Atomistry » Bromine » PDB 5mrm-5o0j » 5nzd
Atomistry »
  Bromine »
    PDB 5mrm-5o0j »
      5nzd »

Bromine in PDB 5nzd: The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.

Protein crystallography data

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121., PDB code: 5nzd 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) 42.15 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.460, 64.613, 84.292, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 24.5

Other elements in 5nzd:

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms
Sodium (Na) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121. (pdb code 5nzd). 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 in Space Group P212121., PDB code: 5nzd:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 5nzd

Go back to Bromine Binding Sites List in 5nzd
Bromine binding site 1 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


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 in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2

b:0.7
occ:1.00
BR A:CBV2 0.0 0.7 1.0
C5 A:CBV2 1.9 89.4 1.0
C4 A:CBV2 3.0 66.5 1.0
C6 A:CBV2 3.0 70.8 1.0
N4 A:CBV2 3.2 60.9 1.0
O3P A:CBV2 3.4 76.0 1.0
C5 A:C1 3.8 69.8 1.0
C6 A:C1 3.9 65.1 1.0
O5' A:C1 4.0 87.3 1.0
C4 A:C1 4.2 61.0 1.0
N3 A:CBV2 4.3 59.9 1.0
N1 A:CBV2 4.3 63.4 1.0
C3' A:C1 4.4 79.2 1.0
N1 A:C1 4.5 58.4 1.0
P A:CBV2 4.7 79.7 1.0
N4 A:C1 4.7 53.6 1.0
N3 A:C1 4.7 60.1 1.0
O5' A:CBV2 4.8 63.5 1.0
MG A:MG104 4.8 85.9 1.0
C2 A:C1 4.8 58.6 1.0
C2 A:CBV2 4.9 57.7 1.0
C2' A:C1 5.0 74.8 1.0

Bromine binding site 2 out of 4 in 5nzd

Go back to Bromine Binding Sites List in 5nzd
Bromine binding site 2 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


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 in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br39

b:70.6
occ:1.00
BR A:CBV39 0.0 70.6 1.0
C5 A:CBV39 1.9 61.5 1.0
C6 A:CBV39 2.9 54.9 1.0
C4 A:CBV39 3.0 54.2 1.0
N4 A:CBV39 3.3 54.7 1.0
N7 A:G38 3.5 71.1 1.0
C5 A:G38 3.5 62.5 1.0
C8 A:G38 3.7 65.9 1.0
O1P A:CBV39 3.8 81.5 1.0
C4 A:G38 3.9 56.7 1.0
N9 A:G38 3.9 59.8 1.0
O4 A:U11 4.0 50.3 1.0
C6 A:G38 4.1 57.9 1.0
N2 A:G10 4.2 55.7 1.0
N1 A:CBV39 4.3 53.5 1.0
N3 A:CBV39 4.3 52.7 1.0
C3' A:G38 4.4 60.0 1.0
C2' A:G38 4.5 62.7 1.0
O5' A:CBV39 4.5 64.9 1.0
O6 A:G38 4.5 55.8 1.0
N3 A:G38 4.6 55.5 1.0
P A:CBV39 4.7 72.9 1.0
N1 A:G38 4.7 58.3 1.0
N1 A:G10 4.7 51.2 1.0
C2 A:G10 4.8 56.9 1.0
C1' A:G38 4.8 63.7 1.0
C2 A:CBV39 4.8 52.4 1.0
C2 A:G38 4.9 54.3 1.0
O3P A:CBV39 5.0 79.4 1.0

Bromine binding site 3 out of 4 in 5nzd

Go back to Bromine Binding Sites List in 5nzd
Bromine binding site 3 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


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 in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br2

b:0.9
occ:1.00
BR B:CBV2 0.0 0.9 1.0
C5 B:CBV2 1.9 76.2 1.0
C4 B:CBV2 3.0 51.6 1.0
C6 B:CBV2 3.0 53.5 1.0
N4 B:CBV2 3.3 55.7 1.0
C5 B:C1 3.4 67.2 1.0
C6 B:C1 3.5 62.3 1.0
O1P B:CBV2 3.6 65.6 1.0
O5' B:C1 3.9 87.5 1.0
C4 B:C1 3.9 70.5 1.0
N1 B:C1 4.1 72.7 1.0
C3' B:C1 4.2 76.6 1.0
N3 B:CBV2 4.3 55.8 1.0
N1 B:CBV2 4.4 53.4 1.0
N3 B:C1 4.5 66.9 1.0
N4 B:C1 4.5 72.9 1.0
C2 B:C1 4.6 72.3 1.0
P B:CBV2 4.7 73.3 1.0
C2' B:C1 4.7 61.4 1.0
O5' B:CBV2 4.7 59.6 1.0
C1' B:C1 4.9 77.6 1.0
C2 B:CBV2 4.9 56.9 1.0
C5' B:C1 4.9 75.2 1.0
O3' B:C1 4.9 83.4 1.0
C4' B:C1 5.0 77.8 1.0

Bromine binding site 4 out of 4 in 5nzd

Go back to Bromine Binding Sites List in 5nzd
Bromine binding site 4 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch in Space Group P212121.


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 in Space Group P212121. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br39

b:55.7
occ:1.00
BR B:CBV39 0.0 55.7 1.0
C5 B:CBV39 1.9 37.3 1.0
C6 B:CBV39 2.9 36.8 1.0
C4 B:CBV39 2.9 38.3 1.0
N4 B:CBV39 3.2 50.6 1.0
N7 B:G38 3.6 44.2 1.0
O4 B:U11 3.7 49.0 1.0
C5 B:G38 3.8 40.2 1.0
C8 B:G38 3.9 40.5 1.0
O1P B:CBV39 4.2 56.0 1.0
N1 B:CBV39 4.3 41.2 1.0
N3 B:CBV39 4.3 39.1 1.0
C6 B:G38 4.3 41.3 1.0
N2 B:G10 4.3 47.6 1.0
C4 B:G38 4.3 37.2 1.0
N9 B:G38 4.4 38.6 1.0
O6 B:G38 4.5 49.8 1.0
C2 B:G10 4.8 55.1 1.0
N1 B:G10 4.8 53.0 1.0
C3' B:G38 4.8 47.7 1.0
C2 B:CBV39 4.8 34.9 1.0
O5' B:CBV39 4.8 49.5 1.0
C4 B:U11 4.9 54.4 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: Mon Jul 7 08:51:35 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy