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Manganese in PDB 6aoc: Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase

Enzymatic activity of Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase

All present enzymatic activity of Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase:
2.7.7.49; 2.7.7.7; 3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase, PDB code: 6aoc was solved by K.A.Kirby, S.G.Sarafianos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.32 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.370, 89.120, 112.730, 105.72, 95.03, 110.72
R / Rfree (%) 18.6 / 22.6

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase (pdb code 6aoc). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase, PDB code: 6aoc:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6aoc

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Manganese binding site 1 out of 4 in the Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:41.8
occ:1.00
 OE1 A:GLU478 2.0 42.4 1.0
OD1 A:ASP498 2.1 43.5 1.0
O1 A:ZW2603 2.1 58.2 1.0
OD1 A:ASP443 2.1 38.5 1.0
O2 A:ZW2603 2.3 50.0 1.0
CG A:ASP498 2.8 35.2 1.0
OD2 A:ASP498 2.9 38.8 1.0
N1 A:ZW2603 2.9 47.3 1.0
C1 A:ZW2603 3.0 52.8 1.0
CD A:GLU478 3.0 48.0 1.0
CG A:ASP443 3.2 41.2 1.0
OE2 A:GLU478 3.3 39.7 1.0
O A:HOH801 3.7 38.5 1.0
OD2 A:ASP443 3.7 38.3 1.0
O A:HOH845 3.7 64.3 1.0
MN A:MN602 3.8 41.5 1.0
O A:HOH730 4.0 59.1 1.0
O A:HOH777 4.1 37.6 1.0
O A:GLY444 4.3 38.2 1.0
CB A:ASP498 4.3 32.8 1.0
C4 A:ZW2603 4.3 61.2 1.0
O A:HOH783 4.4 42.4 1.0
CG A:GLU478 4.4 47.0 1.0
CB A:ASP443 4.5 35.5 1.0
C2 A:ZW2603 4.5 55.1 1.0
N A:GLY444 4.5 35.9 1.0
CA A:ASP443 4.7 33.0 1.0
C A:ASP498 4.7 29.1 1.0
O A:ASP498 4.8 34.9 1.0
O3 A:ZW2603 4.8 47.2 1.0
N A:SER499 4.9 38.5 1.0
CA A:ASP498 4.9 34.5 1.0

Manganese binding site 2 out of 4 in 6aoc

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Manganese binding site 2 out of 4 in the Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:41.5
occ:1.00
 O1 A:ZW2603 2.1 58.2 1.0
OD2 A:ASP443 2.1 38.3 1.0
O A:HOH783 2.1 42.4 1.0
OD1 A:ASP549 2.1 43.2 1.0
O3 A:ZW2603 2.2 47.2 1.0
O A:HOH777 2.2 37.6 1.0
N1 A:ZW2603 2.8 47.3 1.0
C4 A:ZW2603 2.8 61.2 1.0
CG A:ASP443 3.1 41.2 1.0
CG A:ASP549 3.2 41.1 1.0
OD1 A:ASP443 3.4 38.5 1.0
CB A:ASP549 3.6 36.8 1.0
MN A:MN601 3.8 41.8 1.0
OD2 A:ASP498 4.0 38.8 1.0
O A:HOH806 4.0 60.5 1.0
O A:HOH773 4.1 59.0 1.0
NE2 A:HIS539 4.1 55.1 1.0
CA A:ASP549 4.1 31.3 1.0
C1 A:ZW2603 4.1 52.8 1.0
N2 A:ZW2603 4.2 64.9 1.0
O A:GLY444 4.3 38.2 1.0
OD2 A:ASP549 4.3 43.1 1.0
CB A:ASP443 4.5 35.5 1.0
O A:HOH782 4.5 39.0 1.0
CE1 A:HIS539 4.6 55.5 1.0
O2 A:ZW2603 4.6 50.0 1.0
CD2 A:HIS539 4.9 52.5 1.0

Manganese binding site 3 out of 4 in 6aoc

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Manganese binding site 3 out of 4 in the Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:35.1
occ:1.00
 O1 C:ZW2603 1.9 57.5 1.0
OE1 C:GLU478 2.0 44.4 1.0
OD1 C:ASP498 2.1 47.0 1.0
OD1 C:ASP443 2.1 44.8 1.0
O3 C:ZW2603 2.2 49.4 1.0
N1 C:ZW2603 2.8 44.8 1.0
CG C:ASP498 2.8 41.2 1.0
C4 C:ZW2603 2.8 47.6 1.0
OD2 C:ASP498 2.8 40.4 1.0
CD C:GLU478 3.1 36.4 1.0
CG C:ASP443 3.2 41.6 1.0
OE2 C:GLU478 3.5 36.9 1.0
O2 C:EDO622 3.7 93.7 1.0
OD2 C:ASP443 3.8 42.8 1.0
O C:HOH791 3.8 34.6 1.0
MN C:MN602 3.8 42.4 1.0
O C:HOH755 4.0 40.0 1.0
C2 C:EDO622 4.1 92.1 1.0
C1 C:ZW2603 4.1 52.9 1.0
O2 C:EDO623 4.2 61.5 1.0
CB C:ASP498 4.3 33.5 1.0
N2 C:ZW2603 4.3 56.1 1.0
O C:GLY444 4.3 40.7 1.0
CG C:GLU478 4.4 35.9 1.0
CB C:ASP443 4.5 31.5 1.0
N C:GLY444 4.6 34.7 1.0
O C:HOH882 4.6 39.8 1.0
CA C:ASP443 4.7 28.1 1.0
C C:ASP498 4.7 36.6 1.0
O2 C:ZW2603 4.7 53.2 1.0
C1 C:EDO622 4.8 87.8 1.0
O C:ASP498 4.8 34.6 1.0
C1 C:EDO623 4.8 60.6 1.0
C2 C:EDO623 4.9 67.8 1.0
CA C:ASP498 4.9 34.6 1.0
N C:SER499 4.9 34.8 1.0

Manganese binding site 4 out of 4 in 6aoc

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Manganese binding site 4 out of 4 in the Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of An N-Hydroxythienopyrimidine-2,4-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn602

b:42.4
occ:1.00
 OD2 C:ASP443 2.2 42.8 1.0
OD1 C:ASP549 2.2 43.1 1.0
O C:HOH882 2.2 39.8 1.0
O1 C:ZW2603 2.3 57.5 1.0
O2 C:ZW2603 2.3 53.2 1.0
O C:HOH755 2.4 40.0 1.0
N1 C:ZW2603 2.9 44.8 1.0
C1 C:ZW2603 3.0 52.9 1.0
CG C:ASP443 3.1 41.6 1.0
CG C:ASP549 3.2 38.4 1.0
OD1 C:ASP443 3.4 44.8 1.0
CB C:ASP549 3.7 41.5 1.0
MN C:MN601 3.8 35.1 1.0
O C:HOH898 4.0 61.0 1.0
O C:HOH856 4.0 54.8 1.0
OD2 C:ASP498 4.1 40.4 1.0
CA C:ASP549 4.1 41.8 1.0
NE2 C:HIS539 4.2 52.6 1.0
C4 C:ZW2603 4.3 47.6 1.0
O C:GLY444 4.3 40.7 1.0
OD2 C:ASP549 4.3 41.4 1.0
C2 C:ZW2603 4.4 52.7 1.0
CB C:ASP443 4.4 31.5 1.0
O C:HOH769 4.5 42.2 1.0
CE1 C:HIS539 4.7 51.8 1.0
O3 C:ZW2603 4.8 49.4 1.0
O C:ASP549 4.8 42.7 1.0
CG2 C:VAL552 4.9 37.5 1.0
O1 C:EDO622 4.9 86.1 1.0
C C:ASP549 4.9 43.8 1.0
C2 C:EDO622 5.0 92.1 1.0

Reference:

J.Kankanala, K.A.Kirby, A.D.Huber, M.C.Casey, D.J.Wilson, S.G.Sarafianos, Z.Wang. Design, Synthesis and Biological Evaluations of N-Hydroxy Thienopyrimidine-2,4-Diones As Inhibitors of Hiv Reverse Transcriptase-Associated Rnase H. Eur J Med Chem V. 141 149 2017.
ISSN: ISSN 1768-3254
PubMed: 29031062
DOI: 10.1016/J.EJMECH.2017.09.054
Page generated: Tue Dec 15 04:50:37 2020

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