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Strontium in PDB 4msb: Rna 10MER Duplex with Two 2'-5'-Linkages

Protein crystallography data

The structure of Rna 10MER Duplex with Two 2'-5'-Linkages, PDB code: 4msb 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) 30.00 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 96.150, 25.893, 69.722, 90.00, 112.61, 90.00
R / Rfree (%) 18.2 / 24.7

Strontium Binding Sites:

The binding sites of Strontium atom in the Rna 10MER Duplex with Two 2'-5'-Linkages (pdb code 4msb). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 7 binding sites of Strontium where determined in the Rna 10MER Duplex with Two 2'-5'-Linkages, PDB code: 4msb:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7;

Strontium binding site 1 out of 7 in 4msb

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Strontium binding site 1 out of 7 in the Rna 10MER Duplex with Two 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 Two 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr101

b:19.8
occ:0.80
 O B:HOH205 2.6 29.8 1.0
O A:HOH206 2.6 19.5 1.0
O B:HOH202 2.6 23.6 1.0
O A:HOH219 2.6 23.0 1.0
O A:HOH220 2.7 22.1 1.0
O A:HOH223 2.7 26.6 1.0
O A:HOH209 2.7 22.1 1.0
O B:HOH232 2.7 25.8 1.0
O A:HOH233 3.1 32.7 1.0
O A:HOH218 4.1 25.3 1.0
O A:HOH204 4.2 25.2 1.0
O B:HOH204 4.3 25.1 1.0
O A:HOH205 4.5 20.0 1.0
N4 B:C5 4.5 17.1 1.0
O A:HOH222 4.6 23.3 1.0
O A:HOH208 4.6 21.3 1.0
O6 A:G3 4.7 13.5 1.0
O B:HOH209 4.7 29.1 1.0
O B:HOH206 4.7 24.8 1.0
O B:HOH201 4.8 25.1 1.0
O6 A:G4 4.8 17.9 1.0
O6 B:G6 4.9 21.7 1.0
N7 A:G3 4.9 14.7 1.0
O A:HOH202 4.9 25.1 1.0

Strontium binding site 2 out of 7 in 4msb

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Strontium binding site 2 out of 7 in the Rna 10MER Duplex with Two 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 Two 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr101

b:34.6
occ:0.60
 O A:HOH238 2.0 15.9 1.0
O B:HOH214 2.4 31.1 1.0
O B:HOH213 2.5 36.2 1.0
O B:HOH231 2.6 37.4 1.0
O B:HOH206 2.7 24.8 1.0
O A:HOH224 2.8 32.5 1.0
O A:HOH233 3.0 32.7 1.0
O6 B:G4 3.3 24.9 1.0
O6 B:G3 3.7 20.8 1.0
O A:HOH208 4.0 21.3 1.0
C6 B:G4 4.3 20.5 1.0
N7 B:G3 4.3 23.4 1.0
N7 B:G4 4.4 24.4 1.0
C6 B:G3 4.4 19.7 1.0
O B:HOH202 4.4 23.6 1.0
O A:HOH223 4.5 26.6 1.0
N4 A:C7 4.6 23.4 1.0
C5 B:G3 4.6 20.5 1.0
O6 A:G6 4.7 21.5 1.0
O A:HOH248 4.7 34.4 1.0
C5 B:G4 4.7 22.0 1.0
O B:HOH216 4.8 34.6 1.0
N4 B:C5 4.8 17.1 1.0

Strontium binding site 3 out of 7 in 4msb

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Strontium binding site 3 out of 7 in the Rna 10MER Duplex with Two 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 Two 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr101

b:27.7
occ:0.60
 O C:HOH211 2.3 40.2 1.0
O C:HOH226 2.4 47.5 1.0
O D:HOH230 2.5 43.7 1.0
O C:HOH206 2.7 35.6 1.0
O C:HOH224 2.7 26.5 1.0
O D:HOH205 2.7 26.7 1.0
O C:HOH227 2.9 46.3 1.0
O C:HOH222 4.2 40.9 1.0
O C:HOH210 4.3 31.0 1.0
O6 C:G4 4.4 22.2 1.0
O C:HOH201 4.5 35.3 1.0
N4 D:C5 4.6 19.4 1.0
O C:HOH218 4.6 33.0 1.0
O6 D:G6 4.7 25.0 1.0
O D:HOH201 4.8 31.4 1.0
O6 C:G3 4.8 18.5 1.0
O C:HOH219 4.9 32.6 1.0
N7 C:G3 4.9 20.2 1.0
O C:HOH217 5.0 43.2 1.0
N4 C:C5 5.0 23.8 1.0

Strontium binding site 4 out of 7 in 4msb

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Strontium binding site 4 out of 7 in the Rna 10MER Duplex with Two 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 Two 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr101

b:29.8
occ:0.60
 O D:HOH223 1.9 29.8 1.0
O D:HOH219 1.9 23.9 1.0
O C:HOH216 2.6 34.4 1.0
O D:HOH225 2.6 36.1 1.0
O D:HOH210 2.6 22.1 1.0
O C:HOH218 2.6 33.0 1.0
O C:HOH227 2.7 46.3 1.0
O D:HOH224 3.3 29.4 1.0
O D:HOH222 3.5 47.6 1.0
O D:HOH209 4.3 26.9 1.0
O D:HOH214 4.3 37.2 1.0
O6 D:G4 4.4 17.4 1.0
O D:HOH205 4.5 26.7 1.0
O D:HOH207 4.6 26.1 1.0
O6 C:G6 4.6 21.4 1.0
N4 C:C5 4.7 23.8 1.0
O D:HOH216 4.7 38.8 1.0
N7 D:G3 4.8 16.8 1.0
O6 D:G3 4.9 17.7 1.0
N4 D:C5 4.9 19.4 1.0

Strontium binding site 5 out of 7 in 4msb

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Strontium binding site 5 out of 7 in the Rna 10MER Duplex with Two 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 Two 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Sr101

b:40.5
occ:0.70
 O E:HOH202 2.5 32.1 1.0
O F:HOH210 2.5 35.5 1.0
O E:HOH205 2.6 27.1 1.0
O E:HOH225 2.6 37.2 1.0
O E:HOH224 2.6 35.2 1.0
O E:HOH210 2.8 31.4 1.0
O E:HOH209 4.0 33.3 1.0
O F:HOH205 4.4 36.6 1.0
O E:HOH206 4.4 28.1 1.0
O6 F:G6 4.5 20.3 1.0
O F:HOH223 4.7 38.9 1.0
O E:HOH201 4.8 36.0 1.0
O F:HOH204 4.8 34.0 1.0
N7 E:G3 4.9 20.5 1.0
O6 E:G3 4.9 17.3 1.0
O6 E:G4 4.9 21.8 1.0
O E:HOH212 5.0 38.8 1.0

Strontium binding site 6 out of 7 in 4msb

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Strontium binding site 6 out of 7 in the Rna 10MER Duplex with Two 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Rna 10MER Duplex with Two 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Sr102

b:35.5
occ:0.60
 O3' E:G10 2.5 29.4 1.0
O2' E:G10 2.6 33.1 1.0
O E:HOH226 2.8 33.3 1.0
C2' E:G10 3.5 24.9 1.0
C3' E:G10 3.5 24.9 1.0
C4' E:G10 4.3 26.0 1.0
C1' E:G10 4.8 21.8 1.0

Strontium binding site 7 out of 7 in 4msb

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Strontium binding site 7 out of 7 in the Rna 10MER Duplex with Two 2'-5'-Linkages


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Rna 10MER Duplex with Two 2'-5'-Linkages within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Sr101

b:46.2
occ:0.70
 O F:HOH215 2.4 43.9 1.0
O F:HOH206 2.4 38.0 1.0
O F:HOH218 2.5 50.6 1.0
O F:HOH209 2.7 40.3 1.0
O F:HOH205 4.4 36.6 1.0
O6 F:G3 4.5 23.4 1.0
N7 F:G3 4.7 25.1 1.0
O E:HOH222 4.8 45.4 1.0
O6 F:G4 4.8 21.5 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: Fri Oct 11 05:41:06 2024

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