Atomistry » Caesium » PDB 1av2-2j9x » 1i0k
Atomistry »
  Caesium »
    PDB 1av2-2j9x »
      1i0k »

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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy