Fluorine in PDB 5vof: Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban

All present enzymatic activity of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban:
3.4.21.6;

The structure of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban, PDB code: 5vof was solved by S.Krishnaswamy, S.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.05 / 2.25
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	55.744, 164.275, 124.521, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.3

The structure of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Calcium	(Ca)	1 atom
Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Fluorine atom in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban (pdb code 5vof). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 19 binding sites of Fluorine where determined in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban, PDB code: 5vof:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 19 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban within 5.0Å range: probe atom residue distance (Å) B Occ A:F6 b:93.7 occ:1.00 F A:CFL6 0.0 93.7 1.0 C2' A:CFL6 1.3 71.4 1.0 O4' A:CFL7 2.2 70.9 1.0 C1' A:CFL6 2.3 74.6 1.0 C3' A:CFL6 2.4 76.3 1.0 O5' A:CFL7 2.5 73.7 1.0 O2 A:CFL6 2.7 64.4 1.0 N1 A:CFL6 2.7 71.7 1.0 C2 A:CFL6 2.9 66.2 1.0 O3' A:CFL6 2.9 81.4 1.0 C6 A:CFL7 2.9 64.5 1.0 C5' A:CFL7 3.0 76.6 1.0 C4' A:CFL7 3.1 72.9 1.0 C1' A:CFL7 3.3 68.8 1.0 O4' A:CFL6 3.4 75.8 1.0 N1 A:CFL7 3.5 64.8 1.0 P A:CFL7 3.5 77.8 1.0 C4' A:CFL6 3.5 77.6 1.0 C6 A:CFL6 3.7 69.9 1.0 N3 A:CFL6 4.0 62.6 1.0 C5 A:CFL7 4.0 63.3 1.0 C3' A:CFL7 4.1 76.8 1.0 O2P A:CFL7 4.3 80.5 1.0 C2' A:CFL7 4.4 73.3 1.0 O1P A:CFL7 4.5 83.1 1.0 C5 A:CFL6 4.6 65.4 1.0 C4 A:CFL6 4.7 64.7 1.0 C2 A:CFL7 4.8 63.0 1.0 C5' A:CFL6 4.8 82.6 1.0 N2 A:G31 4.9 57.5 1.0

Fluorine binding site 2 out of 19 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban within 5.0Å range: probe atom residue distance (Å) B Occ A:F7 b:89.5 occ:1.00 F A:CFL7 0.0 89.5 1.0 C2' A:CFL7 1.3 73.3 1.0 O4' A:CFL8 2.3 64.0 1.0 C1' A:CFL7 2.4 68.8 1.0 C3' A:CFL7 2.4 76.8 1.0 O2 A:CFL7 2.7 58.7 1.0 N1 A:CFL7 2.9 64.8 1.0 C5' A:CFL8 2.9 70.2 1.0 C2 A:CFL7 3.0 63.0 1.0 C4' A:CFL8 3.0 70.9 1.0 O3' A:CFL7 3.0 79.5 1.0 O5' A:CFL8 3.2 71.2 1.0 O4' A:CFL7 3.5 70.9 1.0 C4' A:CFL7 3.5 72.9 1.0 C1' A:CFL8 3.6 65.1 1.0 C6 A:CFL8 3.6 66.3 1.0 P A:CFL8 3.8 74.3 1.0 C6 A:CFL7 4.0 64.5 1.0 N1 A:CFL8 4.0 63.7 1.0 N3 A:CFL7 4.2 60.8 1.0 C3' A:CFL8 4.3 71.9 1.0 NH1 H:ARG93 4.5 44.6 1.0 C2' A:CFL8 4.6 71.5 1.0 C5 A:CFL8 4.7 66.1 1.0 O1P A:CFL8 4.7 72.2 1.0 O2P A:CFL8 4.7 69.7 1.0 C5' A:CFL7 4.9 76.6 1.0 C5 A:CFL7 5.0 63.3 1.0

