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

Bromine in PDB 5mvl: Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil

Protein crystallography data

The structure of Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil, PDB code: 5mvl was solved by J.S.Hardwick, D.Ptchelkine, S.E.V.Phillips, T.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.67 / 1.41
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 43.517, 43.517, 60.850, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 18.2

Other elements in 5mvl:

The structure of Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil (pdb code 5mvl). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil, PDB code: 5mvl:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 5mvl

Go back to Bromine Binding Sites List in 5mvl
Bromine binding site 1 out of 2 in the Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil


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 An A-Dna Dodecamer Containing 5-Bromouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2

b:23.7
occ:0.37
BR A:BRU2 0.0 23.7 0.4
C5 A:BRU2 1.9 23.3 1.0
C6 A:BRU2 2.9 23.5 1.0
H6 A:BRU2 2.9 28.2 1.0
C4 A:BRU2 3.0 22.9 1.0
O4 A:BRU2 3.2 26.4 1.0
C4 A:DC1 3.7 28.7 1.0
O A:HOH219 3.7 41.0 0.9
N3 A:DC1 3.7 27.6 1.0
C5 A:DC1 3.7 30.2 1.0
C2 A:DC1 3.8 28.7 1.0
N1 A:DC1 3.8 30.3 1.0
O A:HOH220 3.8 26.2 0.7
C6 A:DC1 3.8 29.9 1.0
OP2 A:BRU2 3.9 31.7 1.0
O A:HOH234 3.9 27.2 0.6
O A:HOH211 4.0 27.6 0.5
C3' A:DC1 4.1 32.3 1.0
O A:HOH204 4.2 50.5 1.0
N1 A:BRU2 4.3 22.6 1.0
N4 A:DC1 4.3 29.8 1.0
N3 A:BRU2 4.3 23.4 1.0
O2 A:DC1 4.4 28.4 1.0
C2' A:DC1 4.4 30.9 1.0
O5' A:BRU2 4.5 28.2 1.0
C1' A:DC1 4.7 32.0 1.0
P A:BRU2 4.7 31.2 1.0
C2 A:BRU2 4.8 23.4 1.0
O3' A:DC1 4.9 31.8 1.0
HN3 A:BRU2 5.0 28.1 1.0

Bromine binding site 2 out of 2 in 5mvl

Go back to Bromine Binding Sites List in 5mvl
Bromine binding site 2 out of 2 in the Crystal Structure of An A-Dna Dodecamer Containing 5-Bromouracil


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 An A-Dna Dodecamer Containing 5-Bromouracil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br2

b:24.1
occ:0.38
BR B:BRU2 0.0 24.1 0.4
C5 B:BRU2 1.9 24.3 1.0
C6 B:BRU2 2.9 24.8 1.0
C4 B:BRU2 2.9 24.5 1.0
H6 B:BRU2 3.0 29.8 1.0
O4 B:BRU2 3.1 25.9 1.0
O B:HOH130 3.5 52.6 1.0
O B:HOH110 3.7 30.1 0.8
OP2 B:BRU2 3.8 35.4 1.0
C6 B:DC1 3.8 28.2 1.0
C5 B:DC1 3.8 28.5 1.0
N1 B:DC1 3.8 27.5 1.0
O B:HOH123 3.8 28.8 0.9
C4 B:DC1 3.8 26.6 1.0
C2 B:DC1 3.9 25.5 1.0
N3 B:DC1 3.9 25.6 1.0
C3' B:DC1 4.0 31.8 1.0
O B:HOH105 4.1 39.1 0.8
C2' B:DC1 4.2 28.9 1.0
N1 B:BRU2 4.3 24.3 1.0
N3 B:BRU2 4.3 24.9 1.0
O5' B:DC1 4.4 41.0 1.0
O5' B:BRU2 4.5 30.1 1.0
O2 B:DC1 4.5 24.4 1.0
N4 B:DC1 4.5 26.3 1.0
C1' B:DC1 4.6 28.4 1.0
P B:BRU2 4.6 34.1 1.0
H62 B:DA3 4.7 25.3 1.0
C2 B:BRU2 4.8 23.5 1.0
O3' B:DC1 4.8 33.1 1.0
HN3 B:BRU2 4.9 29.9 1.0

Reference:

J.S.Hardwick, D.Ptchelkine, A.H.El-Sagheer, I.Tear, D.Singleton, S.E.V.Phillips, A.N.Lane, T.Brown. 5-Formylcytosine Does Not Change the Global Structure of Dna. Nat. Struct. Mol. Biol. V. 24 544 2017.
ISSN: ESSN 1545-9985
PubMed: 28504696
DOI: 10.1038/NSMB.3411
Page generated: Thu Jul 11 00:24:52 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy