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Bromine in PDB 1uhx: Crystal Structure of D(Gcgagagc): the Base-Intercalated Duplex

Protein crystallography data

The structure of Crystal Structure of D(Gcgagagc): the Base-Intercalated Duplex, PDB code: 1uhx was solved by J.Kondo, S.I.Umeda, K.Fujita, T.Sunami, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 37.670, 37.670, 65.490, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 27.8

Other elements in 1uhx:

The structure of Crystal Structure of D(Gcgagagc): the Base-Intercalated Duplex also contains other interesting chemical elements:

Cobalt (Co) 1 atom
Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of D(Gcgagagc): the Base-Intercalated Duplex (pdb code 1uhx). 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 Crystal Structure of D(Gcgagagc): the Base-Intercalated Duplex, PDB code: 1uhx:

Bromine binding site 1 out of 1 in 1uhx

Go back to Bromine Binding Sites List in 1uhx
Bromine binding site 1 out of 1 in the Crystal Structure of D(Gcgagagc): the Base-Intercalated Duplex


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 D(Gcgagagc): the Base-Intercalated Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br2

b:14.1
occ:1.00
BR A:CBR2 0.0 14.1 1.0
C5 A:CBR2 1.9 19.0 1.0
C6 A:CBR2 2.9 9.3 1.0
C4 A:CBR2 2.9 18.3 1.0
N4 A:CBR2 3.1 8.8 1.0
O6 A:DG3 3.6 9.5 1.0
N2 A:NCO78 3.6 4.2 0.3
C8 A:DG1 3.6 7.9 1.0
C6 A:DG3 3.7 8.2 1.0
N7 A:DG1 3.9 10.4 1.0
N1 A:DG3 4.0 12.6 1.0
N1 A:CBR2 4.2 12.6 1.0
C2' A:DG1 4.2 13.8 1.0
N3 A:CBR2 4.2 17.9 1.0
N9 A:DG1 4.2 13.4 1.0
C5 A:DG3 4.3 7.3 1.0
O A:HOH12 4.4 20.4 1.0
C5 A:DG1 4.6 14.4 1.0
C2 A:CBR2 4.7 11.8 1.0
C2 A:DG3 4.7 11.0 1.0
C1' A:DG1 4.7 10.0 1.0
C4 A:DG1 4.8 14.7 1.0
N7 A:DG3 4.8 13.2 1.0
C4 A:DG3 4.9 15.8 1.0

Reference:

J.Kondo, S.I.Umeda, K.Fujita, T.Sunami, A.Takenaka. X-Ray Analyses of D(Gcgaxagc) Containing G and T at X: the Base-Intercalated Duplex Is Still Stable Even in Point Mutants at the Fifth Residue. J.Synchrotron Radiat. V. 11 117 2004.
ISSN: ISSN 0909-0495
PubMed: 14646150
DOI: 10.1107/S0909049503023562
Page generated: Wed Jul 10 17:27:10 2024

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