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Manganese in PDB 3qlh: Hiv-1 Reverse Transcriptase in Complex with Manicol at the Rnase H Active Site and TMC278 (Rilpivirine) at the Nnrti Binding Pocket

Enzymatic activity of Hiv-1 Reverse Transcriptase in Complex with Manicol at the Rnase H Active Site and TMC278 (Rilpivirine) at the Nnrti Binding Pocket

All present enzymatic activity of Hiv-1 Reverse Transcriptase in Complex with Manicol at the Rnase H Active Site and TMC278 (Rilpivirine) at the Nnrti Binding Pocket:
2.7.7.49; 2.7.7.7; 3.1.26.13;

Protein crystallography data

The structure of Hiv-1 Reverse Transcriptase in Complex with Manicol at the Rnase H Active Site and TMC278 (Rilpivirine) at the Nnrti Binding Pocket, PDB code: 3qlh was solved by D.M.Himmel, K.Wojtak, J.D.Bauman, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.21 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 163.926, 72.978, 108.377, 90.00, 101.11, 90.00
R / Rfree (%) 23.1 / 25.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Hiv-1 Reverse Transcriptase in Complex with Manicol at the Rnase H Active Site and TMC278 (Rilpivirine) at the Nnrti Binding Pocket (pdb code 3qlh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Hiv-1 Reverse Transcriptase in Complex with Manicol at the Rnase H Active Site and TMC278 (Rilpivirine) at the Nnrti Binding Pocket, PDB code: 3qlh:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 3qlh

Go back to Manganese Binding Sites List in 3qlh
Manganese binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase in Complex with Manicol at the Rnase H Active Site and TMC278 (Rilpivirine) at the Nnrti Binding Pocket


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hiv-1 Reverse Transcriptase in Complex with Manicol at the Rnase H Active Site and TMC278 (Rilpivirine) at the Nnrti Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn556

b:79.5
occ:1.00
 O2 A:MNK1001 1.9 83.8 1.0
O1 A:MNK1001 2.2 0.0 1.0
OD1 A:ASP549 2.3 65.0 1.0
OD2 A:ASP443 2.3 60.4 1.0
C2 A:MNK1001 2.7 91.4 1.0
C1 A:MNK1001 2.9 92.9 1.0
CG A:ASP443 3.2 47.9 1.0
CG A:ASP549 3.4 57.3 1.0
OD1 A:ASP443 3.4 61.7 1.0
MN A:MN557 3.5 56.6 1.0
CB A:ASP549 3.9 54.0 1.0
C3 A:MNK1001 4.0 92.7 1.0
O A:GLY444 4.1 43.3 1.0
OD2 A:ASP498 4.1 45.5 1.0
C7 A:MNK1001 4.2 87.5 1.0
OD2 A:ASP549 4.3 68.9 1.0
O3 A:MNK1001 4.3 91.9 1.0
CA A:ASP549 4.3 47.5 1.0
CB A:ASP443 4.6 41.3 1.0
C12 A:MNK1001 4.7 91.8 1.0
OG A:SER553 4.8 74.5 1.0
NE2 A:HIS539 4.9 66.5 1.0
O A:ASP549 4.9 56.4 1.0
CG A:ASP498 5.0 45.6 1.0

Manganese binding site 2 out of 2 in 3qlh

Go back to Manganese Binding Sites List in 3qlh
Manganese binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase in Complex with Manicol at the Rnase H Active Site and TMC278 (Rilpivirine) at the Nnrti Binding Pocket


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hiv-1 Reverse Transcriptase in Complex with Manicol at the Rnase H Active Site and TMC278 (Rilpivirine) at the Nnrti Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn557

b:56.6
occ:1.00
 OE2 A:GLU478 1.9 56.9 1.0
OD1 A:ASP498 2.0 40.6 1.0
OD1 A:ASP443 2.4 61.7 1.0
O2 A:MNK1001 2.6 83.8 1.0
CG A:ASP498 2.8 45.6 1.0
O3 A:MNK1001 2.9 91.9 1.0
OD2 A:ASP498 2.9 45.5 1.0
CD A:GLU478 3.1 59.6 1.0
CG A:ASP443 3.4 47.9 1.0
MN A:MN556 3.5 79.5 1.0
C2 A:MNK1001 3.6 91.4 1.0
OD2 A:ASP443 3.7 60.4 1.0
OE1 A:GLU478 3.7 75.4 1.0
C3 A:MNK1001 3.7 92.7 1.0
O A:GLY444 4.1 43.3 1.0
CB A:ASP498 4.2 31.6 1.0
CG A:GLU478 4.3 56.6 1.0
N A:GLY444 4.6 34.9 1.0
CB A:ASP443 4.6 41.3 1.0
C A:ASP498 4.7 42.6 1.0
N A:SER499 4.8 40.1 1.0
CA A:ASP498 4.9 38.3 1.0
C1 A:MNK1001 4.9 92.9 1.0
CA A:ASP443 4.9 31.6 1.0
O A:ASP498 5.0 53.7 1.0

Reference:

S.Chung, D.M.Himmel, J.K.Jiang, K.Wojtak, J.D.Bauman, J.W.Rausch, J.A.Wilson, J.A.Beutler, C.J.Thomas, E.Arnold, S.F.Le Grice. Synthesis, Activity, and Structural Analysis of Novel Alpha-Hydroxytropolone Inhibitors of Human Immunodeficiency Virus Reverse Transcriptase-Associated Ribonuclease H. J.Med.Chem. V. 54 4462 2011.
ISSN: ISSN 0022-2623
PubMed: 21568335
DOI: 10.1021/JM2000757
Page generated: Sat Oct 5 17:41:37 2024

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