Fluorine in PDB 8epk: Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)

The structure of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A), PDB code: 8epk was solved by V.N.Kolyadko, S.Krishnaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.24 / 2.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.496, 79.579, 84.317, 90, 101.78, 90
R / Rfree (%)	23.1 / 26.1

The structure of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Magnesium	(Mg)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Fluorine atom in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) (pdb code 8epk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 22 binding sites of Fluorine where determined in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A), PDB code: 8epk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 22 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ E:F6 b:78.8 occ:1.00 F2' E:CFZ6 0.0 78.8 1.0 C2' E:CFZ6 1.4 78.6 1.0 C1' E:CFZ6 2.4 79.7 1.0 C3' E:CFZ6 2.4 77.4 1.0 O3' E:CFZ6 2.7 75.7 1.0 O4' E:CFZ6 3.0 79.3 1.0 C4' E:CFZ6 3.1 78.2 1.0 O B:ILE176 3.3 85.5 1.0 O4' E:UFT7 3.3 76.1 1.0 C5' E:UFT7 3.4 74.2 1.0 N1 E:CFZ6 3.6 80.8 1.0 O5' E:UFT7 3.8 74.4 1.0 C4' E:UFT7 3.8 75.5 1.0 O2 E:CFZ6 3.8 83.4 1.0 P E:UFT7 4.0 74.3 1.0 C B:ILE176 4.0 84.3 1.0 C2 E:CFZ6 4.1 82.4 1.0 CA B:TYR177 4.5 79.5 1.0 N B:TYR177 4.5 81.3 1.0 C5' E:CFZ6 4.6 79.0 1.0 C1' E:UFT7 4.6 77.7 1.0 C6 E:CFZ6 4.6 80.9 1.0 CB B:THR175 4.7 97.2 1.0 N B:ILE176 4.7 90.3 1.0 NE B:ARG165 4.7 94.6 1.0 OP1 E:UFT7 4.8 73.2 1.0 NH2 B:ARG165 4.8 100.3 1.0 C6 E:UFT7 4.8 76.2 1.0 OP2 E:UFT7 4.9 74.8 1.0 OG1 B:THR175 5.0 94.6 1.0

Fluorine binding site 2 out of 22 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ E:F7 b:79.6 occ:1.00 F2' E:UFT7 0.0 79.6 1.0 C2' E:UFT7 1.4 78.0 1.0 C3' E:UFT7 2.4 75.8 1.0 C1' E:UFT7 2.4 77.7 1.0 O3' E:UFT7 2.6 75.8 1.0 NH1 B:ARG165 2.9 98.5 1.0 C4' E:UFT7 2.9 75.5 1.0 O5' E:A2M8 3.0 79.0 1.0 O4' E:UFT7 3.1 76.1 1.0 C5' E:A2M8 3.2 81.0 1.0 CZ B:ARG165 3.4 97.7 1.0 P E:A2M8 3.5 76.0 1.0 N1 E:UFT7 3.6 77.6 1.0 N2 E:G23 3.7 87.1 1.0 NE B:ARG165 3.8 94.6 1.0 O2 E:UFT7 3.9 81.4 1.0 N4 E:OMC24 3.9 96.7 1.0 CD B:ARG165 3.9 91.8 1.0 NH2 B:ARG165 4.1 100.3 1.0 C2 E:UFT7 4.2 79.5 1.0 OP2 E:A2M8 4.2 75.4 1.0 C2 E:G23 4.4 86.2 1.0 C5' E:UFT7 4.4 74.2 1.0 C6 E:UFT7 4.6 76.2 1.0 C4' E:A2M8 4.6 84.0 1.0 OP1 E:A2M8 4.6 75.5 1.0 N1 E:G23 4.7 84.0 1.0 O4' E:A2M8 4.9 86.1 1.0 CG B:ARG165 5.0 93.6 1.0

Fluorine binding site 3 out of 22 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ E:F9 b:102.9 occ:1.00 F2' E:UFT9 0.0 102.9 1.0 C2' E:UFT9 1.4 98.2 1.0 C3' E:UFT9 2.4 96.7 1.0 C1' E:UFT9 2.4 96.4 1.0 O3' E:UFT9 2.7 100.4 1.0 C4' E:UFT9 2.9 96.9 1.0 O4' E:UFT9 3.0 96.1 1.0 N1 E:UFT9 3.6 92.3 1.0 O2 E:UFT9 3.7 95.5 1.0 P E:A2M10 3.9 100.0 1.0 OP1 E:A2M10 4.0 96.9 1.0 C2 E:UFT9 4.1 92.2 1.0 OP2 E:A2M10 4.4 104.4 1.0 C5' E:UFT9 4.4 93.9 1.0 C6 E:UFT9 4.7 89.1 1.0

Fluorine binding site 4 out of 22 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ E:F11 b:155.9 occ:1.00 F2' E:CFZ11 0.0 155.9 1.0 C2' E:CFZ11 1.4 150.8 1.0 C1' E:CFZ11 2.4 152.1 1.0 C3' E:CFZ11 2.4 143.6 1.0 O3' E:CFZ11 2.7 144.0 1.0 O2P E:CFZ12 3.0 154.1 1.0 P E:CFZ12 3.1 147.2 1.0 C4' E:CFZ11 3.2 141.4 1.0 O4' E:CFZ11 3.3 146.0 1.0 N1 E:CFZ11 3.4 153.8 1.0 C6 E:CFZ11 3.9 160.9 1.0 O1P E:CFZ12 4.0 144.3 1.0 O5' E:CFZ12 4.2 141.9 1.0 C2 E:CFZ11 4.5 148.5 1.0 C5' E:CFZ11 4.7 133.5 1.0 O2 E:CFZ11 4.7 142.2 1.0

Fluorine binding site 5 out of 22 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ E:F12 b:119.6 occ:1.00 F2' E:CFZ12 0.0 119.6 1.0 C2' E:CFZ12 1.4 124.2 1.0 C1' E:CFZ12 2.4 125.4 1.0 C3' E:CFZ12 2.4 128.4 1.0 O3' E:CFZ12 2.7 125.8 1.0 N1 E:CFZ12 3.3 125.2 1.0 C4' E:CFZ12 3.4 131.9 1.0 O4' E:CFZ12 3.5 130.7 1.0 C6 E:CFZ12 3.5 120.8 1.0 P E:OMG13 4.0 128.2 1.0 OP2 E:OMG13 4.3 124.7 1.0 C2 E:CFZ12 4.4 129.8 1.0 N7 E:OMG13 4.5 103.1 1.0 C8 E:OMG13 4.6 107.5 1.0 OP1 E:OMG13 4.7 133.0 1.0 O2 E:CFZ12 4.8 134.6 1.0 O2P E:CFZ11 4.8 121.9 1.0 C5 E:CFZ12 4.8 120.4 1.0 C5' E:CFZ12 4.8 138.8 1.0 N3 E:A2M8 4.9 94.1 1.0 O1P E:CFZ11 5.0 117.6 1.0

Fluorine binding site 6 out of 22 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ E:F14 b:111.7 occ:1.00 F2' E:CFZ14 0.0 111.7 1.0 C2' E:CFZ14 1.4 110.3 1.0 C1' E:CFZ14 2.4 107.6 1.0 C3' E:CFZ14 2.4 115.2 1.0 O3' E:CFZ14 2.7 119.7 1.0 C4' E:CFZ14 3.0 117.0 1.0 O4' E:CFZ14 3.1 111.8 1.0 C5' E:OMG15 3.4 115.8 1.0 N1 E:CFZ14 3.6 103.5 1.0 O2 E:CFZ14 3.6 99.1 1.0 O5' E:OMG15 3.8 116.5 1.0 O4' E:OMG15 3.8 107.0 1.0 P E:OMG15 4.0 121.4 1.0 C2 E:CFZ14 4.0 99.5 1.0 C4' E:OMG15 4.2 111.3 1.0 C5' E:CFZ14 4.5 120.9 1.0 C6 E:CFZ14 4.7 104.0 1.0 OP1 E:OMG15 4.8 127.1 1.0 C8 E:OMG15 4.9 106.1 1.0 OP2 E:OMG15 4.9 121.6 1.0

Fluorine binding site 7 out of 22 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ E:F16 b:120.3 occ:1.00 F2' E:UFT16 0.0 120.3 1.0 C2' E:UFT16 1.4 120.3 1.0 C1' E:UFT16 2.4 121.8 1.0 C3' E:UFT16 2.4 115.4 1.0 OP1 E:A2M17 2.6 113.0 1.0 O3' E:UFT16 2.8 111.6 1.0 P E:A2M17 2.9 110.4 1.0 OP2 E:A2M17 3.2 111.0 1.0 C6 E:UFT16 3.2 131.6 1.0 N1 E:UFT16 3.2 127.7 1.0 O4' E:UFT16 3.5 118.9 1.0 C4' E:UFT16 3.6 116.1 1.0 C5' E:UFT16 4.4 119.3 1.0 O5' E:A2M17 4.5 105.2 1.0 OP1 E:UFT16 4.5 122.8 1.0 C5 E:UFT16 4.5 137.7 1.0 C2 E:UFT16 4.6 130.1 1.0 O5' E:UFT16 5.0 116.8 1.0

Fluorine binding site 8 out of 22 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ E:F19 b:76.2 occ:1.00 F2' E:UFT19 0.0 76.2 1.0 C2' E:UFT19 1.4 75.2 1.0 C3' E:UFT19 2.3 76.2 1.0 C1' E:UFT19 2.3 75.5 1.0 O3' E:UFT19 2.4 76.2 1.0 NH1 B:ARG233 2.7 68.9 1.0 C4' E:UFT19 3.1 78.0 1.0 O4' E:UFT19 3.2 77.3 1.0 N1 E:UFT19 3.5 73.9 1.0 O2 E:UFT19 3.7 73.0 1.0 P E:OMG20 3.7 75.5 1.0 CZ B:ARG233 3.8 68.0 1.0 OP1 E:OMG20 3.9 74.2 1.0 C2 E:UFT19 4.0 73.0 1.0 OP2 E:OMG20 4.4 76.2 1.0 C5' E:UFT19 4.5 79.8 1.0 NH2 B:ARG233 4.5 69.0 1.0 C6 E:UFT19 4.6 73.9 1.0 NE B:ARG233 4.6 66.2 1.0 CD B:ARG233 4.7 65.0 1.0 C8 E:OMG20 4.8 81.0 1.0 O5' E:OMG20 4.8 77.2 1.0 N7 E:OMG20 4.8 81.8 1.0

Fluorine binding site 9 out of 22 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ E:F21 b:96.7 occ:1.00 F2' E:CFZ21 0.0 96.7 1.0 C2' E:CFZ21 1.4 93.3 1.0 C1' E:CFZ21 2.3 93.5 1.0 C3' E:CFZ21 2.4 91.0 1.0 O3' E:CFZ21 2.8 91.7 1.0 C4' E:CFZ21 2.9 92.0 1.0 O4' E:CFZ21 3.1 92.6 1.0 O4' E:OMU22 3.3 94.1 1.0 C5' E:OMU22 3.4 93.9 1.0 O5' E:OMU22 3.4 90.9 1.0 N1 E:CFZ21 3.5 91.7 1.0 O2 E:CFZ21 3.6 96.8 1.0 P E:OMU22 3.8 90.1 1.0 C4' E:OMU22 3.8 95.0 1.0 C2 E:CFZ21 4.0 93.3 1.0 C5' E:CFZ21 4.4 89.5 1.0 OP1 E:OMU22 4.6 92.0 1.0 C6 E:CFZ21 4.6 89.1 1.0 C1' E:OMU22 4.7 93.8 1.0 OP2 E:OMU22 4.8 87.2 1.0 C6 E:OMU22 4.8 87.9 1.0

Fluorine binding site 10 out of 22 in the Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Complex of Anticoagulant Rna Aptamer and Human Coagulation Factor Ixa (S195A) within 5.0Å range: probe atom residue distance (Å) B Occ E:F25 b:108.3 occ:1.00 F2' E:CFZ25 0.0 108.3 1.0 C2' E:CFZ25 1.4 105.6 1.0 C1' E:CFZ25 2.4 104.6 1.0 C3' E:CFZ25 2.4 107.6 1.0 O3' E:CFZ25 2.7 110.5 1.0 O4' E:CFZ25 3.0 107.7 1.0 C4' E:CFZ25 3.0 109.8 1.0 N1 E:CFZ25 3.6 101.4 1.0 O2 E:CFZ25 3.8 99.2 1.0 C5' E:UFT26 3.8 106.4 1.0 O4' E:UFT26 4.0 99.3 1.0 C2 E:CFZ25 4.1 98.8 1.0 P E:UFT26 4.2 109.9 1.0 O5' E:UFT26 4.2 106.4 1.0 C4' E:UFT26 4.4 102.6 1.0 C5' E:CFZ25 4.5 110.2 1.0 C6 E:CFZ25 4.7 101.5 1.0 CB B:ALA166 4.7 109.0 1.0 OP1 E:UFT26 5.0 114.4 1.0

V.N.Kolyadko, J.M.Layzer, K.Perry, B.A.Sullenger, S.Krishnaswamy. Allosteric Control of Coagulation Factor Ixa Via Its Exosite II Regulates Blood Clotting Proc.Natl.Acad.Sci.Usa 2024.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.2401136121