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Strontium in PDB 4msr: Rna 10MER Duplex with Six 2'-5'-Linkages

Protein crystallography data

The structure of Rna 10MER Duplex with Six 2'-5'-Linkages, PDB code: 4msr was solved by J.Sheng, L.Li, Engelhart A.E., J.Gan, J.Wang, J.W.Szostak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.75 / 1.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 24.219, 45.504, 81.623, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.7

Strontium Binding Sites:

The binding sites of Strontium atom in the Rna 10MER Duplex with Six 2'-5'-Linkages (pdb code 4msr). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 5 binding sites of Strontium where determined in the Rna 10MER Duplex with Six 2'-5'-Linkages, PDB code: 4msr:
Jump to Strontium binding site number: 1; 2; 3; 4; 5;

Strontium binding site 1 out of 5 in 4msr

Go back to Strontium Binding Sites List in 4msr
Strontium binding site 1 out of 5 in the Rna 10MER Duplex with Six 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Rna 10MER Duplex with Six 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr101

b:12.6
occ:1.00
O A:HOH203 2.5 16.2 1.0
O A:HOH204 2.5 14.7 1.0
O B:HOH222 2.6 14.7 1.0
O A:HOH202 2.6 12.5 1.0
O A:HOH244 2.6 16.0 1.0
O B:HOH204 2.6 11.6 1.0
O B:HOH205 2.6 13.5 1.0
O A:HOH216 2.7 14.8 1.0
O B:HOH229 4.1 18.9 1.0
O6 A:G4 4.2 10.9 0.5
O B:HOH215 4.2 14.8 1.0
O A:HOH219 4.4 21.9 1.0
O6 A:G4 4.4 9.3 0.5
O A:HOH228 4.4 25.9 1.0
O A:HOH240 4.5 17.6 1.0
O A:HOH218 4.5 17.2 1.0
O B:HOH219 4.6 21.1 1.0
N4 B:C5 4.6 10.3 1.0
N7 A:G3 4.6 10.8 0.5
O6 A:G3 4.7 12.4 0.5
O A:HOH253 4.7 25.2 1.0
O B:HOH223 4.8 34.5 1.0
O6 A:G3 4.8 8.8 0.5
O B:HOH203 4.9 12.7 1.0
N7 A:G3 4.9 9.0 0.5
O B:HOH206 5.0 14.6 1.0
N7 A:G4 5.0 9.4 0.5

Strontium binding site 2 out of 5 in 4msr

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Strontium binding site 2 out of 5 in the Rna 10MER Duplex with Six 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Rna 10MER Duplex with Six 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr102

b:13.1
occ:0.40
O A:HOH243 2.2 23.9 1.0
O A:HOH248 2.6 23.9 1.0
OP2 A:G6 2.6 18.5 1.0
O A:HOH242 2.7 21.8 1.0
P A:G6 3.7 18.1 1.0
OP1 A:G6 4.0 21.4 1.0
O A:HOH237 4.6 29.4 1.0
O A:HOH215 4.7 18.4 1.0
O5' A:G6 4.7 16.4 1.0
O2' A:C5 4.8 15.1 1.0
O B:HOH224 4.8 38.9 1.0
O A:HOH207 4.8 23.5 1.0
C2' A:C5 4.8 14.3 1.0
OP2 A:C5 4.9 16.7 1.0

Strontium binding site 3 out of 5 in 4msr

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Strontium binding site 3 out of 5 in the Rna 10MER Duplex with Six 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Rna 10MER Duplex with Six 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr101

b:12.7
occ:1.00
O B:HOH216 2.6 14.3 1.0
O B:HOH203 2.6 12.7 1.0
O A:HOH209 2.6 13.4 1.0
O6 B:G4 2.7 10.9 1.0
O B:HOH219 2.7 21.1 1.0
O6 B:G3 2.7 12.3 1.0
O B:HOH221 2.7 21.9 1.0
O B:HOH214 2.7 19.7 1.0
C6 B:G3 3.7 12.0 1.0
C6 B:G4 3.7 9.9 1.0
N7 B:G4 4.1 11.5 1.0
N4 A:C7 4.1 12.6 1.0
N7 B:G3 4.2 12.0 1.0
C5 B:G4 4.3 10.4 1.0
N4 A:C8 4.3 14.1 1.0
C5 B:G3 4.3 11.7 1.0
O B:HOH202 4.4 13.1 1.0
O B:HOH204 4.6 11.6 1.0
N4 B:C2 4.6 11.1 1.0
O A:HOH218 4.7 17.2 1.0
O A:HOH208 4.8 19.0 1.0
N1 B:G3 4.8 12.0 1.0
O6 A:G6 4.8 11.3 1.0
N1 B:G4 4.9 10.3 1.0
O B:HOH228 5.0 22.6 1.0
O B:HOH205 5.0 13.5 1.0

Strontium binding site 4 out of 5 in 4msr

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Strontium binding site 4 out of 5 in the Rna 10MER Duplex with Six 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Rna 10MER Duplex with Six 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr102

b:15.0
occ:0.80
SR B:SR103 2.4 24.2 0.4
O B:HOH234 2.5 22.6 1.0
O B:HOH237 2.5 19.8 1.0
O B:HOH241 2.6 22.5 1.0
O B:HOH250 2.8 22.6 1.0
O6 B:G10 2.8 16.6 1.0
O B:HOH245 2.9 26.1 1.0
C6 B:G10 3.8 16.8 1.0
N7 B:G10 4.1 14.7 1.0
C5 B:G10 4.3 13.5 1.0
O6 B:G9 4.5 12.9 1.0
N4 A:C1 4.6 18.4 1.0
O B:HOH232 4.8 19.1 1.0
O B:HOH242 4.9 21.0 1.0
O B:HOH238 5.0 24.7 1.0

Strontium binding site 5 out of 5 in 4msr

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Strontium binding site 5 out of 5 in the Rna 10MER Duplex with Six 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Rna 10MER Duplex with Six 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr103

b:24.2
occ:0.40
SR B:SR102 2.4 15.0 0.8
O6 B:G10 2.7 16.6 1.0
O B:HOH237 3.3 19.8 1.0
C6 B:G10 3.4 16.8 1.0
C5 B:G10 4.0 13.5 1.0
N7 B:G10 4.1 14.7 1.0
N1 B:G10 4.4 15.7 1.0
O B:HOH234 4.5 22.6 1.0
O B:HOH250 4.5 22.6 1.0
O B:HOH241 4.7 22.5 1.0
N4 A:C1 4.8 18.4 1.0

Reference:

J.Sheng, L.Li, A.E.Engelhart, J.Gan, J.Wang, J.W.Szostak. Structural Insights Into the Effects of 2'-5' Linkages on the Rna Duplex. Proc.Natl.Acad.Sci.Usa V. 111 3050 2014.
ISSN: ISSN 0027-8424
PubMed: 24516151
DOI: 10.1073/PNAS.1317799111
Page generated: Wed Dec 16 02:24:02 2020

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