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Fluorine in PDB 3dd2: Crystal Structure of An Rna Aptamer Bound to Human Thrombin

Enzymatic activity of Crystal Structure of An Rna Aptamer Bound to Human Thrombin

All present enzymatic activity of Crystal Structure of An Rna Aptamer Bound to Human Thrombin:
3.4.21.5;

Protein crystallography data

The structure of Crystal Structure of An Rna Aptamer Bound to Human Thrombin, PDB code: 3dd2 was solved by S.B.Long, B.A.Sullenger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.35 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.766, 134.017, 44.033, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 25.4

Other elements in 3dd2:

The structure of Crystal Structure of An Rna Aptamer Bound to Human Thrombin also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin (pdb code 3dd2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin, PDB code: 3dd2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 3dd2

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Fluorine binding site 1 out of 10 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


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Stereo pair view

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

b:40.2
occ:1.00
 F B:CFL6 0.0 40.2 1.0
C2' B:CFL6 1.4 39.2 1.0
C1' B:CFL6 2.4 40.1 1.0
C3' B:CFL6 2.4 37.4 1.0
O3' B:CFL6 2.7 36.1 1.0
C4' B:CFL6 3.0 39.3 1.0
CA H:TRP237 3.1 32.3 1.0
O4' B:CFL6 3.2 38.5 1.0
CB H:TRP237 3.2 32.5 1.0
N H:TRP237 3.5 30.4 1.0
OP1 B:A7 3.6 32.8 1.0
N1 B:CFL6 3.6 39.5 1.0
CD1 H:TRP237 3.6 34.7 1.0
P B:A7 3.6 34.0 1.0
O2 B:CFL6 3.8 43.6 1.0
CG H:TRP237 3.8 34.0 1.0
CD H:LYS240 3.9 52.5 1.0
C H:LYS236 4.0 31.2 1.0
C2 B:CFL6 4.1 41.2 1.0
O H:LYS236 4.2 30.4 1.0
OP2 B:A7 4.2 31.2 1.0
CG H:LYS236 4.4 33.2 1.0
C H:TRP237 4.4 32.6 1.0
C5' B:CFL6 4.5 36.7 1.0
CB H:LYS240 4.5 45.1 1.0
C6 B:CFL6 4.6 41.3 1.0
NZ H:LYS240 4.6 56.4 1.0
O B:HOH1028 4.7 54.4 1.0
CB H:LYS236 4.7 31.6 1.0
O H:TRP237 4.8 31.5 1.0
CE H:LYS240 4.9 54.7 1.0
CG H:LYS240 4.9 47.8 1.0
NE1 H:TRP237 4.9 35.8 1.0
O5' B:A7 5.0 33.0 1.0
CD H:LYS236 5.0 33.7 1.0

Fluorine binding site 2 out of 10 in 3dd2

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Fluorine binding site 2 out of 10 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


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Stereo pair view

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

b:41.4
occ:1.00
 F B:CFL11 0.0 41.4 1.0
C2' B:CFL11 1.4 40.1 1.0
C1' B:CFL11 2.4 38.9 1.0
C3' B:CFL11 2.4 41.0 1.0
O3' B:CFL11 2.7 41.5 1.0
C4' B:CFL11 2.9 39.3 1.0
O4' B:CFL11 3.1 39.2 1.0
C5' B:UFT12 3.1 37.6 1.0
O5' B:UFT12 3.5 39.6 1.0
O4' B:UFT12 3.5 35.0 1.0
N1 B:CFL11 3.6 39.2 1.0
C2 B:PEG104 3.6 80.0 1.0
O2 B:CFL11 3.7 36.4 1.0
P B:UFT12 3.8 42.5 1.0
O1 B:PEG104 3.8 78.9 1.0
C4' B:UFT12 3.8 34.9 1.0
O B:HOH1021 4.1 41.3 1.0
C2 B:CFL11 4.1 38.4 1.0
O2 B:PEG104 4.1 81.2 1.0
C1 B:PEG104 4.1 79.4 1.0
C5' B:CFL11 4.4 40.6 1.0
C3 B:PEG104 4.4 81.4 1.0
OP1 B:UFT12 4.5 46.5 1.0
C6 B:CFL11 4.7 37.4 1.0
C6 B:UFT12 4.8 30.1 1.0
OP2 B:UFT12 4.8 42.8 1.0
C1' B:UFT12 4.9 33.0 1.0

Fluorine binding site 3 out of 10 in 3dd2

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Fluorine binding site 3 out of 10 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of An Rna Aptamer Bound to Human Thrombin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F12

b:34.1
occ:1.00
 F2' B:UFT12 0.0 34.1 1.0
C2' B:UFT12 1.4 33.8 1.0
C1' B:UFT12 2.4 33.0 1.0
C3' B:UFT12 2.4 35.4 1.0
O3' B:UFT12 2.6 35.1 1.0
C4' B:UFT12 3.0 34.9 1.0
O4' B:UFT12 3.1 35.0 1.0
C5' B:G13 3.2 36.3 1.0
N1 B:UFT12 3.6 31.0 1.0
O4' B:G13 3.7 35.1 1.0
O B:HOH1024 3.7 51.6 1.0
O5' B:G13 3.8 35.0 1.0
O2 B:UFT12 3.8 30.9 1.0
P B:G13 3.9 35.6 1.0
C4' B:G13 4.0 35.4 1.0
C2 B:UFT12 4.2 30.2 1.0
C5' B:UFT12 4.4 37.6 1.0
OP1 B:G13 4.6 34.1 1.0
O B:HOH1044 4.7 54.0 1.0
C6 B:UFT12 4.7 30.1 1.0
O2' B:A15 4.8 31.5 1.0
N2 B:G16 4.8 29.5 1.0
OP2 B:G13 4.9 31.8 1.0
N3 B:G13 5.0 32.3 1.0

Fluorine binding site 4 out of 10 in 3dd2

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Fluorine binding site 4 out of 10 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of An Rna Aptamer Bound to Human Thrombin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F17

b:61.0
occ:1.00
 F2' B:UFT17 0.0 61.0 1.0
C2' B:UFT17 1.4 60.2 1.0
C1' B:UFT17 2.3 61.1 1.0
C3' B:UFT17 2.4 57.2 1.0
OP1 B:A18 2.6 52.5 1.0
O3' B:UFT17 2.8 53.8 1.0
C4' B:UFT17 2.9 55.8 1.0
O4' B:UFT17 3.0 59.8 1.0
NH1 H:ARG126 3.1 63.3 1.0
P B:A18 3.3 53.5 1.0
CZ H:ARG126 3.5 61.6 1.0
N1 B:UFT17 3.6 63.9 1.0
O2 B:UFT17 3.8 66.1 1.0
NH2 H:ARG126 3.9 61.7 1.0
NE H:ARG126 4.0 60.7 1.0
C2 B:UFT17 4.1 65.3 1.0
O5' B:A18 4.2 47.3 1.0
CD H:ARG126 4.4 54.9 1.0
C5' B:UFT17 4.4 52.4 1.0
OP2 B:A18 4.5 54.0 1.0
C6 B:UFT17 4.7 64.9 1.0
O2P B:CFL19 5.0 39.3 1.0

Fluorine binding site 5 out of 10 in 3dd2

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Fluorine binding site 5 out of 10 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of An Rna Aptamer Bound to Human Thrombin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F19

b:41.4
occ:1.00
 F B:CFL19 0.0 41.4 1.0
C2' B:CFL19 1.4 39.8 1.0
C1' B:CFL19 2.4 37.7 1.0
C3' B:CFL19 2.4 39.3 1.0
O3' B:CFL19 2.7 42.3 1.0
C4' B:CFL19 3.0 39.5 1.0
O4' B:CFL19 3.1 38.5 1.0
C5' B:UFT20 3.3 42.4 1.0
C1 B:PEG104 3.5 79.4 1.0
O5' B:UFT20 3.5 41.8 1.0
N1 B:CFL19 3.6 36.0 1.0
O2 B:CFL19 3.6 36.0 1.0
P B:UFT20 3.8 44.0 1.0
O4' B:UFT20 3.8 42.9 1.0
C2 B:CFL19 4.1 36.5 1.0
C2 B:PEG104 4.1 80.0 1.0
C4' B:UFT20 4.1 44.1 1.0
C5' B:CFL19 4.5 38.6 1.0
O1 B:PEG104 4.6 78.9 1.0
OP1 B:UFT20 4.6 46.6 1.0
C6 B:UFT20 4.7 39.7 1.0
O2 B:PEG104 4.7 81.2 1.0
OP2 B:UFT20 4.7 44.2 1.0
C6 B:CFL19 4.7 35.7 1.0

