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Bromine in PDB 3p59: First Crystal Structure of A Rna Nanosquare

Protein crystallography data

The structure of First Crystal Structure of A Rna Nanosquare, PDB code: 3p59 was solved by S.Dibrov, T.Hermann, J.Mclean, J.Parsons, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.06 / 2.18
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 62.378, 62.378, 126.268, 90.00, 90.00, 120.00
R / Rfree (%) 15.6 / 19.2

Other elements in 3p59:

The structure of First Crystal Structure of A Rna Nanosquare also contains other interesting chemical elements:

Cobalt (Co) 10 atoms
Magnesium (Mg) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the First Crystal Structure of A Rna Nanosquare (pdb code 3p59). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the First Crystal Structure of A Rna Nanosquare, PDB code: 3p59:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 3p59

Go back to Bromine Binding Sites List in 3p59
Bromine binding site 1 out of 4 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br59

b:53.4
occ:1.00
BR A:5BU59 0.0 53.4 1.0
C5 A:5BU59 1.9 26.0 1.0
C4 A:5BU59 2.9 33.5 1.0
C6 A:5BU59 2.9 25.5 1.0
O4 A:5BU59 3.1 43.8 1.0
C6 A:C58 3.6 27.8 1.0
C5 A:C58 3.6 29.4 1.0
N2 B:NCO1 3.7 27.4 1.0
O A:HOH65 3.7 36.3 1.0
N1 A:C58 3.8 26.6 1.0
OP2 A:5BU59 3.9 34.5 1.0
C4 A:C58 3.9 32.6 1.0
C2' A:C58 4.1 26.4 1.0
N3 A:5BU59 4.1 31.0 1.0
C2 A:C58 4.2 24.4 1.0
N1 A:5BU59 4.2 32.2 1.0
N3 A:C58 4.2 31.1 1.0
C3' A:C58 4.2 33.2 1.0
O5' A:5BU59 4.5 42.1 1.0
C1' A:C58 4.6 31.1 1.0
N4 A:C58 4.6 39.2 1.0
C2 A:5BU59 4.7 30.0 1.0
P A:5BU59 4.7 33.6 1.0
O5' A:C58 4.8 44.4 1.0
N4 B:NCO1 4.8 39.5 1.0
O2 A:C58 4.9 26.6 1.0
O3' A:C58 5.0 40.8 1.0

Bromine binding site 2 out of 4 in 3p59

Go back to Bromine Binding Sites List in 3p59
Bromine binding site 2 out of 4 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br59

b:82.2
occ:1.00
BR C:5BU59 0.0 82.2 1.0
C5 C:5BU59 1.9 0.2 1.0
C4 C:5BU59 2.8 0.1 1.0
C6 C:5BU59 2.8 0.7 1.0
O4 C:5BU59 3.0 0.9 1.0
C2 D:A109 3.5 43.6 1.0
N4 C:C58 4.0 43.7 1.0
N1 D:A109 4.1 42.9 1.0
N3 C:5BU59 4.1 0.8 1.0
N1 C:5BU59 4.1 0.2 1.0
N7 C:G60 4.2 50.1 1.0
O D:HOH16 4.4 42.2 1.0
N3 D:A109 4.4 48.4 1.0
C8 C:G60 4.6 54.6 1.0
C2 C:5BU59 4.6 0.3 1.0
C6 D:G110 4.6 95.0 1.0
O6 D:G110 4.7 92.3 1.0
N2 D:NCO1 4.7 0.9 1.0
C4 C:C58 4.7 53.0 1.0
C5 D:G110 4.7 91.4 1.0
N7 D:G110 5.0 84.7 1.0

Bromine binding site 3 out of 4 in 3p59

Go back to Bromine Binding Sites List in 3p59
Bromine binding site 3 out of 4 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br59

b:62.8
occ:1.00
BR E:5BU59 0.0 62.8 1.0
C5 E:5BU59 1.9 27.2 1.0
C4 E:5BU59 2.8 23.2 1.0
C6 E:5BU59 2.8 25.5 1.0
O4 E:5BU59 3.0 27.2 1.0
C5 E:C58 3.4 17.4 1.0
C4 E:C58 3.7 23.9 1.0
N6 F:NCO1 3.7 37.9 1.0
N4 E:C58 3.8 32.5 1.0
N1 E:5BU59 4.1 26.7 1.0
N3 E:5BU59 4.1 16.4 1.0
C6 E:C58 4.1 15.3 1.0
O E:HOH88 4.3 37.3 1.0
N4 F:NCO1 4.3 0.3 1.0
N3 E:C58 4.5 15.5 1.0
OP2 E:5BU59 4.5 26.7 1.0
C2 E:5BU59 4.5 20.1 1.0
N2 F:NCO1 4.6 0.1 1.0
N1 E:C58 4.8 22.0 1.0
C2 E:C58 5.0 10.6 1.0

Bromine binding site 4 out of 4 in 3p59

Go back to Bromine Binding Sites List in 3p59
Bromine binding site 4 out of 4 in the First Crystal Structure of A Rna Nanosquare


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of First Crystal Structure of A Rna Nanosquare within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Br59

b:78.3
occ:1.00
BR G:5BU59 0.0 78.3 1.0
C5 G:5BU59 1.9 44.5 1.0
C4 G:5BU59 2.8 36.9 1.0
C6 G:5BU59 2.8 52.9 1.0
O4 G:5BU59 3.0 36.1 1.0
OP2 G:5BU59 3.7 97.9 1.0
C3' G:C58 3.8 63.2 1.0
N1 G:C58 3.9 69.6 1.0
C6 G:C58 4.0 70.0 1.0
C2' G:C58 4.1 61.4 1.0
N3 G:5BU59 4.1 34.3 1.0
N1 G:5BU59 4.1 52.3 1.0
C2 G:C58 4.1 67.2 1.0
C5 G:C58 4.3 67.5 1.0
O5' G:5BU59 4.3 45.7 1.0
N3 G:C58 4.3 66.7 1.0
C4 G:C58 4.4 66.3 1.0
C1' G:C58 4.5 66.5 1.0
P G:5BU59 4.5 98.5 1.0
C2 G:5BU59 4.6 45.5 1.0
O2 G:C58 4.6 64.2 1.0
C4' G:C58 4.6 61.2 1.0
O3' G:C58 4.7 65.3 1.0
C5' G:C58 4.7 49.8 1.0
O4' G:C58 4.7 66.3 1.0
N2 H:NCO1 5.0 94.8 1.0

Reference:

S.M.Dibrov, J.Mclean, J.Parsons, T.Hermann. Self-Assembling Rna Square. Proc.Natl.Acad.Sci.Usa V. 108 6405 2011.
ISSN: ISSN 0027-8424
PubMed: 21464284
DOI: 10.1073/PNAS.1017999108
Page generated: Sat Dec 12 02:14:34 2020

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