Atomistry » Strontium » PDB 3ilg-4rne » 3p4a
Atomistry »
  Strontium »
    PDB 3ilg-4rne »
      3p4a »

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

Go back to Strontium Binding Sites List in 3p4a
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

Go back to Strontium Binding Sites List in 3p4a
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

Go back to Strontium Binding Sites List in 3p4a
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

Go back to Strontium Binding Sites List in 3p4a
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

Go back to Strontium Binding Sites List in 3p4a
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

Go back to Strontium Binding Sites List in 3p4a
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

Go back to Strontium Binding Sites List in 3p4a
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

Go back to Strontium Binding Sites List in 3p4a
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

Go back to Strontium Binding Sites List in 3p4a
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy