Atomistry » Bromine » PDB 5o62-5q0c » 5o69
Atomistry »
  Bromine »
    PDB 5o62-5q0c »
      5o69 »

Bromine in PDB 5o69: The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine.

Protein crystallography data

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine., PDB code: 5o69 was solved by L.Huang, J.Wang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.32 / 2.32
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.886, 83.886, 67.226, 90.00, 90.00, 120.00
R / Rfree (%) 24.3 / 27

Other elements in 5o69:

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine. (pdb code 5o69). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine., PDB code: 5o69:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 5o69

Go back to Bromine Binding Sites List in 5o69
Bromine binding site 1 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2

b:0.0
occ:1.00
BR A:CBV2 0.0 0.0 1.0
C5 A:CBV2 1.9 0.2 1.0
HN42 A:CBV2 2.7 68.9 1.0
H3' A:C1 2.9 0.3 1.0
C4 A:CBV2 3.0 73.2 1.0
C6 A:CBV2 3.0 87.0 1.0
H6 A:CBV2 3.1 0.4 1.0
N4 A:CBV2 3.2 57.4 1.0
O2P A:CBV2 3.5 83.1 1.0
C5 A:C1 3.5 60.8 1.0
C6 A:C1 3.6 67.2 1.0
H5'' A:C1 3.6 0.7 1.0
H5 A:C1 3.7 73.0 1.0
H6 A:C1 3.7 80.7 1.0
C3' A:C1 3.9 0.4 1.0
C4 A:C1 3.9 64.9 1.0
N1 A:C1 4.0 89.9 1.0
HN41 A:CBV2 4.0 68.9 1.0
H2' A:C1 4.3 0.0 1.0
N3 A:CBV2 4.3 73.3 1.0
N3 A:C1 4.3 75.8 1.0
N1 A:CBV2 4.3 53.1 1.0
C2 A:C1 4.4 74.1 1.0
C5' A:C1 4.4 0.6 1.0
O5' A:CBV2 4.5 79.3 1.0
P A:CBV2 4.5 80.7 1.0
N4 A:C1 4.5 52.3 1.0
C2' A:C1 4.5 97.5 1.0
H41 A:C1 4.6 62.8 1.0
O3' A:C1 4.6 0.9 1.0
C4' A:C1 4.6 0.1 1.0
C1' A:C1 4.7 0.8 1.0
C2 A:CBV2 4.9 48.7 1.0
O5' A:C1 4.9 0.4 1.0
O4' A:C1 4.9 97.1 1.0
O3P A:CBV2 4.9 0.4 1.0

Bromine binding site 2 out of 4 in 5o69

Go back to Bromine Binding Sites List in 5o69
Bromine binding site 2 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br39

b:74.7
occ:1.00
BR A:CBV39 0.0 74.7 1.0
C5 A:CBV39 1.9 47.2 1.0
HN42 A:CBV39 2.9 37.8 1.0
C6 A:CBV39 3.0 41.8 1.0
C4 A:CBV39 3.0 43.8 1.0
H6 A:CBV39 3.0 50.1 1.0
N4 A:CBV39 3.3 31.5 1.0
N7 A:G38 3.5 40.0 1.0
C5 A:G38 3.5 36.9 1.0
O4 A:U11 3.7 45.0 1.0
H3' A:G38 3.7 64.6 1.0
C8 A:G38 3.8 48.4 1.0
H21 A:G10 3.8 43.5 1.0
O2P A:CBV39 3.8 56.5 1.0
C4 A:G38 3.9 32.1 1.0
C6 A:G38 4.0 34.4 1.0
N9 A:G38 4.1 37.7 1.0
N2 A:G10 4.1 36.2 1.0
H2' A:G38 4.1 78.6 1.0
H8 A:G38 4.2 58.1 1.0
HN41 A:CBV39 4.2 37.8 1.0
N1 A:CBV39 4.3 38.1 1.0
O6 A:G38 4.3 44.0 1.0
N3 A:CBV39 4.3 31.6 1.0
H1 A:G10 4.4 58.2 1.0
H22 A:G10 4.4 43.5 1.0
C3' A:G38 4.6 53.8 1.0
N1 A:G38 4.6 32.4 1.0
N3 A:G38 4.6 32.8 1.0
C2 A:G10 4.7 32.7 1.0
O5' A:CBV39 4.7 60.9 1.0
N1 A:G10 4.7 48.5 1.0
C2' A:G38 4.7 65.5 1.0
P A:CBV39 4.8 48.4 1.0
C2 A:CBV39 4.9 29.7 1.0
C2 A:G38 4.9 39.9 1.0
C4 A:U11 4.9 34.6 1.0
O3P A:CBV39 5.0 62.0 1.0
C1' A:G38 5.0 45.8 1.0

