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Silicon in PDB 3qo9: Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti)

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti)

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti):
2.7.7.49; 2.7.7.7; 3.1.26.13; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti), PDB code: 3qo9 was solved by K.Das, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.27 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.760, 72.590, 108.970, 90.00, 98.75, 90.00
R / Rfree (%) 24.4 / 28.6

Silicon Binding Sites:

The binding sites of Silicon atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti) (pdb code 3qo9). This binding sites where shown within 5.0 Angstroms radius around Silicon atom.
In total 2 binding sites of Silicon where determined in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti), PDB code: 3qo9:
Jump to Silicon binding site number: 1; 2;

Silicon binding site 1 out of 2 in 3qo9

Go back to Silicon Binding Sites List in 3qo9
Silicon binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti)


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Si556

b:84.2
occ:1.00
SI1 A:QO9556 0.0 84.2 1.0
O5 A:QO9556 1.7 79.5 1.0
C15 A:QO9556 1.9 72.9 1.0
C14 A:QO9556 1.9 69.7 1.0
C13 A:QO9556 1.9 78.7 1.0
C9 A:QO9556 2.6 74.9 1.0
C17 A:QO9556 2.8 79.6 1.0
C16 A:QO9556 2.8 72.0 1.0
C18 A:QO9556 2.8 78.1 1.0
C8 A:QO9556 3.7 72.0 1.0
C6 A:QO9556 3.8 74.6 1.0
C11 A:QO9556 4.0 71.4 1.0
N2 A:QO9556 4.2 75.5 1.0
O4 A:QO9556 4.2 73.7 1.0
N3 A:QO9556 4.4 72.0 1.0
C3 A:QO9556 4.6 71.2 1.0
C12 A:QO9556 4.7 72.6 1.0
O8 A:QO9556 4.7 77.6 1.0
OH A:TYR318 4.8 62.1 1.0
C4 A:QO9556 4.8 69.9 1.0
S1 A:QO9556 4.8 82.1 1.0
CZ A:TYR318 4.8 64.9 1.0
C7 A:QO9556 4.9 71.5 1.0
O3 A:QO9556 4.9 69.9 1.0
O2 A:QO9556 5.0 73.9 1.0

Silicon binding site 2 out of 2 in 3qo9

Go back to Silicon Binding Sites List in 3qo9
Silicon binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti)


Mono view


Stereo pair view

A full contact list of Silicon with other atoms in the Si binding site number 2 of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with Tsao-T, A Non-Nucleoside Rt Inhibitor (Nnrti) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Si556

b:74.9
occ:1.00
SI2 A:QO9556 0.0 74.9 1.0
O6 A:QO9556 1.7 72.4 1.0
C21 A:QO9556 1.9 75.1 1.0
C20 A:QO9556 1.9 65.1 1.0
C19 A:QO9556 1.9 71.9 1.0
C10 A:QO9556 2.6 67.7 1.0
C22 A:QO9556 2.8 67.3 1.0
C23 A:QO9556 2.8 67.2 1.0
C24 A:QO9556 2.8 69.8 1.0
C3 A:QO9556 3.8 71.2 1.0
C7 A:QO9556 3.9 71.5 1.0
O3 A:QO9556 4.0 69.9 1.0
C5 A:QO9556 4.3 50.4 1.0
C2 A:QO9556 4.5 62.6 1.0
N2 A:QO9556 4.7 75.5 1.0
C6 A:QO9556 4.7 74.6 1.0
C9 A:QO9556 4.8 74.9 1.0
N3 A:QO9556 4.9 72.0 1.0
CE2 A:TRP229 4.9 72.4 1.0
C8 A:QO9556 5.0 72.0 1.0

Reference:

K.Das, J.D.Bauman, A.S.Rim, C.Dharia, A.D.Clark, M.J.Camarasa, J.Balzarini, E.Arnold. Crystal Structure of Tert-Butyldimethylsilyl-Spiroaminooxathioledioxide-Thymine (Tsao-T) in Complex with Hiv-1 Reverse Transcriptase (Rt) Redefines the Elastic Limits of the Non-Nucleoside Inhibitor-Binding Pocket. J.Med.Chem. V. 54 2727 2011.
ISSN: ISSN 0022-2623
PubMed: 21446702
DOI: 10.1021/JM101536X
Page generated: Wed Dec 16 02:09:31 2020

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