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Caesium in PDB 1i0k: 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Cs-Salt

Protein crystallography data

The structure of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Cs-Salt, PDB code: 1i0k 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 (°) 24.870, 44.680, 44.690, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 17.8

Caesium Binding Sites:

The binding sites of Caesium atom in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Cs-Salt (pdb code 1i0k). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 3 binding sites of Caesium where determined in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Cs-Salt, PDB code: 1i0k:
Jump to Caesium binding site number: 1; 2; 3;

Caesium binding site 1 out of 3 in 1i0k

Go back to Caesium Binding Sites List in 1i0k
Caesium binding site 1 out of 3 in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Cs-Salt


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Cs-Salt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs21

b:15.1
occ:1.00
OP1 A:DC10 3.1 13.5 1.0
O3' A:DG9 3.2 10.3 1.0
P A:DC10 3.8 11.4 1.0
O A:HOH272 4.2 28.9 1.0
C3' A:DG9 4.4 8.2 1.0
C5' A:DC10 4.5 8.8 1.0
C4' A:DG9 4.7 8.8 1.0
O5' A:DC10 4.7 9.1 1.0
OP2 A:DC10 5.0 14.7 1.0

Caesium binding site 2 out of 3 in 1i0k

Go back to Caesium Binding Sites List in 1i0k
Caesium binding site 2 out of 3 in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Cs-Salt


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Cs-Salt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs22

b:35.0
occ:1.00
O A:HOH134 2.8 16.7 1.0
O4 A:DT4 2.9 7.7 1.0
O B:HOH202 3.3 20.8 1.0
O6 A:DG3 3.5 9.3 1.0
N7 A:DG3 3.5 9.2 1.0
O A:HOH161 3.7 24.0 1.0
C7 A:DT4 3.7 11.3 1.0
O A:HOH151 3.7 22.9 1.0
C6 A:DG3 3.8 8.7 1.0
N6 A:DA5 3.8 8.6 1.0
C5 A:DG3 3.8 7.8 1.0
O B:HOH225 3.9 26.7 1.0
C4 A:DT4 4.0 7.8 1.0
O A:HOH198 4.1 20.3 1.0
N6 B:DA17 4.2 8.3 1.0
C5 A:DT4 4.4 7.4 1.0
C8 A:DG3 4.5 10.2 1.0
O B:HOH191 4.5 24.6 1.0
O4 B:12616 4.7 8.4 1.0
C6 A:DA5 4.8 7.6 1.0
N1 A:DG3 4.8 7.9 1.0
C4 A:DG3 4.9 8.1 1.0
O A:HOH163 4.9 27.6 1.0
N7 A:DA5 4.9 9.1 1.0

Caesium binding site 3 out of 3 in 1i0k

Go back to Caesium Binding Sites List in 1i0k
Caesium binding site 3 out of 3 in the 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Cs-Salt


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of 1.05 A Structure of the A-Decamer Gcgtatacgc with A Single 2'-O-Methyl-[Tri(Oxyethyl)] Thymine in Place of T6, Medium Cs-Salt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs23

b:65.0
occ:1.00
O3' B:DC20 2.5 10.8 1.0
C3' B:DC20 3.4 8.3 1.0
C4' B:DC20 3.4 7.9 1.0
O B:HOH140 3.6 22.6 1.0
C2' B:DC20 3.8 8.5 1.0
C5' B:DC20 4.4 11.4 1.0
O4' B:DC20 4.5 8.4 1.0
C1' B:DC20 4.7 8.6 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: Sun Dec 13 10:55:26 2020

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