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Rubidium in PDB 1i0n: 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Rb-Salt

Protein crystallography data

The structure of 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Rb-Salt, PDB code: 1i0n was solved by V.Tereshko, C.J.Wilds, G.Minasov, T.P.Prakash, M.A.Maier, A.Howard, Z.Wawrzak, M.Manoharan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 25.160, 44.830, 44.820, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19

Rubidium Binding Sites:

The binding sites of Rubidium atom in the 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Rb-Salt (pdb code 1i0n). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 3 binding sites of Rubidium where determined in the 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Rb-Salt, PDB code: 1i0n:
Jump to Rubidium binding site number: 1; 2; 3;

Rubidium binding site 1 out of 3 in 1i0n

Go back to Rubidium Binding Sites List in 1i0n
Rubidium binding site 1 out of 3 in the 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Rb-Salt


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Rb-Salt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb21

b:15.5
occ:1.00
OP1 A:DC10 2.9 29.5 1.0
O3' A:DG9 3.3 21.8 1.0
P A:DC10 3.7 24.4 1.0
C5' A:DC10 4.3 19.3 1.0
C3' A:DG9 4.5 21.6 1.0
O5' A:DC10 4.6 17.4 1.0
O A:HOH159 4.6 54.4 1.0
C4' A:DG9 4.7 20.0 1.0
OP2 A:DC10 4.9 29.2 1.0

Rubidium binding site 2 out of 3 in 1i0n

Go back to Rubidium Binding Sites List in 1i0n
Rubidium binding site 2 out of 3 in the 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Rb-Salt


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Rb-Salt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb22

b:28.2
occ:1.00
O4 A:DT4 2.7 17.1 1.0
O A:HOH132 3.2 26.6 1.0
O B:HOH232 3.2 42.3 1.0
N6 A:DA5 3.4 18.6 1.0
O6 A:DG3 3.5 18.1 1.0
O A:HOH236 3.5 42.0 1.0
O A:HOH119 3.6 33.3 1.0
C7 A:DT4 3.6 20.6 1.0
C4 A:DT4 3.8 16.3 1.0
N7 A:DG3 3.8 16.8 1.0
C6 A:DG3 3.8 15.5 1.0
O A:HOH123 3.9 36.8 1.0
O A:HOH178 3.9 57.2 1.0
C5 A:DG3 3.9 16.2 1.0
N6 B:DA17 4.1 16.4 1.0
C5 A:DT4 4.2 16.7 1.0
C6 A:DA5 4.4 18.1 1.0
O4 B:12616 4.5 19.4 1.0
N7 A:DA5 4.6 16.6 1.0
O A:HOH202 4.7 32.7 1.0
C8 A:DG3 4.7 20.2 1.0
C5 A:DA5 4.8 15.8 1.0
N1 A:DG3 4.8 16.3 1.0
N6 B:DA15 5.0 17.1 1.0
N3 A:DT4 5.0 14.9 1.0
C4 A:DG3 5.0 15.7 1.0

Rubidium binding site 3 out of 3 in 1i0n

Go back to Rubidium Binding Sites List in 1i0n
Rubidium binding site 3 out of 3 in the 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Rb-Salt


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of 1.3 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Rb-Salt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb23

b:69.0
occ:1.00
OP1 A:DC10 2.7 29.5 1.0
O A:HOH113 2.9 20.2 1.0
OP2 A:DC10 3.2 29.2 1.0
P A:DC10 3.3 24.4 1.0
O5' A:DC10 3.9 17.4 1.0
O A:HOH159 4.0 54.4 1.0
C5' A:DC10 4.7 19.3 1.0
O A:HOH223 4.8 51.7 1.0
O3' A:DG9 4.8 21.8 1.0

Reference:

V.Tereshko, C.J.Wilds, G.Minasov, T.P.Prakash, M.A.Maier, A.Howard, Z.Wawrzak, M.Manoharan, M.Egli. Detection of Alkali Metal Ions in Dna Crystals Using State-of-the-Art X-Ray Diffraction Experiments. Nucleic Acids Res. V. 29 1208 2001.
ISSN: ISSN 0305-1048
PubMed: 11222771
DOI: 10.1093/NAR/29.5.1208
Page generated: Wed Dec 16 02:06:35 2020

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