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Bromine in PDB 1d3r: Crystal Structure of Triplex Dna

Protein crystallography data

The structure of Crystal Structure of Triplex Dna, PDB code: 1d3r was solved by S.Rhee, Z.-J.Han, K.Liu, H.T.Todd Miles, D.R.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 53.800, 53.800, 43.100, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 27.5

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Triplex Dna (pdb code 1d3r). 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 Triplex Dna, PDB code: 1d3r:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 1d3r

Go back to Bromine Binding Sites List in 1d3r
Bromine binding site 1 out of 4 in the Crystal Structure of Triplex Dna


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 Triplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2

b:24.0
occ:1.00
BR A:BRU2 0.0 24.0 1.0
C5 A:BRU2 1.5 23.6 1.0
C6 A:BRU2 2.5 24.0 1.0
C4 A:BRU2 2.7 23.1 1.0
O4 A:BRU2 3.0 23.6 1.0
C2' A:DC1 3.4 26.0 1.0
C6 A:DC1 3.5 19.5 1.0
O A:HOH137 3.5 30.2 1.0
O C:HOH105 3.6 29.1 1.0
O C:HOH175 3.6 31.9 1.0
O5' A:DC1 3.7 25.1 1.0
C5 A:DC1 3.7 17.3 1.0
O C:HOH123 3.8 24.3 1.0
O A:HOH100 3.8 6.6 1.0
N1 A:BRU2 3.9 26.4 1.0
N3 A:BRU2 3.9 22.6 1.0
O A:HOH180 4.0 27.7 1.0
OP2 A:BRU2 4.0 26.4 1.0
O A:HOH112 4.0 26.9 1.0
N1 A:DC1 4.0 21.4 1.0
O A:HOH130 4.1 34.7 1.0
C3' A:DC1 4.1 26.3 1.0
O A:HOH118 4.3 25.6 1.0
C1' A:DC1 4.4 24.2 1.0
C4 A:DC1 4.4 17.5 1.0
C2 A:BRU2 4.4 24.2 1.0
C2 A:DC1 4.7 19.8 1.0
C5' A:DC1 4.7 25.2 1.0
O5' A:BRU2 4.8 27.2 1.0
P A:BRU2 4.9 26.0 1.0
N3 A:DC1 4.9 19.4 1.0
C4' A:DC1 4.9 25.9 1.0

Bromine binding site 2 out of 4 in 1d3r

Go back to Bromine Binding Sites List in 1d3r
Bromine binding site 2 out of 4 in the Crystal Structure of Triplex Dna


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 Triplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br5

b:33.2
occ:1.00
BR A:BRU5 0.0 33.2 1.0
C5 A:BRU5 1.5 30.1 1.0
C6 A:BRU5 2.5 31.5 1.0
C4 A:BRU5 2.6 30.1 1.0
O4 A:BRU5 3.0 29.6 1.0
O A:HOH212 3.4 43.6 1.0
O A:HOH312 3.6 44.1 1.0
C6 A:DC4 3.6 26.1 1.0
N1 A:BRU5 3.8 32.9 1.0
N3 A:BRU5 3.8 28.6 1.0
O A:HOH160 3.9 34.4 1.0
C5 A:DC4 3.9 27.9 1.0
C2' A:DC4 3.9 30.2 1.0
N1 A:DC4 3.9 28.0 1.0
O A:HOH110 4.3 29.2 1.0
O A:HOH313 4.3 47.4 1.0
C1' A:DC4 4.3 29.6 1.0
C2 A:BRU5 4.4 31.4 1.0
O A:HOH157 4.4 53.7 1.0
C4 A:DC4 4.5 27.5 1.0
C2 A:DC4 4.5 26.9 1.0
N3 A:DC4 4.8 27.6 1.0
N4 A:DC6 4.9 23.7 1.0
C1' A:BRU5 5.0 34.9 1.0