Fluorine binding site 6 out of 10 in 3dd2

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Fluorine binding site 6 out of 10 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of An Rna Aptamer Bound to Human Thrombin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F20

b:46.8
occ:1.00
 F2' B:UFT20 0.0 46.8 1.0
C2' B:UFT20 1.4 44.5 1.0
C1' B:UFT20 2.3 43.4 1.0
C3' B:UFT20 2.4 45.0 1.0
O3' B:UFT20 2.7 47.7 1.0
C4' B:UFT20 3.0 44.1 1.0
O4' B:UFT20 3.1 42.9 1.0
C5' B:UFT21 3.2 48.2 1.0
O4' B:UFT21 3.2 49.3 1.0
O5' B:UFT21 3.5 46.3 1.0
N1 B:UFT20 3.6 42.0 1.0
O2 B:UFT20 3.6 41.8 1.0
C4' B:UFT21 3.8 48.9 1.0
P B:UFT21 3.8 48.3 1.0
C2 B:UFT20 4.0 40.8 1.0
O B:HOH1031 4.1 58.4 1.0
O B:HOH1021 4.4 41.3 1.0
C6 B:UFT21 4.4 44.8 1.0
C5' B:UFT20 4.4 42.4 1.0
C1' B:UFT21 4.5 48.2 1.0
OP1 B:UFT21 4.6 51.1 1.0
C6 B:UFT20 4.7 39.7 1.0
OP2 B:UFT21 4.8 46.8 1.0
N1 B:UFT21 4.8 45.6 1.0

Fluorine binding site 7 out of 10 in 3dd2

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Fluorine binding site 7 out of 10 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of An Rna Aptamer Bound to Human Thrombin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F21

b:50.2
occ:1.00
 F2' B:UFT21 0.0 50.2 1.0
C2' B:UFT21 1.4 48.7 1.0
C1' B:UFT21 2.4 48.2 1.0
C3' B:UFT21 2.4 50.0 1.0
O3' B:UFT21 2.8 50.5 1.0
C4' B:UFT21 3.0 48.9 1.0
O4' B:UFT21 3.1 49.3 1.0
C5' B:A22 3.3 53.3 1.0
O4' B:A22 3.4 53.8 1.0
O5' B:A22 3.5 52.6 1.0
N1 B:UFT21 3.6 45.6 1.0
P B:A22 3.9 51.5 1.0
O2 B:UFT21 3.9 45.2 1.0
C4' B:A22 3.9 54.1 1.0
C2 B:UFT21 4.1 44.9 1.0
C5' B:UFT21 4.4 48.2 1.0
C6 B:UFT21 4.6 44.8 1.0
C1' B:A22 4.7 52.9 1.0
OP1 B:A22 4.7 54.4 1.0
OP2 B:A22 4.8 50.7 1.0
C8 B:A22 4.8 49.1 1.0
N9 B:A22 5.0 50.4 1.0

Fluorine binding site 8 out of 10 in 3dd2

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Fluorine binding site 8 out of 10 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of An Rna Aptamer Bound to Human Thrombin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F23

b:55.8
occ:1.00
 F B:CFL23 0.0 55.8 1.0
C2' B:CFL23 1.4 54.5 1.0
C1' B:CFL23 2.4 53.2 1.0
C3' B:CFL23 2.4 55.4 1.0
O3' B:CFL23 2.8 57.1 1.0
C4' B:CFL23 3.0 55.3 1.0
O4' B:CFL23 3.1 53.6 1.0
C5' B:CFL24 3.1 54.6 1.0
O4' B:CFL24 3.4 52.5 1.0
O5' B:CFL24 3.4 56.1 1.0
N1 B:CFL23 3.6 50.6 1.0
O2 B:CFL23 3.7 50.8 1.0
O4 B:PEG103 3.7 64.5 1.0
C4' B:CFL24 3.8 54.2 1.0
P B:CFL24 3.8 58.4 1.0
C2 B:CFL23 4.1 50.1 1.0
C5' B:CFL23 4.5 54.9 1.0
C6 B:CFL24 4.6 44.9 1.0
C6 B:CFL23 4.7 50.2 1.0
O2P B:CFL24 4.7 60.3 1.0
C1' B:CFL24 4.7 50.6 1.0
C4 B:PEG103 4.8 63.6 1.0
O1P B:CFL24 4.8 57.5 1.0

Fluorine binding site 9 out of 10 in 3dd2

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Fluorine binding site 9 out of 10 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of An Rna Aptamer Bound to Human Thrombin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F24

b:53.2
occ:1.00
 F B:CFL24 0.0 53.2 1.0
C2' B:CFL24 1.4 53.1 1.0
C1' B:CFL24 2.4 50.6 1.0
C3' B:CFL24 2.4 54.5 1.0
O3' B:CFL24 2.8 57.5 1.0
C4' B:CFL24 3.0 54.2 1.0
O4' B:CFL24 3.1 52.5 1.0
O4' B:CFL25 3.2 55.4 1.0
C5' B:CFL25 3.2 55.9 1.0
O1 B:PEG103 3.3 63.4 1.0
O5' B:CFL25 3.5 57.0 1.0
N1 B:CFL24 3.6 47.1 1.0
O2 B:CFL24 3.6 45.7 1.0
C4' B:CFL25 3.7 56.8 1.0
P B:CFL25 3.9 58.4 1.0
C2 B:CFL24 4.0 45.8 1.0
C2 B:PEG103 4.1 63.0 1.0
C1 B:PEG103 4.3 63.3 1.0
C1' B:CFL25 4.5 53.9 1.0
C6 B:CFL25 4.5 47.0 1.0
C5' B:CFL24 4.5 54.6 1.0
C6 B:CFL24 4.7 44.9 1.0
O2P B:CFL25 4.8 60.2 1.0
O1P B:CFL25 4.8 57.9 1.0
N1 B:CFL25 4.9 48.9 1.0

Fluorine binding site 10 out of 10 in 3dd2

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Fluorine binding site 10 out of 10 in the Crystal Structure of An Rna Aptamer Bound to Human Thrombin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of An Rna Aptamer Bound to Human Thrombin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F25

b:57.1
occ:1.00
 F B:CFL25 0.0 57.1 1.0
C2' B:CFL25 1.4 56.1 1.0
C1' B:CFL25 2.3 53.9 1.0
C3' B:CFL25 2.4 57.4 1.0
O3' B:CFL25 2.7 62.2 1.0
C4' B:CFL25 3.0 56.8 1.0
O4' B:CFL25 3.1 55.4 1.0
N1 B:CFL25 3.6 48.9 1.0
O2 B:CFL25 3.6 47.9 1.0
C2 B:CFL25 4.0 47.8 1.0
O5' B:DT26 4.1 62.8 1.0
P B:DT26 4.1 64.7 1.0
C5' B:CFL25 4.5 55.9 1.0
C6 B:CFL25 4.6 47.0 1.0
OP2 B:DT26 4.9 62.1 1.0
OP1 B:DT26 5.0 65.0 1.0

Reference:

S.B.Long, M.B.Long, R.R.White, B.A.Sullenger. Crystal Structure of An Rna Aptamer Bound to Thrombin. Rna V. 14 2504 2008.
ISSN: ISSN 1355-8382
PubMed: 18971322
DOI: 10.1261/RNA.1239308
Page generated: Wed Jul 31 17:53:59 2024

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