Bromine in PDB 7xkm: Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions

The structure of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions, PDB code: 7xkm was solved by J.Kondo, A.Ono, T.Atsugi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.96 / 2.79
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	77.461, 77.461, 123.722, 90, 90, 120
R / Rfree (%)	18.7 / 21.7

The structure of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions also contains other interesting chemical elements:

Silver

(Ag)

23 atoms

The binding sites of Bromine atom in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions (pdb code 7xkm). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions, PDB code: 7xkm:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Br6 b:75.1 occ:1.00 BR A:BRU6 0.0 75.1 1.0 C5 A:BRU6 1.9 35.6 1.0 C6 A:BRU6 2.9 39.2 1.0 C4 A:BRU6 3.0 37.9 1.0 O4 A:BRU6 3.2 35.0 1.0 N4 A:DC7 3.6 41.2 1.0 C6 A:DC5 3.9 37.9 1.0 C2' A:DC5 4.0 46.4 1.0 C4 A:DC7 4.2 42.8 1.0 C5 A:DC5 4.2 38.2 1.0 N1 A:BRU6 4.3 43.3 1.0 N3 A:BRU6 4.3 36.9 1.0 N1 A:DC5 4.3 35.9 1.0 C5 A:DC7 4.4 41.4 1.0 C1' A:DC5 4.7 41.9 1.0 C2 A:BRU6 4.8 40.1 1.0 C4 A:DC5 4.9 35.3 1.0 C2 A:DC5 5.0 38.2 1.0

Bromine binding site 2 out of 8 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Br8 b:85.3 occ:1.00 BR A:BRU8 0.0 85.3 1.0 C5 A:BRU8 1.9 44.6 1.0 C6 A:BRU8 2.9 43.6 1.0 C4 A:BRU8 2.9 45.9 1.0 O4 A:BRU8 3.1 50.5 1.0 C2' A:DC7 3.5 47.9 1.0 C6 A:DC7 3.7 41.3 1.0 N4 A:DC9 4.0 49.0 1.0 N1 A:DC7 4.1 43.2 1.0 OP2 A:BRU8 4.2 49.0 1.0 C5 A:DC7 4.2 41.4 1.0 N1 A:BRU8 4.3 39.1 1.0 N3 A:BRU8 4.3 38.6 1.0 C1' A:DC7 4.3 43.3 1.0 C4 A:DC9 4.6 40.4 1.0 C3' A:DC7 4.8 47.8 1.0 C2 A:BRU8 4.8 38.6 1.0 C2 A:DC7 4.9 41.4 1.0 C4 A:DC7 4.9 42.8 1.0 C5 A:DC9 5.0 43.0 1.0

Bromine binding site 3 out of 8 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Br6 b:65.1 occ:1.00 BR B:BRU6 0.0 65.1 1.0 C5 B:BRU6 1.9 43.0 1.0 C6 B:BRU6 2.9 42.3 1.0 C4 B:BRU6 3.0 40.4 1.0 O4 B:BRU6 3.2 44.1 1.0 N4 B:DC7 3.7 39.4 1.0 C2' B:DC5 4.0 43.8 1.0 C6 B:DC5 4.2 39.2 1.0 N1 B:BRU6 4.3 39.8 1.0 N3 B:BRU6 4.3 36.5 1.0 C4 B:DC7 4.3 40.8 1.0 N1 B:DC5 4.5 40.4 1.0 C5 B:DC5 4.5 38.5 1.0 C5 B:DC7 4.6 39.5 1.0 OP2 B:BRU6 4.7 43.0 1.0 C2 B:BRU6 4.8 37.6 1.0 C1' B:DC5 4.9 42.9 1.0

Bromine binding site 4 out of 8 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Br8 b:67.1 occ:1.00 BR B:BRU8 0.0 67.1 1.0 C5 B:BRU8 1.9 38.4 1.0 C6 B:BRU8 3.0 40.0 1.0 C4 B:BRU8 3.0 37.9 1.0 O4 B:BRU8 3.2 38.5 1.0 C6 B:DC7 3.7 39.9 1.0 C5 B:DC7 3.9 39.5 1.0 N1 B:DC7 4.1 35.2 1.0 C2' B:DC7 4.1 42.6 1.0 N1 B:BRU8 4.3 36.3 1.0 N3 B:BRU8 4.3 34.1 1.0 N4 B:DC9 4.4 35.8 1.0 C4 B:DC7 4.4 40.8 1.0 C2 B:DC7 4.6 31.7 1.0 C1' B:DC7 4.6 38.2 1.0 N3 B:DC7 4.8 35.9 1.0 C2 B:BRU8 4.8 35.4 1.0

Bromine binding site 5 out of 8 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Br6 b:72.6 occ:1.00 BR C:BRU6 0.0 72.6 1.0 C5 C:BRU6 2.0 46.7 1.0 C4 C:BRU6 3.0 47.4 1.0 C6 C:BRU6 3.0 42.7 1.0 O4 C:BRU6 3.1 46.1 1.0 N4 C:DC7 3.8 46.7 1.0 C6 C:DC5 3.8 41.8 1.0 C5 C:DC5 4.0 40.3 1.0 C2' C:DC5 4.1 39.7 1.0 N3 C:BRU6 4.3 41.3 1.0 N1 C:BRU6 4.3 45.8 1.0 N1 C:DC5 4.4 41.8 1.0 C4 C:DC7 4.4 44.3 1.0 C5 C:DC7 4.7 42.0 1.0 C4 C:DC5 4.8 41.6 1.0 C2 C:BRU6 4.9 42.9 1.0 C1' C:DC5 4.9 42.3 1.0

Bromine binding site 6 out of 8 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Br8 b:85.1 occ:1.00 BR C:BRU8 0.0 85.1 1.0 C5 C:BRU8 2.0 45.9 1.0 C6 C:BRU8 3.0 46.2 1.0 C4 C:BRU8 3.0 47.7 1.0 O4 C:BRU8 3.2 52.3 1.0 C6 C:DC7 4.0 43.4 1.0 C5 C:DC7 4.1 42.0 1.0 N4 C:DC9 4.2 49.9 1.0 C2' C:DC7 4.3 44.1 1.0 N1 C:BRU8 4.4 43.5 1.0 N3 C:BRU8 4.4 43.7 1.0 N1 C:DC7 4.4 45.5 1.0 C4 C:DC7 4.7 44.3 1.0 C4 C:DC9 4.7 47.6 1.0 C5 C:DC9 4.8 45.6 1.0 C2 C:BRU8 4.9 45.7 1.0 C1' C:DC7 5.0 45.4 1.0 C2 C:DC7 5.0 43.0 1.0

Bromine binding site 7 out of 8 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range: probe atom residue distance (Å) B Occ D:Br6 b:62.9 occ:1.00 BR D:BRU6 0.0 62.9 1.0 C5 D:BRU6 2.0 40.6 1.0 C6 D:BRU6 3.0 38.5 1.0 C4 D:BRU6 3.0 38.2 1.0 O4 D:BRU6 3.2 42.6 1.0 O C:HOH202 3.3 30.4 1.0 N4 D:DC7 3.6 38.4 1.0 C6 D:DC5 3.9 40.3 1.0 C5 D:DC5 4.1 41.4 1.0 C2' D:DC5 4.1 46.0 1.0 N1 D:BRU6 4.3 38.6 1.0 N3 D:BRU6 4.3 37.6 1.0 N1 D:DC5 4.4 38.8 1.0 C4 D:DC7 4.4 39.3 1.0 C5 D:DC7 4.7 44.0 1.0 C4 D:DC5 4.7 41.0 1.0 C1' D:DC5 4.9 40.8 1.0 C2 D:BRU6 4.9 38.6 1.0

Bromine binding site 8 out of 8 in the Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of Dna-Ag(I) Rod Comprising A One-Dimensional Array of 11 Silver Ions within 5.0Å range: probe atom residue distance (Å) B Occ D:Br8 b:72.3 occ:1.00 BR D:BRU8 0.0 72.3 1.0 C5 D:BRU8 2.0 41.5 1.0 C6 D:BRU8 2.9 39.2 1.0 C4 D:BRU8 3.1 39.3 1.0 O4 D:BRU8 3.4 41.0 1.0 C6 D:DC7 3.8 41.9 1.0 C5 D:DC7 3.9 44.0 1.0 N4 D:DC9 4.0 36.9 1.0 C2' D:DC7 4.2 37.4 1.0 N1 D:BRU8 4.3 40.1 1.0 N1 D:DC7 4.3 40.9 1.0 N3 D:BRU8 4.4 32.5 1.0 C4 D:DC9 4.5 35.8 1.0 C4 D:DC7 4.6 39.3 1.0 C5 D:DC9 4.6 35.7 1.0 C1' D:DC7 4.8 42.0 1.0 C2 D:BRU8 4.9 39.0 1.0 C2 D:DC7 4.9 37.8 1.0

T.Atsugi, A.Ono, M.Tasaka, N.Eguchi, S.Fujiwara, J.Kondo. A Novel Ag I -Dna Rod Comprising A One-Dimensional Array of 11 Silver Ions Within A Double Helical Structure. Angew.Chem.Int.Ed.Engl. V. 61 04798 2022.
ISSN: ESSN 1521-3773
PubMed: 35641885
DOI: 10.1002/ANIE.202204798