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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5vof:

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

Fluorine (F) 19 atoms
Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban, PDB code: 5vof:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5vof

Go back to Magnesium Binding Sites List in 5vof
Magnesium binding site 1 out of 2 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg101

b:43.2
occ:1.00
O1P A:CFL22 1.7 79.7 1.0
O A:HOH202 1.9 49.5 1.0
O A:HOH207 2.0 68.0 1.0
OP2 A:UFT23 2.2 92.2 1.0
O A:HOH203 2.2 45.0 1.0
OP1 A:A10 2.8 63.6 1.0
P A:CFL22 3.1 75.7 1.0
P A:UFT23 3.6 86.0 1.0
P A:A10 3.9 68.7 1.0
O2P A:CFL22 4.0 78.9 1.0
O5' A:CFL22 4.0 82.6 1.0
O3' A:A21 4.2 79.3 1.0
OP2 A:A10 4.2 64.2 1.0
C5' A:CFL22 4.3 85.9 1.0
O3' A:CFL22 4.3 89.4 1.0
C3' A:CFL22 4.3 89.0 1.0
O5' A:UFT23 4.5 84.8 1.0
O5' A:A10 4.6 68.3 1.0
O2P A:CFL9 4.6 76.4 1.0
OP1 A:UFT23 4.6 91.0 1.0
O3' A:CFL9 4.8 78.5 1.0
C5' A:A10 4.8 64.5 1.0
O6 A:G25 4.8 0.3 1.0
C5 A:UFT23 4.8 82.4 1.0
C4' A:CFL22 4.9 90.3 1.0

Magnesium binding site 2 out of 2 in 5vof

Go back to Magnesium Binding Sites List in 5vof
Magnesium binding site 2 out of 2 in the Desgla-XAS195A Bound to Aptamer 11F7T and Rivaroxaban


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg102

b:50.5
occ:1.00
OP2 A:A10 1.5 64.2 1.0
O A:HOH212 1.9 45.2 1.0
O A:HOH208 2.4 42.4 1.0
O4 A:UFT24 2.4 74.5 1.0
P A:A10 2.7 68.7 1.0
O5' A:A10 3.2 68.3 1.0
N1 A:G25 3.6 92.4 1.0
C4 A:UFT24 3.6 78.8 1.0
N2 A:G25 3.7 0.6 1.0
F A:CFL9 3.9 93.0 1.0
O4 A:UFT23 3.9 82.0 1.0
O3' A:CFL9 4.0 78.5 1.0
OP1 A:A10 4.0 63.6 1.0
O A:HOH203 4.0 45.0 1.0
C2 A:G25 4.1 95.5 1.0
N3 A:UFT24 4.4 79.1 1.0
OP2 A:G11 4.5 69.2 1.0
C3' A:CFL9 4.5 74.9 1.0
C6 A:G25 4.5 84.5 1.0
C5 A:UFT24 4.6 79.4 1.0
C5' A:A10 4.6 64.5 1.0
O A:HOH207 4.6 68.0 1.0
O6 A:G25 4.6 0.3 1.0
O6 A:G13 4.7 71.5 1.0
C2' A:CFL9 4.7 70.9 1.0
C4 A:UFT23 4.8 83.1 1.0
C5 A:UFT23 5.0 82.4 1.0

Reference:

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
Page generated: Mon Dec 14 21:18:36 2020

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