Atomistry » Barium » PDB 1djh-2x6b » 2dqo
Atomistry »
  Barium »
    PDB 1djh-2x6b »
      2dqo »

Barium in PDB 2dqo: Crystal Structure of D(Cxctxcttc):R(Gaagaagag) Where X Is 5- (N-Aminohexyl)Carbamoyl-2'-O-Methyluridine

Protein crystallography data

The structure of Crystal Structure of D(Cxctxcttc):R(Gaagaagag) Where X Is 5- (N-Aminohexyl)Carbamoyl-2'-O-Methyluridine, PDB code: 2dqo was solved by E.C.M.Juan, J.Kondo, T.Ito, Y.Ueno, A.Matsuda, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.30
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 51.400, 51.400, 44.200, 90.00, 90.00, 120.00
R / Rfree (%) 21.6 / 27.6

Other elements in 2dqo:

The structure of Crystal Structure of D(Cxctxcttc):R(Gaagaagag) Where X Is 5- (N-Aminohexyl)Carbamoyl-2'-O-Methyluridine also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of D(Cxctxcttc):R(Gaagaagag) Where X Is 5- (N-Aminohexyl)Carbamoyl-2'-O-Methyluridine (pdb code 2dqo). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 2 binding sites of Barium where determined in the Crystal Structure of D(Cxctxcttc):R(Gaagaagag) Where X Is 5- (N-Aminohexyl)Carbamoyl-2'-O-Methyluridine, PDB code: 2dqo:
Jump to Barium binding site number: 1; 2;

Barium binding site 1 out of 2 in 2dqo

Go back to Barium Binding Sites List in 2dqo
Barium binding site 1 out of 2 in the Crystal Structure of D(Cxctxcttc):R(Gaagaagag) Where X Is 5- (N-Aminohexyl)Carbamoyl-2'-O-Methyluridine


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of D(Cxctxcttc):R(Gaagaagag) Where X Is 5- (N-Aminohexyl)Carbamoyl-2'-O-Methyluridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba101

b:43.4
occ:1.00
O B:HOH220 2.7 38.6 1.0
O B:HOH227 2.7 26.9 1.0
O B:HOH216 2.9 19.1 1.0
O B:HOH221 2.9 24.9 1.0
O6 B:G13 3.0 28.6 1.0
N7 B:G13 3.0 26.8 1.0
O A:HOH232 3.0 44.1 1.0
N7 B:A12 3.2 36.9 1.0
O B:HOH213 3.6 31.5 1.0
C6 B:G13 3.6 27.2 1.0
C5 B:G13 3.6 28.0 1.0
C5 B:A12 3.9 36.5 1.0
N6 B:A12 4.0 37.4 1.0
C8 B:A12 4.0 37.4 1.0
C8 B:G13 4.2 27.4 1.0
C6 B:A12 4.2 36.5 1.0
N6 B:A14 4.6 25.8 1.0
O A:HOH209 4.7 24.4 1.0
C4 B:A12 4.8 36.8 1.0
N9 B:A12 4.9 38.4 1.0
O B:HOH209 4.9 35.7 1.0
C4 B:G13 5.0 28.2 1.0

Barium binding site 2 out of 2 in 2dqo

Go back to Barium Binding Sites List in 2dqo
Barium binding site 2 out of 2 in the Crystal Structure of D(Cxctxcttc):R(Gaagaagag) Where X Is 5- (N-Aminohexyl)Carbamoyl-2'-O-Methyluridine


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of D(Cxctxcttc):R(Gaagaagag) Where X Is 5- (N-Aminohexyl)Carbamoyl-2'-O-Methyluridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba102

b:51.2
occ:1.00
N7 B:A17 3.0 25.6 1.0
O B:HOH218 3.1 18.6 1.0
C5 B:A17 3.7 23.6 1.0
N6 B:A17 3.7 23.1 1.0
C8 B:A17 3.9 24.6 1.0
C6 B:A17 4.1 23.7 1.0
C4 B:A17 4.8 23.7 1.0
N9 B:A17 4.8 24.8 1.0
N7 B:G18 4.9 27.5 1.0
OP2 B:A17 5.0 25.0 1.0

Reference:

E.C.M.Juan, J.Kondo, T.Kurihara, T.Ito, Y.Ueno, A.Matsuda, A.Takenaka. Crystal Structures of Dna:Dna and Dna:Rna Duplexes Containing 5-(N-Aminohexyl)Carbamoyl-Modified Uracils Reveal the Basis For Properties As Antigene and Antisense Molecules Nucleic Acids Res. V. 35 1969 2007.
ISSN: ISSN 0305-1048
PubMed: 17341465
DOI: 10.1093/NAR/GKL821
Page generated: Tue Oct 27 17:00:16 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy