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Rubidium in PDB 1i0m: 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt

Protein crystallography data

The structure of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt, PDB code: 1i0m 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 / 1.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 24.820, 45.260, 43.970, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 17

Other elements in 1i0m:

The structure of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt (pdb code 1i0m). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 3 binding sites of Rubidium where determined in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt, PDB code: 1i0m:
Jump to Rubidium binding site number: 1; 2; 3;

Rubidium binding site 1 out of 3 in 1i0m

Go back to Rubidium Binding Sites List in 1i0m
Rubidium binding site 1 out of 3 in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb21

b:14.7
occ:1.00
OP1 A:DC10 3.0 12.2 1.0
O3' A:DG9 3.0 11.0 1.0
P A:DC10 3.7 11.6 1.0
C3' A:DG9 4.2 10.3 1.0
C5' A:DC10 4.5 12.3 1.0
C4' A:DG9 4.5 10.0 1.0
O5' A:DC10 4.6 11.4 1.0
O A:HOH244 4.7 30.0 1.0
OP2 A:DC10 4.8 13.5 1.0
O A:HOH175 4.9 25.9 1.0
C2' A:DG9 4.9 11.4 1.0

Rubidium binding site 2 out of 3 in 1i0m

Go back to Rubidium Binding Sites List in 1i0m
Rubidium binding site 2 out of 3 in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb22

b:30.0
occ:1.00
O A:HOH136 3.0 19.8 1.0
O4 A:DT4 3.0 10.2 1.0
O A:HOH208 3.3 22.2 1.0
O6 A:DG3 3.3 11.2 1.0
O B:HOH308 3.3 24.6 1.0
N7 A:DG3 3.4 11.8 1.0
O A:HOH164 3.6 24.6 1.0
C6 A:DG3 3.6 11.0 1.0
C5 A:DG3 3.7 11.4 1.0
O B:HOH219 3.7 28.1 1.0
O B:HOH282 3.7 27.4 1.0
C7 A:DT4 3.8 12.4 1.0
O A:HOH305 3.9 28.9 1.0
O A:HOH347 4.0 31.3 1.0
C4 A:DT4 4.0 11.5 1.0
N6 A:DA5 4.0 11.4 1.0
N6 B:DA17 4.3 10.7 1.0
C8 A:DG3 4.3 12.4 1.0
C5 A:DT4 4.4 10.9 1.0
N1 A:DG3 4.7 10.8 1.0
C4 A:DG3 4.7 9.4 1.0
O A:HOH194 4.8 25.0 1.0
O A:HOH135 4.9 17.4 1.0
O4 B:12516 4.9 11.7 1.0
O B:HOH341 5.0 30.2 1.0
O A:HOH311 5.0 30.7 1.0

Rubidium binding site 3 out of 3 in 1i0m

Go back to Rubidium Binding Sites List in 1i0m
Rubidium binding site 3 out of 3 in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Fluoroethyl Thymine in Place of T6, High Rb-Salt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Rb23

b:69.0
occ:1.00
O A:HOH185 1.7 28.6 1.0
O A:HOH175 2.5 25.9 1.0
O A:HOH195 2.7 33.4 1.0
OP2 A:DC10 2.8 13.5 1.0
P A:DC10 3.9 11.6 1.0
OP1 A:DC10 3.9 12.2 1.0
O A:HOH317 4.1 29.8 1.0
O A:HOH159 4.1 23.3 1.0
O A:HOH302 4.1 30.9 1.0
O A:HOH165 4.7 27.8 1.0
O A:HOH338 4.8 35.0 1.0
O3' A:DG9 4.8 11.0 1.0
OP1 A:DG9 5.0 15.5 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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