Atomistry » Bromine » PDB 5mrm-5o0j » 5nz3
Atomistry »
  Bromine »
    PDB 5mrm-5o0j »
      5nz3 »

Bromine in PDB 5nz3: The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine

Protein crystallography data

The structure of The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine, PDB code: 5nz3 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) 48.78 / 2.06
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.491, 83.491, 66.071, 90.00, 90.00, 120.00
R / Rfree (%) 21.9 / 27.4

Other elements in 5nz3:

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

Magnesium (Mg) 5 atoms
Sodium (Na) 4 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine (pdb code 5nz3). 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 Methylguanidine, PDB code: 5nz3:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 5nz3

Go back to Bromine Binding Sites List in 5nz3
Bromine binding site 1 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine


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

b:70.7
occ:1.00
BR A:CBV2 0.0 70.7 1.0
C5 A:CBV2 1.9 57.6 1.0
HN41 A:CBV2 2.8 68.6 1.0
H3' A:C1 2.9 0.4 1.0
C6 A:CBV2 3.0 58.9 1.0
C4 A:CBV2 3.0 56.5 1.0
H6 A:CBV2 3.0 70.6 1.0
N4 A:CBV2 3.2 57.2 1.0
O2P A:CBV2 3.3 67.0 1.0
C6 A:C1 3.5 87.7 1.0
C5 A:C1 3.6 75.8 1.0
O5' A:C1 3.7 0.1 1.0
O A:HOH213 3.7 56.4 1.0
H6 A:C1 3.8 0.2 1.0
H5 A:C1 3.8 90.9 1.0
C3' A:C1 3.8 1.0 1.0
N1 A:C1 3.9 93.8 1.0
C4 A:C1 3.9 70.8 1.0
HO5' A:C1 4.0 0.5 1.0
H2' A:C1 4.0 0.9 1.0
HN42 A:CBV2 4.1 68.6 1.0
N3 A:C1 4.2 69.7 1.0
C2 A:C1 4.2 79.5 1.0
N3 A:CBV2 4.3 54.1 1.0
N1 A:CBV2 4.3 59.4 1.0
O5' A:CBV2 4.3 63.1 1.0
P A:CBV2 4.4 68.9 1.0
C2' A:C1 4.4 0.4 1.0
N4 A:C1 4.6 64.4 1.0
O3' A:C1 4.6 94.7 1.0
C1' A:C1 4.6 0.2 1.0
C4' A:C1 4.7 0.3 1.0
C5' A:C1 4.7 0.7 1.0
H41 A:C1 4.7 77.3 1.0
MG A:MG104 4.7 30.0 1.0
C2 A:CBV2 4.8 54.0 1.0
O4' A:C1 4.8 0.3 1.0
O3P A:CBV2 4.9 77.2 1.0

Bromine binding site 2 out of 4 in 5nz3

Go back to Bromine Binding Sites List in 5nz3
Bromine binding site 2 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine


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 Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br39

b:39.4
occ:1.00
BR A:CBV39 0.0 39.4 1.0
C5 A:CBV39 1.9 42.5 1.0
HN42 A:CBV39 2.9 75.1 1.0
C6 A:CBV39 2.9 45.1 1.0
H6 A:CBV39 3.0 54.1 1.0
C4 A:CBV39 3.0 35.2 1.0
N4 A:CBV39 3.3 62.6 1.0
N7 A:G38 3.5 34.6 1.0
H3' A:G38 3.6 60.4 1.0
C5 A:G38 3.6 40.0 1.0
O2P A:CBV39 3.7 39.3 1.0
C8 A:G38 3.7 36.5 1.0
O4 A:U11 3.8 34.1 1.0
C4 A:G38 4.0 36.3 1.0
H21 A:G10 4.0 45.8 1.0
N9 A:G38 4.0 35.8 1.0
H8 A:G38 4.1 43.9 1.0
C6 A:G38 4.1 34.6 1.0
HN41 A:CBV39 4.2 75.1 1.0
N1 A:CBV39 4.2 36.9 1.0
NA A:NA106 4.3 65.2 1.0
N3 A:CBV39 4.3 39.6 1.0
H2' A:G38 4.3 56.0 1.0
N2 A:G10 4.4 38.2 1.0
C3' A:G38 4.5 50.3 1.0
O6 A:G38 4.5 47.0 1.0
H1 A:G10 4.6 54.6 1.0
O5' A:CBV39 4.6 33.0 1.0
H22 A:G10 4.7 45.8 1.0
N3 A:G38 4.8 40.1 1.0
C2' A:G38 4.8 46.6 1.0
N1 A:G38 4.8 42.0 1.0
C2 A:CBV39 4.8 34.0 1.0
P A:CBV39 4.8 40.0 1.0
C2 A:G10 4.9 41.8 1.0
N1 A:G10 4.9 45.5 1.0
C1' A:G38 5.0 38.4 1.0
O5' A:G38 5.0 43.1 1.0

