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Strontium in PDB 3p4a: 2'Fluoro Modified Rna Octamer FA2U2

Protein crystallography data

The structure of 2'Fluoro Modified Rna Octamer FA2U2, PDB code: 3p4a was solved by M.Manoharan, A.Akinc, R.K.Pandey, J.Qin, P.Hadwiger, M.John, K.Mills, K.Charisse, M.A.Maier, L.Nechev, E.M.Greene, P.S.Pallan, E.Rozners, K.G.Rajeev, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.20
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 43.245, 43.245, 60.791, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 23.4

Other elements in 3p4a:

The structure of 2'Fluoro Modified Rna Octamer FA2U2 also contains other interesting chemical elements:

Fluorine (F) 52 atoms
Magnesium (Mg) 2 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the 2'Fluoro Modified Rna Octamer FA2U2 (pdb code 3p4a). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 9 binding sites of Strontium where determined in the 2'Fluoro Modified Rna Octamer FA2U2, PDB code: 3p4a:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Strontium binding site 1 out of 9 in 3p4a

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Strontium binding site 1 out of 9 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr705

b:32.1
occ:1.00
 O A:HOH815 2.0 20.8 0.5
O C:HOH921 2.4 42.6 1.0
O C:HOH895 2.4 52.0 1.0
OP2 A:GF2108 2.4 14.5 1.0
O A:HOH964 2.6 30.8 1.0
O A:HOH821 2.7 24.9 1.0
P A:GF2108 3.7 13.0 1.0
O A:HOH774 4.2 15.3 0.5
OP1 A:GF2108 4.3 13.9 1.0
O A:HOH741 4.5 17.1 1.0
O3' A:CFZ107 4.7 12.8 1.0
O5' C:CFZ301 4.7 15.8 1.0
O5' A:GF2108 4.8 10.9 1.0
O5' A:CFZ107 4.8 13.5 1.0
O2P A:CFZ107 4.8 14.7 1.0
C3' A:CFZ107 5.0 12.6 1.0

Strontium binding site 2 out of 9 in 3p4a

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Strontium binding site 2 out of 9 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr704

b:18.9
occ:0.50
 O B:HOH846 2.2 35.6 1.0
O A:HOH975 2.2 35.5 1.0
O B:HOH996 2.3 27.4 1.0
O B:HOH927 2.3 26.3 1.0
O4 B:UFT213 2.6 16.0 1.0
O B:HOH823 2.8 31.0 1.0
O B:HOH836 2.9 40.9 1.0
C4 B:UFT213 3.7 14.4 1.0
O B:HOH834 4.1 32.5 1.0
C5 B:UFT213 4.2 14.7 1.0
O B:HOH851 4.3 32.7 1.0
O A:HOH845 4.4 33.2 1.0
N6 A:AF2104 4.4 15.1 1.0
N7 B:AF2212 4.6 12.6 1.0
N6 B:AF2212 4.6 10.9 1.0
O4 B:UFT214 4.7 14.3 1.0
O B:HOH791 4.7 30.7 1.0
O B:HOH790 4.7 27.9 1.0
N3 B:UFT213 4.9 13.5 1.0
O B:HOH953 4.9 58.1 1.0

Strontium binding site 3 out of 9 in 3p4a

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Strontium binding site 3 out of 9 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr701

b:21.1
occ:1.00
 O C:HOH768 2.1 24.8 0.6
O C:HOH886 2.1 49.7 1.0
O C:HOH832 2.5 37.3 1.0
O D:HOH764 2.6 22.3 1.0
O C:HOH800 2.7 17.4 0.6
O C:HOH875 2.8 30.2 1.0
O4 C:UFT305 3.3 25.3 1.0
SR C:SR707 3.3 23.1 1.0
O C:HOH853 4.2 27.5 1.0
N6 C:AF2304 4.2 23.6 1.0
C4 C:UFT305 4.3 24.3 1.0
O C:HOH761 4.4 32.8 1.0
N7 C:AF2304 4.4 17.4 1.0
O D:HOH867 4.4 26.4 0.7
O C:HOH721 4.5 25.6 1.0
O4 C:UFT306 4.5 16.7 0.9
C5 C:UFT305 4.5 20.7 1.0
O C:HOH728 4.6 14.9 1.0
O C:HOH818 4.6 27.5 1.0
O4 C:UFT306 4.6 18.9 0.1
O C:HOH752 4.8 33.0 1.0
O C:HOH857 4.8 36.2 1.0
O D:HOH748 4.9 21.6 1.0
C6 C:AF2304 4.9 24.9 1.0
C5 C:AF2304 5.0 18.2 1.0

Strontium binding site 4 out of 9 in 3p4a

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Strontium binding site 4 out of 9 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sr707

b:23.1
occ:1.00
 O C:HOH844 2.6 31.5 1.0
O C:HOH728 2.6 14.9 1.0
O C:HOH853 2.9 27.5 1.0
O C:HOH768 2.9 24.8 0.6
SR C:SR701 3.3 21.1 1.0
O C:HOH800 3.5 17.4 0.6
O C:HOH875 3.8 30.2 1.0
O C:HOH819 4.3 25.1 1.0
O C:HOH886 4.3 49.7 1.0
O D:HOH764 4.3 22.3 1.0
O C:HOH857 4.4 36.2 1.0
O C:HOH866 4.5 35.7 1.0
N7 C:AF2303 4.5 10.2 1.0
OP2 C:AF2303 4.6 15.3 1.0
O C:HOH752 4.7 33.0 1.0
O C:HOH765 4.8 21.3 1.0
OP2 C:GF2302 4.9 11.3 1.0

Strontium binding site 5 out of 9 in 3p4a

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Strontium binding site 5 out of 9 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr702

b:20.7
occ:1.00
 O D:HOH767 2.0 27.3 0.7
O C:HOH797 2.5 32.1 1.0
O C:HOH765 2.6 21.3 1.0
O D:HOH950 2.7 29.0 1.0
O D:HOH835 2.8 30.7 1.0
O D:HOH867 2.8 26.4 0.7
O4 D:UFT413 3.1 28.1 0.2
O4 D:UFT413 3.1 24.2 0.8
O C:HOH857 3.2 36.2 1.0
SR D:SR708 3.3 23.3 1.0
O D:HOH812 4.1 23.9 1.0
O D:HOH920 4.1 30.1 1.0
C4 D:UFT413 4.1 21.9 0.8
C4 D:UFT413 4.2 25.0 0.2
O D:HOH916 4.4 35.3 1.0
N7 D:AF2412 4.4 17.9 1.0
N6 D:AF2412 4.4 22.3 1.0
C5 D:UFT413 4.5 19.1 0.8
O4 D:UFT414 4.5 18.0 1.0
O D:HOH720 4.6 14.4 1.0
O C:HOH800 4.6 17.4 0.6
O D:HOH903 4.6 23.9 1.0
C5 D:UFT413 4.8 20.5 0.2
O C:HOH747 4.9 20.4 1.0
N6 C:AF2304 4.9 23.6 1.0
O D:HOH764 5.0 22.3 1.0

Strontium binding site 6 out of 9 in 3p4a

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Strontium binding site 6 out of 9 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Sr708

b:23.3
occ:1.00
 O D:HOH963 2.5 39.7 1.0
O D:HOH862 2.5 34.7 1.0
O C:HOH857 2.6 36.2 1.0
O D:HOH812 2.6 23.9 1.0
O D:HOH720 2.6 14.4 1.0
O D:HOH767 2.7 27.3 0.7
O C:HOH797 2.9 32.1 1.0
SR D:SR702 3.3 20.7 1.0
O D:HOH867 3.6 26.4 0.7
O D:HOH809 4.3 27.8 1.0
O C:HOH765 4.3 21.3 1.0
OP2 D:AF2411 4.5 11.0 0.7
N7 D:AF2411 4.5 10.3 1.0
OP2 D:GF2410 4.6 12.3 0.3
O D:HOH764 4.8 22.3 1.0
O D:HOH950 4.8 29.0 1.0
OP2 D:GF2410 4.9 10.4 0.7

Strontium binding site 7 out of 9 in 3p4a

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Strontium binding site 7 out of 9 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Sr703

b:18.9
occ:0.50
 O E:HOH873 2.3 28.3 0.7
O E:HOH897 2.4 23.0 0.6
O E:HOH949 2.5 33.6 0.7
O E:HOH837 2.5 28.1 0.7
O4 E:UFT505 2.7 17.4 1.0
O E:HOH804 3.0 23.0 1.0
O F:HOH960 3.0 40.8 1.0
O E:HOH937 3.1 22.7 0.5
C4 E:UFT505 3.7 14.7 1.0
O E:HOH879 4.2 34.2 1.0
C5 E:UFT505 4.2 14.4 1.0
O F:HOH865 4.4 41.5 1.0
N6 F:AF2612 4.4 14.1 1.0
O F:HOH999 4.4 40.6 1.0
N7 E:AF2504 4.6 12.7 1.0
N6 E:AF2504 4.6 11.3 1.0
O E:HOH938 4.7 50.9 1.0
O4 E:UFT506 4.7 15.3 1.0
O E:HOH829 4.8 26.9 1.0
O E:HOH781 4.9 31.1 1.0
N3 E:UFT505 4.9 14.0 1.0

Strontium binding site 8 out of 9 in 3p4a

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Strontium binding site 8 out of 9 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Sr709

b:28.7
occ:0.50
 O E:HOH922 1.9 32.1 1.0
O E:HOH884 2.8 59.6 1.0
O E:HOH948 2.8 40.6 1.0
O E:HOH787 2.8 21.1 1.0
O E:HOH710 3.2 38.8 0.3
O E:HOH924 3.3 35.0 1.0
F2' E:UFT506 4.9 15.0 1.0
O4' E:CFZ507 4.9 13.8 1.0
O2 E:UFT506 4.9 14.7 1.0

Strontium binding site 9 out of 9 in 3p4a

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Strontium binding site 9 out of 9 in the 2'Fluoro Modified Rna Octamer FA2U2


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of 2'Fluoro Modified Rna Octamer FA2U2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Sr706

b:18.7
occ:0.50
 O F:HOH995 2.0 34.0 1.0
OP2 F:GF2616 2.5 15.2 1.0
O F:HOH902 2.5 29.3 1.0
O F:HOH813 2.7 24.8 1.0
O F:HOH843 3.4 40.2 1.0
P F:GF2616 3.7 13.0 1.0
OP1 F:GF2616 4.3 13.6 1.0
O F:HOH749 4.5 17.0 1.0
O3' F:CFZ615 4.6 12.7 1.0
O5' F:GF2616 4.8 10.9 1.0
O5' F:CFZ615 4.8 13.5 1.0
O2P F:CFZ615 4.8 14.7 1.0
C3' F:CFZ615 5.0 12.3 1.0

Reference:

P.S.Pallan, E.M.Greene, P.A.Jicman, R.K.Pandey, M.Manoharan, E.Rozners, M.Egli. Unexpected Origins of the Enhanced Pairing Affinity of 2'-Fluoro-Modified Rna. Nucleic Acids Res. V. 39 3482 2011.
ISSN: ISSN 0305-1048
PubMed: 21183463
DOI: 10.1093/NAR/GKQ1270
Page generated: Fri Oct 11 05:22:20 2024

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