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Caesium in PDB 5dea: Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Cesium Bound Form.

Protein crystallography data

The structure of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Cesium Bound Form., PDB code: 5dea was solved by N.Vasilyev, A.Polonskaia, J.C.Darnell, R.B.Darnell, D.J.Patel, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.87 / 2.80
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.570, 129.870, 36.790, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.6

Other elements in 5dea:

The structure of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Cesium Bound Form. also contains other interesting chemical elements:

Potassium (K) 4 atoms

Caesium Binding Sites:

The binding sites of Caesium atom in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Cesium Bound Form. (pdb code 5dea). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 3 binding sites of Caesium where determined in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Cesium Bound Form., PDB code: 5dea:
Jump to Caesium binding site number: 1; 2; 3;

Caesium binding site 1 out of 3 in 5dea

Go back to Caesium Binding Sites List in 5dea
Caesium binding site 1 out of 3 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Cesium Bound Form.


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Cesium Bound Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs103

b:42.8
occ:0.52
O6 A:G29 3.0 15.2 1.0
O6 A:G18 3.1 13.5 1.0
O6 A:G9 3.1 13.2 1.0
N1 A:A17 3.1 10.5 1.0
O4 A:U8 3.2 20.1 1.0
O6 A:G26 3.3 17.6 1.0
O6 A:G6 3.3 19.3 1.0
K A:K102 3.7 11.9 1.0
C6 A:G6 3.8 23.9 1.0
C2 A:A17 3.8 8.6 1.0
C6 A:G18 3.8 10.2 1.0
N1 A:G18 3.9 7.3 1.0
C6 A:G9 3.9 16.1 1.0
C6 A:G26 4.0 18.9 1.0
C6 A:G29 4.0 15.4 1.0
N1 A:G6 4.1 21.0 1.0
C6 A:A17 4.1 19.1 1.0
N1 A:G9 4.1 16.6 1.0
C4 A:U8 4.1 19.4 1.0
N1 A:G26 4.2 18.7 1.0
N6 A:A17 4.2 20.1 1.0
N7 A:G29 4.2 19.6 1.0
N3 A:U8 4.2 24.9 1.0
C5 A:G29 4.5 21.1 1.0
C5 A:G6 4.6 25.9 1.0
O2 A:U28 4.7 11.5 1.0
N4 A:C30 4.8 14.7 1.0

Caesium binding site 2 out of 3 in 5dea

Go back to Caesium Binding Sites List in 5dea
Caesium binding site 2 out of 3 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Cesium Bound Form.


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Cesium Bound Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cs103

b:41.3
occ:0.50
O6 C:G29 2.9 26.1 1.0
O6 C:G18 3.0 27.1 1.0
O C:HOH202 3.0 16.7 1.0
O4 C:U8 3.1 22.4 1.0
O6 C:G9 3.1 17.7 1.0
N1 C:A17 3.2 11.0 1.0
O6 C:G6 3.3 28.3 1.0
O6 C:G26 3.4 23.8 1.0
C6 C:G6 3.7 12.5 1.0
K C:K101 3.7 19.4 1.0
C6 C:G18 3.8 22.9 1.0
C2 C:A17 3.9 10.7 1.0
C6 C:G29 3.9 24.2 1.0
N1 C:G18 3.9 19.4 1.0
C6 C:G9 4.0 14.1 1.0
N1 C:G6 4.0 12.8 1.0
C4 C:U8 4.0 19.3 1.0
C6 C:A17 4.1 27.9 1.0
N3 C:U8 4.1 19.2 1.0
N6 C:A17 4.1 11.3 1.0
C6 C:G26 4.2 25.6 1.0
N1 C:G9 4.2 13.3 1.0
N7 C:G29 4.2 18.1 1.0
C5 C:G29 4.4 26.3 1.0
N1 C:G26 4.5 17.4 1.0
C5 C:G6 4.5 13.8 1.0
N4 C:C30 4.7 17.8 1.0
C2 C:G6 4.9 19.4 1.0
O C:HOH204 4.9 2.7 1.0

Caesium binding site 3 out of 3 in 5dea

Go back to Caesium Binding Sites List in 5dea
Caesium binding site 3 out of 3 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Cesium Bound Form.


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Cesium Bound Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cs104

b:0.0
occ:1.00
O C:HOH205 3.2 35.9 1.0
O2' C:G6 3.9 35.2 1.0
O3' C:G6 3.9 48.4 1.0
OP2 C:G7 4.0 38.2 1.0
OP2 C:A13 4.3 41.0 1.0
OP2 C:U8 4.4 27.1 1.0
OP1 C:G15 4.6 41.5 1.0
P C:G7 4.6 38.1 1.0
C2' C:G6 4.7 24.8 1.0
C1' C:G6 4.7 22.1 1.0
C5' C:G7 4.9 14.6 1.0
C3' C:G6 4.9 31.3 1.0

Reference:

N.Vasilyev, A.Polonskaia, J.C.Darnell, R.B.Darnell, D.J.Patel, A.Serganov. Crystal Structure Reveals Specific Recognition of A G-Quadruplex Rna By A Beta-Turn in the Rgg Motif of Fmrp. Proc.Natl.Acad.Sci.Usa V. 112 E5391 2015.
ISSN: ESSN 1091-6490
PubMed: 26374839
DOI: 10.1073/PNAS.1515737112
Page generated: Sun Dec 13 10:56:43 2020

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