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Fluorine in PDB 5do4: Thrombin-Rna Aptamer Complex

Enzymatic activity of Thrombin-Rna Aptamer Complex

All present enzymatic activity of Thrombin-Rna Aptamer Complex:
3.4.21.5;

Protein crystallography data

The structure of Thrombin-Rna Aptamer Complex, PDB code: 5do4 was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.30 / 1.86
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.663, 139.166, 44.511, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.4

Other elements in 5do4:

The structure of Thrombin-Rna Aptamer Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Thrombin-Rna Aptamer Complex (pdb code 5do4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Thrombin-Rna Aptamer Complex, PDB code: 5do4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5do4

Go back to Fluorine Binding Sites List in 5do4
Fluorine binding site 1 out of 8 in the Thrombin-Rna Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Thrombin-Rna Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F6

b:35.2
occ:1.00
 F2' A:CFZ6 0.0 35.2 1.0
C2' A:CFZ6 1.4 35.2 1.0
C1' A:CFZ6 2.4 35.3 1.0
C3' A:CFZ6 2.4 35.6 1.0
O3' A:CFZ6 2.6 35.2 1.0
C4' A:CFZ6 3.0 34.1 1.0
CA H:TRP249 3.1 27.5 1.0
O4' A:CFZ6 3.2 34.8 1.0
CB H:TRP249 3.3 29.4 1.0
N H:TRP249 3.4 27.2 1.0
N1 A:CFZ6 3.5 37.9 1.0
OP1 A:A7 3.6 28.2 1.0
CD1 H:TRP249 3.6 30.5 1.0
P A:A7 3.6 32.0 1.0
O2 A:CFZ6 3.7 41.1 1.0
CG H:TRP249 3.9 30.6 1.0
C H:LYS248 4.0 28.9 1.0
C2 A:CFZ6 4.0 36.9 1.0
CD H:LYS252 4.1 52.7 1.0
O H:LYS248 4.2 29.6 1.0
OP2 A:A7 4.3 33.6 1.0
C6 A:CFZ6 4.4 39.2 1.0
C H:TRP249 4.5 30.1 1.0
C5' A:CFZ6 4.5 32.2 1.0
CB H:LYS252 4.5 38.1 1.0
CG H:LYS248 4.5 33.0 1.0
CB H:LYS248 4.8 30.0 1.0
NZ H:LYS252 4.8 60.5 1.0
O H:TRP249 4.8 29.8 1.0
NE1 H:TRP249 4.9 28.2 1.0
CG H:LYS252 4.9 46.4 1.0
O5' A:A7 5.0 32.4 1.0

Fluorine binding site 2 out of 8 in 5do4

Go back to Fluorine Binding Sites List in 5do4
Fluorine binding site 2 out of 8 in the Thrombin-Rna Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Thrombin-Rna Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F11

b:43.0
occ:1.00
 F2' A:CFZ11 0.0 43.0 1.0
C2' A:CFZ11 1.4 41.0 1.0
C1' A:CFZ11 2.3 40.5 1.0
C3' A:CFZ11 2.4 41.4 1.0
O3' A:CFZ11 2.8 40.6 1.0
C4' A:CFZ11 2.9 42.6 1.0
O4' A:CFZ11 3.1 40.6 1.0
C5' A:UMS12 3.3 44.9 1.0
O4' A:UMS12 3.5 45.9 1.0
N1 A:CFZ11 3.6 41.6 1.0
O2 A:CFZ11 3.6 32.1 1.0
O5' A:UMS12 3.6 51.3 1.0
O A:HOH216 3.7 43.5 1.0
P A:UMS12 3.8 43.2 1.0
C4' A:UMS12 3.9 47.6 1.0
C2 A:CFZ11 4.0 37.5 1.0
C5' A:CFZ11 4.4 41.1 1.0
OP1 A:UMS12 4.5 50.5 1.0
C6 A:CFZ11 4.7 39.1 1.0
C1' A:UMS12 4.8 43.2 1.0
OP2 A:UMS12 4.9 42.3 1.0
C6 A:UMS12 5.0 38.4 1.0

Fluorine binding site 3 out of 8 in 5do4

Go back to Fluorine Binding Sites List in 5do4
Fluorine binding site 3 out of 8 in the Thrombin-Rna Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Thrombin-Rna Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F17

b:34.5
occ:1.00
 F2' A:UFT17 0.0 34.5 1.0
C2' A:UFT17 1.4 35.5 1.0
C3' A:UFT17 2.4 35.3 1.0
C1' A:UFT17 2.4 38.8 1.0
O3' A:UFT17 2.8 37.1 1.0
C4' A:UFT17 2.9 34.2 1.0
O4' A:UFT17 3.2 33.6 1.0
O5' A:ADS18 3.2 33.2 1.0
CD H:ARG123 3.5 57.8 1.0
N1 A:UFT17 3.6 43.2 1.0
P A:ADS18 3.6 35.9 1.0
NE H:ARG123 3.7 71.1 1.0
NH1 H:ARG123 3.8 73.6 1.0
O2 A:UFT17 3.9 39.9 1.0
CZ H:ARG123 3.9 75.5 1.0
C2 A:UFT17 4.2 42.0 1.0
C5' A:UFT17 4.4 34.5 1.0
C5' A:ADS18 4.4 33.6 1.0
O2P A:CFZ19 4.5 35.9 1.0
C6 A:UFT17 4.6 43.0 1.0
NH2 H:ARG123 4.7 79.8 1.0
CG H:ARG123 4.7 49.3 1.0
S3P A:ADS18 4.8 35.0 1.0

Fluorine binding site 4 out of 8 in 5do4

Go back to Fluorine Binding Sites List in 5do4
Fluorine binding site 4 out of 8 in the Thrombin-Rna Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Thrombin-Rna Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F19

b:40.7
occ:1.00
 F2' A:CFZ19 0.0 40.7 1.0
C2' A:CFZ19 1.4 40.9 1.0
C3' A:CFZ19 2.3 38.4 1.0
C1' A:CFZ19 2.3 36.6 1.0
O3' A:CFZ19 2.6 39.0 1.0
C4' A:CFZ19 3.0 36.3 1.0
O4' A:CFZ19 3.0 34.2 1.0
C5' A:UFT20 3.3 42.7 1.0
O5' A:UFT20 3.3 44.3 1.0
P A:UFT20 3.6 43.2 1.0
N1 A:CFZ19 3.6 37.0 1.0
O2 A:CFZ19 3.6 38.3 1.0
O4' A:UFT20 3.6 42.3 1.0
C4' A:UFT20 4.0 44.0 1.0
C2 A:CFZ19 4.0 37.1 1.0
O A:HOH214 4.3 37.1 1.0
C5' A:CFZ19 4.5 37.6 1.0
OP1 A:UFT20 4.5 46.5 1.0
C6 A:UFT20 4.5 43.0 1.0
OP2 A:UFT20 4.6 44.6 1.0
C6 A:CFZ19 4.7 37.3 1.0
O5' A:CFZ19 4.9 35.3 1.0
C1' A:UFT20 4.9 45.6 1.0

Fluorine binding site 5 out of 8 in 5do4

Go back to Fluorine Binding Sites List in 5do4
Fluorine binding site 5 out of 8 in the Thrombin-Rna Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Thrombin-Rna Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F20

b:46.9
occ:1.00
 F2' A:UFT20 0.0 46.9 1.0
C2' A:UFT20 1.4 50.2 1.0
C1' A:UFT20 2.4 45.6 1.0
C3' A:UFT20 2.4 46.4 1.0
O3' A:UFT20 2.7 46.4 1.0
C4' A:UFT20 3.0 44.0 1.0
O4' A:UFT20 3.1 42.3 1.0
O4' A:UMS21 3.2 50.2 1.0
C5' A:UMS21 3.3 46.9 1.0
O5' A:UMS21 3.5 45.6 1.0
N1 A:UFT20 3.6 43.9 1.0
O2 A:UFT20 3.7 41.0 1.0
C4' A:UMS21 3.7 50.0 1.0
P A:UMS21 3.8 47.5 1.0
C2 A:UFT20 4.1 43.4 1.0
O A:HOH216 4.4 43.5 1.0
C6 A:UMS21 4.4 47.1 1.0
C5' A:UFT20 4.4 42.7 1.0
C1' A:UMS21 4.4 49.6 1.0
OP1 A:UMS21 4.7 56.9 1.0
C6 A:UFT20 4.7 43.0 1.0
OP2 A:UMS21 4.8 39.7 1.0
N1 A:UMS21 4.8 51.1 1.0

Fluorine binding site 6 out of 8 in 5do4

Go back to Fluorine Binding Sites List in 5do4
Fluorine binding site 6 out of 8 in the Thrombin-Rna Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Thrombin-Rna Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F23

b:56.6
occ:1.00
 F2' A:CFZ23 0.0 56.6 1.0
C2' A:CFZ23 1.4 54.9 1.0
C3' A:CFZ23 2.3 56.2 1.0
C1' A:CFZ23 2.4 52.5 1.0
O3' A:CFZ23 2.6 61.7 1.0
C4' A:CFZ23 2.9 57.3 1.0
O4' A:CFZ23 3.1 53.2 1.0
O4' A:CFZ24 3.4 55.1 1.0
C5' A:CFZ24 3.4 55.3 1.0
N1 A:CFZ23 3.5 48.9 1.0
O5' A:CFZ24 3.6 56.3 1.0
O2 A:CFZ23 3.6 50.2 1.0
P A:CFZ24 3.7 58.1 1.0
C4' A:CFZ24 3.9 54.1 1.0
C2 A:CFZ23 4.0 49.1 1.0
C5' A:CFZ23 4.4 57.7 1.0
C6 A:CFZ23 4.6 47.1 1.0
C6 A:CFZ24 4.6 51.9 1.0
O2P A:CFZ24 4.6 61.5 1.0
O1P A:CFZ24 4.6 76.9 1.0
C1' A:CFZ24 4.7 56.0 1.0
O5' A:CFZ23 5.0 53.2 1.0

Fluorine binding site 7 out of 8 in 5do4

Go back to Fluorine Binding Sites List in 5do4
Fluorine binding site 7 out of 8 in the Thrombin-Rna Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Thrombin-Rna Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F24

b:52.0
occ:1.00
 F2' A:CFZ24 0.0 52.0 1.0
C2' A:CFZ24 1.4 56.2 1.0
C1' A:CFZ24 2.4 56.0 1.0
C3' A:CFZ24 2.4 55.6 1.0
O3' A:CFZ24 2.7 60.2 1.0
C4' A:CFZ24 3.0 54.1 1.0
O4' A:CFZ24 3.1 55.1 1.0
O4' A:CFZ25 3.4 52.7 1.0
C5' A:CFZ25 3.4 48.5 1.0
N1 A:CFZ24 3.6 52.4 1.0
O2 A:CFZ24 3.6 47.0 1.0
O5' A:CFZ25 3.7 44.6 1.0
P A:CFZ25 3.8 53.0 1.0
C4' A:CFZ25 3.9 54.4 1.0
C2 A:CFZ24 4.0 48.6 1.0
C5' A:CFZ24 4.4 55.3 1.0
C6 A:CFZ24 4.6 51.9 1.0
C1' A:CFZ25 4.7 47.8 1.0
C6 A:CFZ25 4.7 43.7 1.0
O1P A:CFZ25 4.7 70.3 1.0
O2P A:CFZ25 4.8 49.7 1.0

Fluorine binding site 8 out of 8 in 5do4

Go back to Fluorine Binding Sites List in 5do4
Fluorine binding site 8 out of 8 in the Thrombin-Rna Aptamer Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Thrombin-Rna Aptamer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F25

b:54.2
occ:1.00
 F2' A:CFZ25 0.0 54.2 1.0
C2' A:CFZ25 1.4 52.9 1.0
C3' A:CFZ25 2.4 55.3 1.0
C1' A:CFZ25 2.4 47.8 1.0
O3' A:CFZ25 2.6 63.5 1.0
C4' A:CFZ25 3.0 54.4 1.0
O4' A:CFZ25 3.2 52.7 1.0
N1 A:CFZ25 3.6 45.0 1.0
O2 A:CFZ25 3.7 43.0 1.0
C2 A:CFZ25 4.0 39.9 1.0
C5' A:CFZ25 4.5 48.5 1.0
C6 A:CFZ25 4.6 43.7 1.0

Reference:

N.D.Abeydeera, M.Egli, N.Cox, K.Mercier, J.N.Conde, P.S.Pallan, D.M.Mizurini, M.Sierant, F.E.Hibti, T.Hassell, T.Wang, F.W.Liu, H.M.Liu, C.Martinez, A.K.Sood, T.P.Lybrand, C.Frydman, R.Q.Monteiro, R.H.Gomer, B.Nawrot, X.Yang. Evoking Picomolar Binding in Rna By A Single Phosphorodithioate Linkage. Nucleic Acids Res. V. 44 8052 2016.
ISSN: ESSN 1362-4962
PubMed: 27566147
DOI: 10.1093/NAR/GKW725
Page generated: Thu Aug 1 08:46:37 2024

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