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Barium in PDB 439d: 5'-R(*Cp*Up*Gp*Gp*Gp*Cp*Gp*G)-3', 5'- R(*Cp*Cp*Gp*Cp*Cp*Up*Gp*G)-3'

Protein crystallography data

The structure of 5'-R(*Cp*Up*Gp*Gp*Gp*Cp*Gp*G)-3', 5'- R(*Cp*Cp*Gp*Cp*Cp*Up*Gp*G)-3', PDB code: 439d was solved by M.Perbandt, S.Lorenz, M.Vallazza, V.A.Erdmann, C.Betzel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.60
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 41.969, 41.969, 127.137, 90.00, 90.00, 120.00
R / Rfree (%) 22.4 / 27.1

Barium Binding Sites:

The binding sites of Barium atom in the 5'-R(*Cp*Up*Gp*Gp*Gp*Cp*Gp*G)-3', 5'- R(*Cp*Cp*Gp*Cp*Cp*Up*Gp*G)-3' (pdb code 439d). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total only one binding site of Barium was determined in the 5'-R(*Cp*Up*Gp*Gp*Gp*Cp*Gp*G)-3', 5'- R(*Cp*Cp*Gp*Cp*Cp*Up*Gp*G)-3', PDB code: 439d:

Barium binding site 1 out of 1 in 439d

Go back to Barium Binding Sites List in 439d
Barium binding site 1 out of 1 in the 5'-R(*Cp*Up*Gp*Gp*Gp*Cp*Gp*G)-3', 5'- R(*Cp*Cp*Gp*Cp*Cp*Up*Gp*G)-3'


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of 5'-R(*Cp*Up*Gp*Gp*Gp*Cp*Gp*G)-3', 5'- R(*Cp*Cp*Gp*Cp*Cp*Up*Gp*G)-3' within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba101

b:27.9
occ:0.50
O A:HOH12 2.6 33.5 1.0
O A:HOH13 2.7 38.4 1.0
N7 A:G82 2.7 29.6 1.0
O6 A:G82 2.9 34.4 1.0
O A:HOH60 3.0 30.3 1.0
O A:HOH1 3.3 38.6 1.0
C5 A:G82 3.5 21.4 1.0
O B:HOH20 3.5 47.3 1.0
C6 A:G82 3.6 33.5 1.0
N7 A:G81 3.6 21.6 1.0
C8 A:G82 3.9 23.1 1.0
O6 A:G81 4.1 25.9 1.0
C5 A:G81 4.2 25.7 1.0
C8 A:G81 4.3 24.3 1.0
C6 A:G81 4.5 24.0 1.0
O6 A:G83 4.7 30.1 1.0
C4 A:G82 4.8 22.2 1.0
N4 B:C94 4.8 23.3 1.0
OP2 A:G81 5.0 24.7 1.0
N1 A:G82 5.0 31.4 1.0
O A:HOH14 5.0 39.5 1.0
N7 A:G83 5.0 24.5 1.0
N9 A:G82 5.0 26.8 1.0

Reference:

M.Perbandt, M.Vallazza, C.Lippmann, C.Betzel, V.A.Erdmann. Structure of An Rna Duplex with An Unusual G.C Pair in Wobble-Like Conformation at 1.6 A Resolution. Acta Crystallogr.,Sect.D V. 57 219 2001.
ISSN: ISSN 0907-4449
PubMed: 11173467
DOI: 10.1107/S0907444900017042
Page generated: Sat Dec 12 01:56:02 2020

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