Bromine binding site 3 out of 4 in 5o69

Go back to Bromine Binding Sites List in 5o69
Bromine binding site 3 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br2

b:0.2
occ:1.00
BR B:CBV2 0.0 0.2 1.0
C5 B:CBV2 1.9 0.6 1.0
HO5' B:C1 2.7 0.6 1.0
H3' B:C1 2.8 0.0 1.0
HN42 B:CBV2 2.9 0.8 1.0
C6 B:CBV2 3.0 90.4 1.0
C4 B:CBV2 3.0 98.2 1.0
H6 B:CBV2 3.0 0.5 1.0
N4 B:CBV2 3.3 88.2 1.0
O5' B:C1 3.3 0.5 1.0
C6 B:C1 3.5 90.2 1.0
C5 B:C1 3.5 89.7 1.0
O1P B:CBV2 3.6 0.2 1.0
H6 B:C1 3.7 0.2 1.0
H5 B:C1 3.8 0.6 1.0
C3' B:C1 3.8 0.8 1.0
N1 B:C1 3.8 0.8 1.0
C4 B:C1 3.9 90.1 1.0
H2' B:C1 4.0 0.2 1.0
HN41 B:CBV2 4.1 0.8 1.0
C2 B:C1 4.2 0.7 1.0
N3 B:C1 4.2 0.4 1.0
N3 B:CBV2 4.3 93.9 1.0
N1 B:CBV2 4.3 91.4 1.0
C2' B:C1 4.4 0.0 1.0
O5' B:CBV2 4.4 0.5 1.0
C5' B:C1 4.5 0.1 1.0
P B:CBV2 4.5 0.1 1.0
C1' B:C1 4.5 0.3 1.0
C4' B:C1 4.6 0.7 1.0
N4 B:C1 4.6 96.0 1.0
O3' B:C1 4.6 0.6 1.0
H41 B:C1 4.7 0.2 1.0
O4' B:C1 4.8 0.7 1.0
C2 B:CBV2 4.9 91.2 1.0
O3P B:CBV2 4.9 0.3 1.0
H5'' B:C1 4.9 0.5 1.0
O2 B:C1 5.0 0.1 1.0

Bromine binding site 4 out of 4 in 5o69

Go back to Bromine Binding Sites List in 5o69
Bromine binding site 4 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Agmatine. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br39

b:72.2
occ:1.00
BR B:CBV39 0.0 72.2 1.0
C5 B:CBV39 1.9 45.0 1.0
HN42 B:CBV39 2.8 54.0 1.0
C6 B:CBV39 2.9 44.5 1.0
C4 B:CBV39 3.0 44.2 1.0
H6 B:CBV39 3.0 53.4 1.0
N4 B:CBV39 3.2 45.0 1.0
N7 B:G38 3.5 67.3 1.0
C5 B:G38 3.5 67.3 1.0
O3P B:CBV39 3.7 70.1 1.0
H3' B:G38 3.8 74.0 1.0
C8 B:G38 3.8 58.5 1.0
O4 B:U11 3.9 54.8 1.0
C4 B:G38 3.9 52.2 1.0
C6 B:G38 4.0 79.8 1.0
N9 B:G38 4.0 57.2 1.0
HN41 B:CBV39 4.1 54.0 1.0
H2' B:G38 4.1 72.5 1.0
H21 B:G10 4.1 99.3 1.0
H8 B:G38 4.2 70.2 1.0
N1 B:CBV39 4.3 81.1 1.0
N3 B:CBV39 4.3 43.3 1.0
O6 B:G38 4.4 70.4 1.0
O1P B:CBV39 4.4 84.0 1.0
N2 B:G10 4.5 82.8 1.0
H1 B:G10 4.5 0.3 1.0
C3' B:G38 4.6 61.7 1.0
N3 B:G38 4.6 61.6 1.0
N1 B:G38 4.6 71.3 1.0
C2' B:G38 4.7 60.4 1.0
O5' B:CBV39 4.8 81.3 1.0
H22 B:G10 4.8 99.3 1.0
N1 B:G10 4.8 86.9 1.0
C2 B:CBV39 4.8 55.3 1.0
C2 B:G10 4.9 77.3 1.0
C2 B:G38 4.9 71.6 1.0
P B:CBV39 4.9 69.5 1.0
C1' B:G38 5.0 65.8 1.0

Reference:

L.Huang, J.Wang, T.J.Wilson, D.M.J.Lilley. Structure of the Guanidine III Riboswitch. Cell Chem Biol V. 24 1407 2017.
ISSN: ESSN 2451-9456
PubMed: 28988949
DOI: 10.1016/J.CHEMBIOL.2017.08.021
Page generated: Thu Jul 11 00:35:48 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy