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Bromine in PDB 1dp7: Cocrystal Structure of Rfx-Dbd in Complex with Its Cognate X-Box Binding Site

Protein crystallography data

The structure of Cocrystal Structure of Rfx-Dbd in Complex with Its Cognate X-Box Binding Site, PDB code: 1dp7 was solved by K.S.Gajiwala, H.Chen, F.Cornille, B.P.Roques, W.Reith, B.Mach, S.K.Burley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.843, 42.752, 52.277, 90.00, 109.21, 90.00
R / Rfree (%) 19.2 / 22.8

Bromine Binding Sites:

The binding sites of Bromine atom in the Cocrystal Structure of Rfx-Dbd in Complex with Its Cognate X-Box Binding Site (pdb code 1dp7). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Cocrystal Structure of Rfx-Dbd in Complex with Its Cognate X-Box Binding Site, PDB code: 1dp7:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 1dp7

Go back to Bromine Binding Sites List in 1dp7
Bromine binding site 1 out of 2 in the Cocrystal Structure of Rfx-Dbd in Complex with Its Cognate X-Box Binding Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Cocrystal Structure of Rfx-Dbd in Complex with Its Cognate X-Box Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br3

b:24.1
occ:1.00
BR D:BRU3 0.0 24.1 1.0
C5 D:BRU3 2.1 14.7 1.0
C6 D:BRU3 3.0 13.2 1.0
C4 D:BRU3 3.0 12.5 1.0
O4 D:BRU3 3.2 16.4 1.0
O D:HOH61 3.5 37.5 1.0
C8 D:DG2 3.6 14.6 1.0
N7 D:DG2 4.0 16.3 1.0
C2' D:DG2 4.1 16.9 1.0
N9 D:DG2 4.2 16.0 1.0
O D:HOH22 4.2 38.1 1.0
N1 D:BRU3 4.2 13.2 1.0
N3 D:BRU3 4.3 12.2 1.0
O4 D:DT4 4.7 13.8 1.0
C1' D:DG2 4.7 16.1 1.0
C5 D:DG2 4.7 14.0 1.0
C2 D:BRU3 4.8 11.9 1.0
C4 D:DG2 4.8 12.9 1.0

Bromine binding site 2 out of 2 in 1dp7

Go back to Bromine Binding Sites List in 1dp7
Bromine binding site 2 out of 2 in the Cocrystal Structure of Rfx-Dbd in Complex with Its Cognate X-Box Binding Site


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Cocrystal Structure of Rfx-Dbd in Complex with Its Cognate X-Box Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br9

b:15.1
occ:1.00
BR D:BRU9 0.0 15.1 1.0
C5 D:BRU9 2.1 12.1 1.0
C4 D:BRU9 2.9 10.3 1.0
C6 D:BRU9 3.0 13.1 1.0
O4 D:BRU9 3.1 12.9 1.0
O D:HOH30 3.2 16.5 1.0
C8 D:DA8 3.6 11.4 1.0
CZ P:TYR67 3.6 12.2 1.0
NH1 P:ARG19 3.7 14.0 1.0
N7 D:DA8 3.7 10.5 1.0
O P:HOH572 3.7 34.3 1.0
CE2 P:TYR67 3.7 11.7 1.0
OH P:TYR67 3.8 12.4 1.0
OP2 D:BRU9 3.8 12.8 1.0
N9 D:DA8 4.1 10.8 1.0
O P:HOH512 4.1 21.2 1.0
C5 D:DA8 4.1 10.3 1.0
CE1 P:TYR67 4.1 11.7 1.0
N3 D:BRU9 4.2 11.8 1.0
C3' D:DA8 4.2 10.6 1.0
O D:HOH33 4.2 17.1 1.0
N1 D:BRU9 4.3 13.7 1.0
CD2 P:TYR67 4.3 13.2 1.0
O5' D:DA8 4.3 11.0 1.0
C4 D:DA8 4.3 10.0 1.0
C2' D:DA8 4.4 12.2 1.0
OP2 D:DA8 4.5 11.7 1.0
CD1 P:TYR67 4.6 11.7 1.0
O5' D:BRU9 4.7 12.8 1.0
CG P:TYR67 4.8 9.8 1.0
C2 D:BRU9 4.8 11.2 1.0
P D:BRU9 4.8 11.1 1.0
C1' D:DA8 4.8 11.2 1.0
CZ P:ARG19 4.9 14.1 1.0
C6 D:DA8 4.9 10.1 1.0

Reference:

K.S.Gajiwala, H.Chen, F.Cornille, B.P.Roques, W.Reith, B.Mach, S.K.Burley. Structure of the Winged-Helix Protein HRFX1 Reveals A New Mode of Dna Binding. Nature V. 403 916 2000.
ISSN: ISSN 0028-0836
PubMed: 10706293
DOI: 10.1038/35002634
Page generated: Sat Dec 12 01:59:59 2020

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