Atomistry » Barium » PDB 2y5y-4e60 » 439d
Atomistry »
  Barium »
    PDB 2y5y-4e60 »
      439d »

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: Mon Jul 7 02:17:18 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy