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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: Wed Jul 10 15:02:03 2024

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