Bromine binding site 3 out of 4 in 5nz3

Go back to Bromine Binding Sites List in 5nz3
Bromine binding site 3 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine


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 Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br2

b:99.0
occ:1.00
BR B:CBV2 0.0 99.0 1.0
C5 B:CBV2 1.9 99.4 1.0
HN41 B:CBV2 2.8 0.2 1.0
C4 B:CBV2 3.0 0.3 1.0
C6 B:CBV2 3.0 97.4 1.0
H3' B:C1 3.0 0.3 1.0
H6 B:CBV2 3.1 0.9 1.0
N4 B:CBV2 3.2 0.1 1.0
C5 B:C1 3.5 89.3 1.0
O1P B:CBV2 3.6 0.6 1.0
C6 B:C1 3.6 1.0 1.0
C4 B:C1 3.7 87.9 1.0
N1 B:C1 3.8 0.4 1.0
H5 B:C1 3.8 0.2 1.0
H6 B:C1 3.9 0.4 1.0
C3' B:C1 3.9 0.9 1.0
H2' B:C1 3.9 0.9 1.0
N3 B:C1 3.9 99.1 1.0
C2 B:C1 4.0 0.1 1.0
O5' B:C1 4.0 0.0 1.0
HN42 B:CBV2 4.1 0.2 1.0
N3 B:CBV2 4.3 0.2 1.0
HO5' B:C1 4.3 0.4 1.0
N4 B:C1 4.3 88.7 1.0
N1 B:CBV2 4.3 98.0 1.0
C2' B:C1 4.3 0.6 1.0
P B:CBV2 4.5 0.7 1.0
H41 B:C1 4.6 0.5 1.0
C1' B:C1 4.6 0.2 1.0
O5' B:CBV2 4.6 96.6 1.0
H5'2 B:CBV2 4.7 0.4 1.0
O3' B:C1 4.7 0.2 1.0
O2 B:C1 4.7 0.2 1.0
H42 B:C1 4.8 0.5 1.0
C4' B:C1 4.8 0.3 1.0
C2 B:CBV2 4.9 99.9 1.0
O4' B:C1 4.9 0.3 1.0
O3P B:CBV2 4.9 0.6 1.0
C5' B:C1 5.0 0.9 1.0

Bromine binding site 4 out of 4 in 5nz3

Go back to Bromine Binding Sites List in 5nz3
Bromine binding site 4 out of 4 in the The Structure of the Thermobifida Fusca Guanidine III Riboswitch with Methylguanidine


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 Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br39

b:63.2
occ:1.00
BR B:CBV39 0.0 63.2 1.0
C5 B:CBV39 1.9 53.1 1.0
HN42 B:CBV39 2.6 66.5 1.0
C4 B:CBV39 2.9 54.1 1.0
C6 B:CBV39 3.0 53.6 1.0
N4 B:CBV39 3.1 55.4 1.0
H6 B:CBV39 3.1 64.3 1.0
N7 B:G38 3.5 60.6 1.0
H3' B:G38 3.6 82.0 1.0
C5 B:G38 3.6 69.3 1.0
C8 B:G38 3.8 62.4 1.0
O1P B:CBV39 3.8 47.7 1.0
O4 B:U11 3.9 59.3 1.0
HN41 B:CBV39 3.9 66.5 1.0
C4 B:G38 4.0 64.9 1.0
N9 B:G38 4.1 69.9 1.0
C6 B:G38 4.1 66.5 1.0
H2' B:G38 4.1 85.1 1.0
H21 B:G10 4.1 79.9 1.0
H8 B:G38 4.1 74.8 1.0
N3 B:CBV39 4.2 54.8 1.0
N1 B:CBV39 4.3 69.3 1.0
C3' B:G38 4.5 68.3 1.0
O6 B:G38 4.5 74.2 1.0
MG B:MG101 4.5 30.0 1.0
N2 B:G10 4.5 66.6 1.0
O5' B:CBV39 4.5 55.3 1.0
H1 B:G10 4.7 84.2 1.0
C2' B:G38 4.7 70.9 1.0
P B:CBV39 4.7 55.5 1.0
N3 B:G38 4.8 63.6 1.0
N1 B:G38 4.8 76.5 1.0
C2 B:CBV39 4.8 61.1 1.0
H22 B:G10 4.8 79.9 1.0
C1' B:G38 5.0 73.8 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: Sat Dec 12 02:28:38 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy