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Sodium 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:

Barium (Ba) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2dqo

Go back to Sodium Binding Sites List in 2dqo
Sodium binding site 1 out of 3 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 Sodium with other atoms in the Na 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
A:Na203

b:23.1
occ:1.00
O A:HOH206 2.5 44.0 1.0
OP2 A:OMU5 2.7 35.4 1.0
O1Y A:CMY105 2.8 30.1 1.0
O A:HOH213 2.8 44.3 1.0
C1Y A:CMY105 3.7 30.6 1.0
P A:OMU5 4.0 35.6 1.0
C2Y A:CMY105 4.1 34.1 1.0
O5' A:OMU5 4.2 32.5 1.0
N1Y A:CMY105 4.4 30.4 1.0
C5 A:OMU5 4.7 29.4 1.0
C6 A:OMU5 4.9 28.4 1.0
OP2 A:DC6 4.9 34.6 1.0
OP1 A:OMU5 5.0 36.9 1.0

Sodium binding site 2 out of 3 in 2dqo

Go back to Sodium Binding Sites List in 2dqo
Sodium binding site 2 out of 3 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 Sodium with other atoms in the Na 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:Na201

b:21.8
occ:1.00
O B:HOH217 2.4 34.9 1.0
O B:HOH211 2.5 32.0 1.0
O B:HOH212 2.9 26.1 1.0
O B:HOH205 3.2 25.5 1.0
N7 B:A15 3.2 23.0 1.0
C8 B:A15 4.0 22.7 1.0
C5 B:A15 4.2 23.1 1.0
OP2 B:A15 4.2 32.5 1.0
O B:HOH215 4.3 57.1 1.0
N6 B:A15 4.3 20.4 1.0
C6 B:A15 4.7 22.6 1.0
O B:HOH218 4.7 18.6 1.0
N7 B:G16 4.8 24.3 1.0
C7Y A:CMY102 4.9 57.9 1.0

Sodium binding site 3 out of 3 in 2dqo

Go back to Sodium Binding Sites List in 2dqo
Sodium binding site 3 out of 3 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 Sodium with other atoms in the Na binding site number 3 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:Na202

b:18.8
occ:1.00
O B:HOH228 2.8 40.2 1.0
OP2 B:G18 4.4 30.2 1.0
OP1 B:A17 5.0 31.5 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 Dec 15 05:47:35 2020

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