Fluorine binding site 3 out of 19 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban within 5.0Å range: probe atom residue distance (Å) B Occ A:F8 b:85.1 occ:1.00 F A:CFL8 0.0 85.1 1.0 C2' A:CFL8 1.4 71.5 1.0 O4' A:CFL9 2.3 71.5 1.0 C3' A:CFL8 2.4 71.9 1.0 C1' A:CFL8 2.4 65.1 1.0 O5' A:CFL9 2.6 80.9 1.0 O2 A:CFL8 2.8 61.3 1.0 N1 A:CFL8 2.8 63.7 1.0 C2 A:CFL8 3.0 63.6 1.0 O3' A:CFL8 3.1 70.6 1.0 C4' A:CFL9 3.2 75.1 1.0 P A:CFL9 3.4 71.8 1.0 C5' A:CFL9 3.4 76.3 1.0 C1' A:CFL9 3.4 67.9 1.0 C6 A:CFL9 3.5 67.7 1.0 O4' A:CFL8 3.5 64.0 1.0 C4' A:CFL8 3.5 70.9 1.0 CB H:ASN92 3.7 49.3 1.0 N1 A:CFL9 3.8 70.5 1.0 ND2 H:ASN92 3.8 51.7 1.0 C6 A:CFL8 3.9 66.3 1.0 O2P A:CFL9 3.9 76.4 1.0 N3 A:CFL8 4.1 64.4 1.0 O H:ASN92 4.1 46.5 1.0 CG H:ASN92 4.3 51.0 1.0 C3' A:CFL9 4.4 74.9 1.0 C5 A:CFL9 4.5 70.8 1.0 CA H:ASN92 4.6 46.9 1.0 C2' A:CFL9 4.6 70.9 1.0 O1P A:CFL9 4.6 81.2 1.0 C H:ASN92 4.6 44.8 1.0 C5 A:CFL8 4.8 66.1 1.0 C5' A:CFL8 4.8 70.2 1.0 C4 A:CFL8 4.9 65.3 1.0

Fluorine binding site 4 out of 19 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban within 5.0Å range: probe atom residue distance (Å) B Occ A:F9 b:93.0 occ:1.00 F A:CFL9 0.0 93.0 1.0 C2' A:CFL9 1.4 70.9 1.0 C3' A:CFL9 2.4 74.9 1.0 C1' A:CFL9 2.4 67.9 1.0 O2 A:CFL9 2.7 73.6 1.0 N1 A:CFL9 2.8 70.5 1.0 N2 A:G25 2.9 0.6 1.0 C2 A:CFL9 3.0 71.2 1.0 O3' A:CFL9 3.1 78.5 1.0 N1 A:G25 3.2 92.4 1.0 OP2 A:A10 3.4 64.2 1.0 C2 A:G25 3.4 95.5 1.0 O4' A:CFL9 3.5 71.5 1.0 C4' A:CFL9 3.6 75.1 1.0 P A:A10 3.6 68.7 1.0 O6 A:G11 3.8 58.7 1.0 O A:HOH208 3.8 42.4 1.0 MG A:MG102 3.9 50.5 1.0 C6 A:CFL9 3.9 67.7 1.0 N3 A:CFL9 4.1 73.6 1.0 N7 A:G11 4.1 61.0 1.0 C6 A:G25 4.2 84.5 1.0 OP1 A:A10 4.6 63.6 1.0 O6 A:G25 4.6 0.3 1.0 C6 A:G11 4.6 59.7 1.0 N3 A:G25 4.6 78.7 1.0 O5' A:A10 4.6 68.3 1.0 C5 A:G11 4.7 58.9 1.0 C5 A:CFL9 4.8 70.8 1.0 C5' A:CFL9 4.9 76.3 1.0 C4 A:CFL9 4.9 73.0 1.0 O4 A:UFT24 4.9 74.5 1.0 O A:HOH212 5.0 45.2 1.0

Fluorine binding site 5 out of 19 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban within 5.0Å range: probe atom residue distance (Å) B Occ A:F12 b:94.4 occ:1.00 F A:CFL12 0.0 94.4 1.0 C2' A:CFL12 1.3 73.6 1.0 C3' A:CFL12 2.3 76.5 1.0 C1' A:CFL12 2.3 70.3 1.0 N1 A:CFL12 2.7 67.3 1.0 O2 A:CFL12 2.7 70.1 1.0 O5' A:G13 2.8 86.7 1.0 O4' A:G13 2.9 75.8 1.0 C2 A:CFL12 2.9 67.6 1.0 O3' A:CFL12 3.0 77.3 1.0 C5' A:G13 3.2 86.0 1.0 P A:G13 3.4 84.9 1.0 O4' A:CFL12 3.4 67.9 1.0 C4' A:G13 3.4 83.8 1.0 C4' A:CFL12 3.5 73.1 1.0 C6 A:CFL12 3.7 66.8 1.0 N3 A:CFL12 4.0 66.2 1.0 C1' A:G13 4.2 78.7 1.0 OP2 A:G13 4.3 83.8 1.0 C8 A:G13 4.3 71.9 1.0 OP1 A:G13 4.3 76.6 1.0 N9 A:G13 4.6 75.3 1.0 C5 A:CFL12 4.7 66.0 1.0 C5' A:CFL12 4.7 70.7 1.0 C4 A:CFL12 4.7 68.8 1.0 C3' A:G13 4.9 87.5 1.0 O5' A:CFL12 5.0 72.3 1.0

Fluorine binding site 6 out of 19 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban within 5.0Å range: probe atom residue distance (Å) B Occ A:F17 b:0.6 occ:1.00 F2' A:UFT17 0.0 0.6 1.0 C2' A:UFT17 1.4 0.1 1.0 C1' A:UFT17 2.3 0.3 1.0 C3' A:UFT17 2.3 0.8 1.0 O5' A:A18 2.6 0.5 1.0 O3' A:UFT17 2.7 0.4 1.0 C4' A:UFT17 3.0 0.5 1.0 C2' A:A18 3.0 0.5 1.0 O4' A:UFT17 3.1 0.8 1.0 P A:A18 3.3 0.5 1.0 C3' A:A18 3.4 0.4 1.0 N1 A:UFT17 3.5 0.4 1.0 C5' A:A18 3.7 0.8 1.0 O2' A:A18 3.8 0.4 1.0 C4' A:A18 3.9 0.5 1.0 C6 A:UFT17 4.0 0.8 1.0 C8 A:A18 4.1 0.3 1.0 C1' A:A18 4.1 0.8 1.0 O4' A:A18 4.2 0.5 1.0 OP2 A:A18 4.2 0.8 1.0 OP1 A:A18 4.3 0.8 1.0 N9 A:A18 4.4 0.7 1.0 C5' A:UFT17 4.5 0.5 1.0 C2 A:UFT17 4.5 0.9 1.0 O3' A:A18 4.6 0.8 1.0 O2 A:UFT17 4.8 0.4 1.0

Fluorine binding site 7 out of 19 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban within 5.0Å range: probe atom residue distance (Å) B Occ A:F20 b:0.2 occ:1.00 F2' A:UFT20 0.0 0.2 1.0 C2' A:UFT20 1.4 0.8 1.0 OP2 A:A21 2.2 86.1 1.0 C3' A:UFT20 2.3 0.5 1.0 C1' A:UFT20 2.4 0.0 1.0 O2 A:UFT20 2.6 0.9 1.0 O3' A:UFT20 2.7 92.6 1.0 P A:A21 3.0 84.0 1.0 N1 A:UFT20 3.3 0.2 1.0 C2 A:UFT20 3.3 96.5 1.0 O4' A:UFT20 3.5 0.8 1.0 C4' A:UFT20 3.6 1.0 1.0 O5' A:A21 4.1 78.0 1.0 OP2 A:UFT20 4.1 0.2 1.0 C5' A:A21 4.2 74.7 1.0 OP1 A:A21 4.2 86.4 1.0 C5' A:UFT20 4.5 0.8 1.0 C6 A:UFT20 4.6 95.7 1.0 N3 A:UFT20 4.6 93.2 1.0 O5' A:UFT20 4.7 0.5 1.0

Fluorine binding site 8 out of 19 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban within 5.0Å range: probe atom residue distance (Å) B Occ A:F22 b:98.7 occ:1.00 F A:CFL22 0.0 98.7 1.0 C2' A:CFL22 1.4 92.5 1.0 C1' A:CFL22 2.4 91.8 1.0 O2 A:CFL22 2.4 89.5 1.0 C3' A:CFL22 2.5 89.0 1.0 O4' A:UFT23 2.7 89.5 1.0 N1 A:CFL22 2.8 87.4 1.0 C2 A:CFL22 2.8 87.3 1.0 C6 A:UFT23 3.0 84.1 1.0 O3' A:CFL22 3.1 89.4 1.0 O5' A:UFT23 3.3 84.8 1.0 O4' A:CFL22 3.5 89.3 1.0 N1 A:UFT23 3.5 87.9 1.0 C4' A:CFL22 3.6 90.3 1.0 C1' A:UFT23 3.6 89.9 1.0 C5' A:UFT23 3.6 88.8 1.0 C4' A:UFT23 3.7 91.4 1.0 C5 A:UFT23 3.8 82.4 1.0 C6 A:CFL22 4.0 85.4 1.0 N3 A:CFL22 4.0 86.7 1.0 P A:UFT23 4.1 86.0 1.0 N2 A:G15 4.3 98.5 1.0 C2 A:UFT23 4.7 87.9 1.0 C3' A:UFT23 4.7 87.6 1.0 OP2 A:UFT23 4.8 92.2 1.0 C4 A:UFT23 4.8 83.1 1.0 C5' A:CFL22 4.9 85.9 1.0 C5 A:CFL22 4.9 84.8 1.0 C2' A:UFT23 4.9 88.3 1.0 C4 A:CFL22 4.9 86.5 1.0

Fluorine binding site 9 out of 19 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban within 5.0Å range: probe atom residue distance (Å) B Occ A:F23 b:91.7 occ:1.00 F2' A:UFT23 0.0 91.7 1.0 C2' A:UFT23 1.4 88.3 1.0 C1' A:UFT23 2.3 89.9 1.0 C3' A:UFT23 2.4 87.6 1.0 O3' A:UFT23 2.8 89.5 1.0 C4' A:UFT23 3.0 91.4 1.0 O4' A:UFT23 3.1 89.5 1.0 C5' A:UFT24 3.3 86.8 1.0 O4' A:UFT24 3.4 83.8 1.0 N1 A:UFT23 3.5 87.9 1.0 O2 A:UFT23 3.5 87.6 1.0 O5' A:UFT24 3.6 83.9 1.0 C4' A:UFT24 3.9 86.9 1.0 P A:UFT24 3.9 87.2 1.0 C2 A:UFT23 3.9 87.9 1.0 C5' A:UFT23 4.5 88.8 1.0 C6 A:UFT23 4.6 84.1 1.0 C1' A:UFT24 4.7 84.2 1.0 OP1 A:UFT24 4.8 89.5 1.0 C6 A:UFT24 4.8 81.0 1.0 OP2 A:UFT24 5.0 81.6 1.0

Fluorine binding site 10 out of 19 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban within 5.0Å range: probe atom residue distance (Å) B Occ A:F24 b:83.6 occ:1.00 F2' A:UFT24 0.0 83.6 1.0 C2' A:UFT24 1.4 83.3 1.0 C1' A:UFT24 2.3 84.2 1.0 C3' A:UFT24 2.4 84.1 1.0 O3' A:UFT24 2.7 87.2 1.0 C4' A:UFT24 3.0 86.9 1.0 O4' A:UFT24 3.1 83.8 1.0 C5' A:G25 3.5 83.3 1.0 N1 A:UFT24 3.5 81.8 1.0 O2 A:UFT24 3.7 78.5 1.0 O4' A:G25 3.7 83.8 1.0 O5' A:G25 3.9 82.2 1.0 P A:G25 4.0 87.5 1.0 C2 A:UFT24 4.0 79.7 1.0 C4' A:G25 4.1 85.6 1.0 C5' A:UFT24 4.5 86.8 1.0 C6 A:UFT24 4.6 81.0 1.0 C8 A:G25 4.8 79.8 1.0 OP1 A:G25 4.8 90.2 1.0 C1' A:G25 4.9 82.4 1.0 N9 A:G25 4.9 79.2 1.0 OP2 A:G25 5.0 78.2 1.0

R.Gunaratne, S.Kumar, J.W.Frederiksen, S.Stayrook, J.L.Lohrmann, K.Perry, K.M.Bompiani, C.V.Chabata, N.K.Thalji, M.D.Ho, G.Arepally, R.M.Camire, S.Krishnaswamy, B.A.Sullenger. Combination of Aptamer and Drug For Reversible Anticoagulation in Cardiopulmonary Bypass. Nat. Biotechnol. V. 36 606 2018.
ISSN: ISSN 1546-1696
PubMed: 29863725
DOI: 10.1038/NBT.4153