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Bromine in PDB 1iha: Structure of the Hybrid Rna/Dna R-Gcuucggc-D[Br]U in Presence of Rh(NH3)6+++

Protein crystallography data

The structure of Structure of the Hybrid Rna/Dna R-Gcuucggc-D[Br]U in Presence of Rh(NH3)6+++, PDB code: 1iha was solved by W.B.Cruse, P.Saludjian, A.Neuman, T.Prange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 1.75 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 53.800, 19.400, 50.310, 90.00, 109.90, 90.00
R / Rfree (%) 16.1 / 19.6

Other elements in 1iha:

The structure of Structure of the Hybrid Rna/Dna R-Gcuucggc-D[Br]U in Presence of Rh(NH3)6+++ also contains other interesting chemical elements:

Rhodium (Rh) 2 atoms
Chlorine (Cl) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Structure of the Hybrid Rna/Dna R-Gcuucggc-D[Br]U in Presence of Rh(NH3)6+++ (pdb code 1iha). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Structure of the Hybrid Rna/Dna R-Gcuucggc-D[Br]U in Presence of Rh(NH3)6+++, PDB code: 1iha:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in 1iha

Go back to Bromine Binding Sites List in 1iha
Bromine binding site 1 out of 3 in the Structure of the Hybrid Rna/Dna R-Gcuucggc-D[Br]U in Presence of Rh(NH3)6+++


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of the Hybrid Rna/Dna R-Gcuucggc-D[Br]U in Presence of Rh(NH3)6+++ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br9

b:21.6
occ:1.00
BR A:BRU9 0.0 21.6 1.0
C5 A:BRU9 1.9 13.6 1.0
C6 A:BRU9 2.8 13.7 1.0
C4 A:BRU9 2.9 15.4 1.0
O4 A:BRU9 3.1 18.8 1.0
OP1 A:BRU9 3.6 11.4 1.0
O A:HOH102 3.7 23.6 1.0
N1 A:BRU9 4.1 11.0 1.0
N3 A:BRU9 4.2 10.7 1.0
OP2 A:BRU9 4.4 10.9 1.0
P A:BRU9 4.4 11.5 1.0
C2 A:BRU9 4.7 12.1 1.0

Bromine binding site 2 out of 3 in 1iha

Go back to Bromine Binding Sites List in 1iha
Bromine binding site 2 out of 3 in the Structure of the Hybrid Rna/Dna R-Gcuucggc-D[Br]U in Presence of Rh(NH3)6+++


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of the Hybrid Rna/Dna R-Gcuucggc-D[Br]U in Presence of Rh(NH3)6+++ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br9

b:32.5
occ:0.50
BR B:BRU9 0.0 32.5 0.5
C4 B:BRU9 0.2 33.9 0.5
N3 B:BRU9 1.2 37.8 0.5
O4 B:BRU9 1.4 35.7 0.5
C5 B:BRU9 1.5 34.5 0.5
C5 B:BRU9 1.9 34.5 0.5
C2 B:BRU9 2.2 35.4 0.5
C6 B:BRU9 2.4 38.2 0.5
N1 B:BRU9 2.7 32.2 0.5
C6 B:BRU9 2.8 38.7 0.5
C4 B:BRU9 2.9 31.8 0.5
BR B:BRU9 3.1 34.6 0.5
O4 B:BRU9 3.1 33.5 0.5
O B:HOH156 3.2 29.6 1.0
O2 B:BRU9 3.3 33.1 0.5
C3' B:C8 3.4 59.5 1.0
C2' B:C8 3.7 43.0 1.0
O3' B:C8 3.8 44.5 1.0
N1 B:BRU9 4.1 39.9 0.5
N3 B:BRU9 4.1 38.3 0.5
C1' B:BRU9 4.2 46.8 0.5
O2' B:C8 4.3 36.7 1.0
C4' B:C8 4.6 49.7 1.0
C2 B:BRU9 4.7 37.1 0.5
O4' B:BRU9 4.7 45.4 0.5
N1 B:C8 4.9 36.9 1.0
C2 B:C8 4.9 36.6 1.0
C1' B:C8 5.0 33.6 1.0

Bromine binding site 3 out of 3 in 1iha

Go back to Bromine Binding Sites List in 1iha
Bromine binding site 3 out of 3 in the Structure of the Hybrid Rna/Dna R-Gcuucggc-D[Br]U in Presence of Rh(NH3)6+++


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of the Hybrid Rna/Dna R-Gcuucggc-D[Br]U in Presence of Rh(NH3)6+++ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br9

b:34.6
occ:0.50
BR B:BRU9 0.0 34.6 0.5
C5 B:BRU9 1.9 34.5 0.5
O B:HOH156 2.7 29.6 1.0
C6 B:BRU9 2.9 38.2 0.5
C4 B:BRU9 2.9 33.9 0.5
BR B:BRU9 3.1 32.5 0.5
O4 B:BRU9 3.1 35.7 0.5
C5' B:C8 3.7 44.1 1.0
C3' B:C8 3.9 59.5 1.0
N1 B:BRU9 4.1 32.2 0.5
N3 B:BRU9 4.2 37.8 0.5
C4' B:C8 4.3 49.7 1.0
C5 B:BRU9 4.5 34.5 0.5
O3' B:C8 4.6 44.5 1.0
C6 B:BRU9 4.6 38.7 0.5
C2 B:BRU9 4.7 35.4 0.5
OP2 B:C8 4.9 22.7 1.0
C2' B:C8 4.9 43.0 1.0
O5' B:C8 5.0 35.2 1.0
C6 B:C8 5.0 31.2 1.0

Reference:

W.Cruse, P.Saludjian, A.Neuman, T.Prange. Destabilizing Effect of A Fluorouracil Extra Base in A Hybrid Rna Duplex Compared with Bromo and Chloro Analogues. Acta Crystallogr.,Sect.D V. 57 1609 2001.
ISSN: ISSN 0907-4449
PubMed: 11679725
DOI: 10.1107/S0907444901012318
Page generated: Sat Dec 12 02:01:46 2020

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