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Bromine in PDB 406d: 5'-R(*Cp*Ap*Cp*Cp*Gp*Gp*Ap*Up*Gp*Gp*Up*(Bro) Up*Cp*Gp*Gp*Up*G)-3'

Protein crystallography data

The structure of 5'-R(*Cp*Ap*Cp*Cp*Gp*Gp*Ap*Up*Gp*Gp*Up*(Bro) Up*Cp*Gp*Gp*Up*G)-3', PDB code: 406d was solved by S.A.Shah, A.T.Brunger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.80
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 39.627, 39.627, 91.018, 90.00, 90.00, 120.00
R / Rfree (%) 26.2 / 29.4

Bromine Binding Sites:

The binding sites of Bromine atom in the 5'-R(*Cp*Ap*Cp*Cp*Gp*Gp*Ap*Up*Gp*Gp*Up*(Bro) Up*Cp*Gp*Gp*Up*G)-3' (pdb code 406d). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the 5'-R(*Cp*Ap*Cp*Cp*Gp*Gp*Ap*Up*Gp*Gp*Up*(Bro) Up*Cp*Gp*Gp*Up*G)-3', PDB code: 406d:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 406d

Go back to Bromine Binding Sites List in 406d
Bromine binding site 1 out of 2 in the 5'-R(*Cp*Ap*Cp*Cp*Gp*Gp*Ap*Up*Gp*Gp*Up*(Bro) Up*Cp*Gp*Gp*Up*G)-3'


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of 5'-R(*Cp*Ap*Cp*Cp*Gp*Gp*Ap*Up*Gp*Gp*Up*(Bro) Up*Cp*Gp*Gp*Up*G)-3' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br12

b:6.8
occ:1.00
BR A:5BU12 0.0 6.8 1.0
C5 A:5BU12 1.9 6.8 1.0
C4 A:5BU12 2.8 6.8 1.0
C6 A:5BU12 2.8 6.8 1.0
O4 A:5BU12 3.1 6.8 1.0
C5 A:U11 3.4 4.3 1.0
C6 A:U11 3.6 4.3 1.0
OP2 A:5BU12 3.7 12.3 1.0
C4 A:U11 3.9 4.3 1.0
N3 A:5BU12 4.1 6.8 1.0
N1 A:5BU12 4.1 6.8 1.0
OP2 A:U11 4.2 12.0 1.0
N1 A:U11 4.2 4.3 1.0
C3' A:U11 4.4 12.0 1.0
O4 A:U11 4.4 4.3 1.0
O5' A:5BU12 4.4 12.3 1.0
O5' A:U11 4.4 12.0 1.0
N3 A:U11 4.5 4.3 1.0
P A:5BU12 4.6 12.3 1.0
C2 A:5BU12 4.7 6.8 1.0
C2 A:U11 4.7 4.3 1.0
C2' A:U11 4.8 12.0 1.0
P A:U11 5.0 12.0 1.0

Bromine binding site 2 out of 2 in 406d

Go back to Bromine Binding Sites List in 406d
Bromine binding site 2 out of 2 in the 5'-R(*Cp*Ap*Cp*Cp*Gp*Gp*Ap*Up*Gp*Gp*Up*(Bro) Up*Cp*Gp*Gp*Up*G)-3'


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of 5'-R(*Cp*Ap*Cp*Cp*Gp*Gp*Ap*Up*Gp*Gp*Up*(Bro) Up*Cp*Gp*Gp*Up*G)-3' within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br29

b:9.6
occ:1.00
BR E:5BU29 0.0 9.6 1.0
C5 E:5BU29 1.9 9.6 1.0
C6 E:5BU29 2.8 9.6 1.0
C4 E:5BU29 2.9 9.6 1.0
O4 E:5BU29 3.2 9.6 1.0
OP2 E:5BU29 3.2 14.5 1.0
C5 E:U28 3.5 3.3 1.0
C6 E:U28 3.7 3.3 1.0
N1 E:5BU29 4.1 9.6 1.0
C4 E:U28 4.1 3.3 1.0
N3 E:5BU29 4.2 9.6 1.0
O5' E:5BU29 4.3 14.5 1.0
C3' E:U28 4.3 10.0 1.0
P E:5BU29 4.3 14.5 1.0
N1 E:U28 4.4 3.3 1.0
O5' E:U28 4.5 10.0 1.0
OP2 E:U28 4.5 10.0 1.0
O E:HOH49 4.6 13.1 1.0
O4 E:U28 4.6 3.3 1.0
C2 E:5BU29 4.7 9.6 1.0
N3 E:U28 4.7 3.3 1.0
C2' E:U28 4.8 10.0 1.0
O3' E:U28 4.9 10.0 1.0
C2 E:U28 4.9 3.3 1.0

Reference:

S.A.Shah, A.T.Brunger. The 1.8 A Crystal Structure of A Statically Disordered 17 Base-Pair Rna Duplex: Principles of Rna Crystal Packing and Its Effect on Nucleic Acid Structure. J.Mol.Biol. V. 285 1577 1999.
ISSN: ISSN 0022-2836
PubMed: 9917398
DOI: 10.1006/JMBI.1998.2385
Page generated: Sat Dec 12 02:17:06 2020

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