Bromine binding site 3 out of 4 in 1d3r

Go back to Bromine Binding Sites List in 1d3r
Bromine binding site 3 out of 4 in the Crystal Structure of Triplex Dna


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 Triplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br32

b:27.8
occ:1.00
BR C:BRU32 0.0 27.8 1.0
C5 C:BRU32 1.5 28.2 1.0
C6 C:BRU32 2.5 29.3 1.0
C4 C:BRU32 2.7 29.0 1.0
O4 C:BRU32 3.1 30.8 1.0
C2' C:DC31 3.6 31.6 1.0
C6 C:DC31 3.7 30.4 1.0
O A:HOH104 3.8 23.1 1.0
N1 C:BRU32 3.8 30.3 1.0
N3 C:BRU32 3.9 29.8 1.0
O C:HOH105 3.9 29.1 1.0
O A:HOH100 3.9 6.6 1.0
OP2 C:BRU32 3.9 31.1 1.0
C5 C:DC31 3.9 30.2 1.0
O5' C:DC31 3.9 30.8 1.0
C3' C:DC31 4.0 31.4 1.0
O A:HOH186 4.0 31.7 1.0
N1 C:DC31 4.1 30.7 1.0
O A:HOH180 4.1 27.7 1.0
O A:HOH118 4.1 25.6 1.0
C5' C:DC31 4.1 31.6 1.0
O C:HOH123 4.2 24.3 1.0
C2 C:BRU32 4.4 30.5 1.0
C4 C:DC31 4.5 29.2 1.0
C1' C:DC31 4.5 30.9 1.0
C2 C:DC31 4.6 29.4 1.0
C4' C:DC31 4.6 31.4 1.0
N3 C:DC31 4.8 28.5 1.0
O5' C:BRU32 4.9 31.2 1.0
P C:BRU32 4.9 31.6 1.0
O C:HOH317 4.9 48.7 1.0
O3' C:DC31 5.0 32.1 1.0
O4' C:DC31 5.0 30.8 1.0

Bromine binding site 4 out of 4 in 1d3r

Go back to Bromine Binding Sites List in 1d3r
Bromine binding site 4 out of 4 in the Crystal Structure of Triplex Dna


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 Triplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br35

b:32.0
occ:1.00
BR C:BRU35 0.0 32.0 1.0
C5 C:BRU35 1.5 32.0 1.0
C6 C:BRU35 2.5 33.3 1.0
C4 C:BRU35 2.6 30.5 1.0
O4 C:BRU35 3.0 28.5 1.0
O C:HOH161 3.4 33.3 1.0
C6 C:DC34 3.6 26.8 1.0
O C:HOH210 3.6 35.7 1.0
O C:HOH109 3.8 18.8 1.0
N1 C:BRU35 3.8 34.3 1.0
N3 C:BRU35 3.8 30.8 1.0
C5 C:DC34 3.9 24.8 1.0
N1 C:DC34 4.0 30.0 1.0
C2' C:DC34 4.0 33.1 1.0
O C:HOH101 4.1 15.8 1.0
O C:HOH182 4.1 39.0 1.0
O C:HOH305 4.2 42.8 1.0
C2 C:BRU35 4.4 32.7 1.0
C1' C:DC34 4.4 32.2 1.0
C4 C:DC34 4.5 24.1 1.0
O C:HOH204 4.6 33.8 1.0
C2 C:DC34 4.6 28.4 1.0
N4 C:DC36 4.7 23.2 1.0
N3 C:DC34 4.9 25.7 1.0

Reference:

S.Rhee, Z.Han, K.Liu, H.T.Miles, D.R.Davies. Structure of A Triple Helical Dna with A Triplex-Duplex Junction. Biochemistry V. 38 16810 1999.
ISSN: ISSN 0006-2960
PubMed: 10606513
DOI: 10.1021/BI991811M
Page generated: Sat Dec 12 01:59:46 2020

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