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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: Sat Dec 12 02:17:08 2020

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