Bromine in PDB 5w1z: Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)

The structure of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4), PDB code: 5w1z was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.24 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	24.884, 32.798, 34.034, 90.25, 107.32, 111.04
R / Rfree (%)	20.7 / 23.4

The structure of Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Sodium	(Na)	4 atoms

The binding sites of Bromine atom in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4) (pdb code 5w1z). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4), PDB code: 5w1z:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


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 Inosine-Substituted Decamer Duplex Dna (I4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br8 b:48.4 occ:0.50 BR A:BRU8 0.0 48.4 0.5 C5 A:BRU8 1.8 21.9 1.0 C6 A:BRU8 2.8 20.7 1.0 C4 A:BRU8 2.8 17.2 1.0 O4 A:BRU8 2.9 19.3 1.0 O A:HOH218 3.1 23.0 1.0 O C:HOH202 3.5 33.0 1.0 O B:HOH133 3.6 31.3 1.0 O A:HOH234 3.7 25.9 1.0 O D:HOH206 3.8 27.3 1.0 O A:HOH207 3.8 29.0 1.0 C6 A:DC7 3.9 16.3 1.0 N3 A:BRU8 4.0 18.3 1.0 N1 A:BRU8 4.0 18.7 1.0 O A:HOH222 4.0 27.4 1.0 O B:HOH118 4.1 24.0 1.0 C5 A:DC7 4.1 19.0 1.0 OP1 D:DI20 4.1 24.2 1.0 N1 A:DC7 4.2 16.1 1.0 C2' A:DC7 4.2 21.1 1.0 O D:HOH222 4.2 25.8 1.0 C2 A:BRU8 4.4 18.0 1.0 C4 A:DC7 4.6 16.1 1.0 C2 A:DC7 4.6 18.0 1.0 N4 B:DC12 4.6 19.4 1.0 C1' A:DC7 4.7 17.3 1.0 O6 A:DI9 4.8 18.0 1.0 N3 A:DC7 4.9 15.8 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


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 Inosine-Substituted Decamer Duplex Dna (I4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Br18 b:49.1 occ:0.50 BR B:BRU18 0.0 49.1 0.5 C5 B:BRU18 1.8 22.6 1.0 C4 B:BRU18 2.8 19.0 1.0 C6 B:BRU18 2.8 22.1 1.0 O4 B:BRU18 2.9 17.4 1.0 O B:HOH114 3.4 27.2 1.0 O B:HOH122 3.6 33.0 1.0 O B:HOH140 3.8 28.3 1.0 C6 B:DC17 3.9 16.7 1.0 O B:HOH117 3.9 27.6 1.0 N3 B:BRU18 4.0 19.4 1.0 C5 B:DC17 4.0 17.7 1.0 N1 B:BRU18 4.0 19.4 1.0 N1 B:DC17 4.1 19.1 1.0 C2' B:DC17 4.2 22.3 1.0 O A:HOH220 4.4 24.2 1.0 C4 B:DC17 4.5 15.3 1.0 C2 B:BRU18 4.5 20.1 1.0 C2 B:DC17 4.6 18.3 1.0 N3 B:DC17 4.7 15.8 1.0 C1' B:DC17 4.7 20.1 1.0 O6 B:DI19 4.8 18.1 1.0 N4 A:DC2 4.9 17.1 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


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 Inosine-Substituted Decamer Duplex Dna (I4) within 5.0Å range: probe atom residue distance (Å) B Occ C:Br8 b:54.7 occ:0.50 BR C:BRU8 0.0 54.7 0.5 C5 C:BRU8 1.8 23.3 1.0 C4 C:BRU8 2.8 20.7 1.0 C6 C:BRU8 2.9 20.3 1.0 O4 C:BRU8 3.0 23.0 1.0 O C:HOH228 3.8 28.7 1.0 O C:HOH206 4.0 14.9 0.5 N3 C:BRU8 4.0 18.8 1.0 C6 C:DC7 4.1 16.4 1.0 N1 C:BRU8 4.1 19.2 1.0 O D:HOH220 4.2 30.4 1.0 C5 C:DC7 4.2 15.6 1.0 O C:HOH236 4.5 40.7 1.0 N4 D:DC12 4.6 18.7 1.0 C2 C:BRU8 4.6 19.2 1.0 C2' C:DC7 4.6 21.3 1.0 N1 C:DC7 4.6 17.2 1.0 O C:HOH203 4.8 33.8 1.0 C4 C:DC7 4.8 15.8 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of Inosine-Substituted Decamer Duplex Dna (I4)


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 Inosine-Substituted Decamer Duplex Dna (I4) within 5.0Å range: probe atom residue distance (Å) B Occ D:Br18 b:44.5 occ:0.50 BR D:BRU18 0.0 44.5 0.5 C5 D:BRU18 1.8 23.6 1.0 C4 D:BRU18 2.8 21.3 1.0 C6 D:BRU18 2.8 20.9 1.0 O4 D:BRU18 2.9 23.8 1.0 C6 D:DC17 3.7 16.6 1.0 C5 D:DC17 3.8 15.2 1.0 O D:HOH223 3.9 31.8 1.0 O D:HOH242 4.0 28.4 1.0 N3 D:BRU18 4.0 20.9 1.0 N1 D:BRU18 4.0 19.2 1.0 O D:HOH215 4.1 31.0 1.0 N1 D:DC17 4.3 15.1 1.0 O C:HOH220 4.3 39.4 1.0 C4 D:DC17 4.4 14.9 1.0 C2' D:DC17 4.5 21.9 1.0 C2 D:BRU18 4.5 18.4 1.0 N4 C:DC2 4.6 21.6 1.0 C2 D:DC17 4.8 15.8 1.0 N3 D:DC17 4.9 14.8 1.0 O D:HOH205 4.9 31.6 1.0 C1' D:DC17 5.0 18.9 1.0

J.P.Peters, E.A.Kowal, P.S.Pallan, M.Egli, L.J.Maher 3Rd.. Comparative Analysis of Inosine-Substituted Duplex Dna By Circular Dichroism and X-Ray Crystallography. J. Biomol. Struct. Dyn. V. 36 2753 2018.
ISSN: ESSN 1538-0254
PubMed: 28818035
DOI: 10.1080/07391102.2017.1369164