Atomistry » Bromine » PDB 3x41-4alu » 421d
Atomistry »
  Bromine »
    PDB 3x41-4alu »
      421d »

Bromine in PDB 421d: 5'-D(*Tp*Tp*Cp*Tp*Tp*(Bro)Cp*Tp*Tp*C)-3', 5'- R(*Gp*Ap*Ap*Gp*Ap*Ap*Gp*Ap*A)-3'

Protein crystallography data

The structure of 5'-D(*Tp*Tp*Cp*Tp*Tp*(Bro)Cp*Tp*Tp*C)-3', 5'- R(*Gp*Ap*Ap*Gp*Ap*Ap*Gp*Ap*A)-3', PDB code: 421d was solved by Y.Xiong, M.Sundaralingam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.80
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 48.080, 48.080, 42.880, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 23.7

Bromine Binding Sites:

The binding sites of Bromine atom in the 5'-D(*Tp*Tp*Cp*Tp*Tp*(Bro)Cp*Tp*Tp*C)-3', 5'- R(*Gp*Ap*Ap*Gp*Ap*Ap*Gp*Ap*A)-3' (pdb code 421d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total only one binding site of Bromine was determined in the 5'-D(*Tp*Tp*Cp*Tp*Tp*(Bro)Cp*Tp*Tp*C)-3', 5'- R(*Gp*Ap*Ap*Gp*Ap*Ap*Gp*Ap*A)-3', PDB code: 421d:

Bromine binding site 1 out of 1 in 421d

Go back to Bromine Binding Sites List in 421d
Bromine binding site 1 out of 1 in the 5'-D(*Tp*Tp*Cp*Tp*Tp*(Bro)Cp*Tp*Tp*C)-3', 5'- R(*Gp*Ap*Ap*Gp*Ap*Ap*Gp*Ap*A)-3'


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of 5'-D(*Tp*Tp*Cp*Tp*Tp*(Bro)Cp*Tp*Tp*C)-3', 5'- R(*Gp*Ap*Ap*Gp*Ap*Ap*Gp*Ap*A)-3' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br6

b:31.2
occ:1.00
BR A:CBR6 0.0 31.2 1.0
C5 A:CBR6 1.9 21.3 1.0
H42 A:CBR6 2.6 0.0 1.0
C6 A:CBR6 2.8 21.7 1.0
C4 A:CBR6 2.9 22.9 1.0
N4 A:CBR6 3.1 20.0 1.0
H2 A:HOH111 3.5 0.0 1.0
C5 A:DT5 3.6 14.7 1.0
OP2 A:CBR6 3.6 27.0 1.0
C6 A:DT5 3.6 18.8 1.0
H1 A:HOH111 3.8 0.0 1.0
O A:HOH111 3.8 54.3 1.0
H1 A:HOH128 3.9 0.0 1.0
O A:HOH125 3.9 58.8 1.0
C7 A:DT5 4.0 13.4 1.0
C4 A:DT5 4.0 16.4 1.0
N1 A:DT5 4.1 20.8 1.0
N1 A:CBR6 4.1 21.4 1.0
C7 A:DT7 4.1 13.0 1.0
H41 A:CBR6 4.1 0.0 1.0
N3 A:CBR6 4.1 21.3 1.0
C3' A:DT5 4.1 22.0 1.0
H1 A:HOH125 4.3 0.0 1.0
N3 A:DT5 4.3 18.7 1.0
C2 A:DT5 4.4 20.9 1.0
C2' A:DT5 4.4 20.5 1.0
O A:HOH128 4.4 51.8 1.0
O5' A:CBR6 4.4 25.4 1.0
O4 A:DT7 4.5 16.1 1.0
H2 A:HOH128 4.5 0.0 1.0
P A:CBR6 4.5 28.2 1.0
O4 A:DT5 4.6 19.2 1.0
C2 A:CBR6 4.6 17.4 1.0
H2 A:HOH125 4.8 0.0 1.0
C1' A:DT5 4.8 19.8 1.0
O5' A:DT5 4.8 29.5 1.0
C5 A:DT7 4.8 14.3 1.0
O3' A:DT5 4.9 26.6 1.0
H3 A:DT5 4.9 0.0 1.0
C4 A:DT7 4.9 13.5 1.0

Reference:

Y.Xiong, M.Sundaralingam. Crystal Structure and Conformation of A Dna-Rna Hybrid Duplex with A Polypurine Rna Strand: D(TTCTTBR5CTTC)-R(Gaagaagaa). Structure V. 6 1493 1998.
ISSN: ISSN 0969-2126
PubMed: 9862803
DOI: 10.1016/S0969-2126(98)00148-8
Page generated: Wed Jul 10 20:43:56 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy