.7 0.4
C5 H:DG6 3.2 29.4 1.0
O6 H:DG6 3.6 24.7 1.0
C6 H:DG6 3.7 24.8 1.0
N9 H:DG6 4.2 27.6 1.0
C4 H:DG6 4.3 29.1 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: Sun Dec 13 11:16:15 2020

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