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Manganese in PDB 5uv5: Crystal Structure of A 2-Hydroxyisoquinoline-1,3-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase

Enzymatic activity of Crystal Structure of A 2-Hydroxyisoquinoline-1,3-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase

All present enzymatic activity of Crystal Structure of A 2-Hydroxyisoquinoline-1,3-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 A 2-Hydroxyisoquinoline-1,3-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase, PDB code: 5uv5 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) 62.43 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 68.990, 88.670, 108.860, 105.53, 93.41, 110.13
R / Rfree (%) 23.2 / 28.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of A 2-Hydroxyisoquinoline-1,3-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase (pdb code 5uv5). 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 A 2-Hydroxyisoquinoline-1,3-Dione Rnase H Active Site Inhibitor with Multiple Binding Modes to Hiv Reverse Transcriptase, PDB code: 5uv5:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5uv5

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Manganese binding site 1 out of 4 in the Crystal Structure of A 2-Hydroxyisoquinoline-1,3-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 A 2-Hydroxyisoquinoline-1,3-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:85.5
occ:1.00
 O3 A:Y55603 2.1 79.7 1.0
OD1 A:ASP443 2.2 41.4 1.0
OD1 A:ASP498 2.2 63.6 1.0
OE2 A:GLU478 2.2 49.3 1.0
OD2 A:ASP498 2.2 62.0 1.0
CG A:ASP498 2.5 61.4 1.0
O1 A:Y55603 2.7 89.1 1.0
N A:Y55603 3.0 85.2 1.0
CD A:GLU478 3.1 52.2 1.0
CG A:ASP443 3.2 40.9 1.0
C1 A:Y55603 3.3 86.5 1.0
MN A:MN602 3.3 61.4 1.0
OE1 A:GLU478 3.3 53.1 1.0
OD2 A:ASP443 3.6 39.1 1.0
O A:GLY444 3.9 58.0 1.0
CB A:ASP498 3.9 54.7 1.0
C5 A:Y55603 4.2 88.5 1.0
N A:GLY444 4.4 56.2 1.0
CG A:GLU478 4.5 51.3 1.0
CB A:ASP443 4.5 45.8 1.0
O2 A:Y55603 4.5 98.2 1.0
C2 A:Y55603 4.6 82.9 1.0
C A:ASP498 4.8 55.7 1.0
CA A:ASP443 4.8 45.8 1.0
CA A:ASP498 4.9 52.4 1.0
C A:GLY444 4.9 62.5 1.0
CB A:ALA538 5.0 34.3 1.0

Manganese binding site 2 out of 4 in 5uv5

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Manganese binding site 2 out of 4 in the Crystal Structure of A 2-Hydroxyisoquinoline-1,3-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 A 2-Hydroxyisoquinoline-1,3-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:61.4
occ:1.00
 OD1 A:ASP549 2.1 59.0 1.0
OD2 A:ASP443 2.2 39.1 1.0
O3 A:Y55603 2.3 79.7 1.0
O2 A:Y55603 2.7 98.2 1.0
CG A:ASP443 3.1 40.9 1.0
CG A:ASP549 3.2 59.4 1.0
MN A:MN601 3.3 85.5 1.0
N A:Y55603 3.3 85.2 1.0
OD1 A:ASP443 3.3 41.4 1.0
OD2 A:ASP498 3.4 62.0 1.0
C5 A:Y55603 3.4 88.5 1.0
CB A:ASP549 4.0 60.5 1.0
O A:GLY444 4.0 58.0 1.0
OD2 A:ASP549 4.2 55.3 1.0
CE1 A:HIS539 4.4 66.6 1.0
CA A:ASP549 4.5 62.8 1.0
CB A:ASP443 4.5 45.8 1.0
CG A:ASP498 4.6 61.4 1.0
C1 A:Y55603 4.6 86.5 1.0
CG2 A:VAL552 4.9 90.8 1.0
NE2 A:HIS539 4.9 66.7 1.0
O1 A:Y55603 4.9 89.1 1.0
C4 A:Y55603 4.9 82.6 1.0
OE2 A:GLU478 5.0 49.3 1.0

Manganese binding site 3 out of 4 in 5uv5

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Manganese binding site 3 out of 4 in the Crystal Structure of A 2-Hydroxyisoquinoline-1,3-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 A 2-Hydroxyisoquinoline-1,3-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:93.5
occ:1.00
 OD2 C:ASP498 2.1 62.7 1.0
OE2 C:GLU478 2.1 54.1 1.0
OD1 C:ASP498 2.2 55.1 1.0
OD1 C:ASP443 2.2 53.7 1.0
O3 C:Y55603 2.4 91.9 1.0
CG C:ASP498 2.4 56.3 1.0
O2 C:Y55603 2.5 95.5 1.0
CD C:GLU478 2.9 46.7 1.0
OE1 C:GLU478 3.1 37.4 1.0
C5 C:Y55603 3.2 93.3 1.0
N C:Y55603 3.3 91.9 1.0
CG C:ASP443 3.3 45.6 1.0
MN C:MN602 3.7 75.2 1.0
OD2 C:ASP443 3.8 43.2 1.0
CB C:ASP498 3.9 50.8 1.0
O C:GLY444 4.2 62.7 1.0
CG C:GLU478 4.3 46.3 1.0
C C:ASP498 4.4 48.0 1.0
N C:GLY444 4.5 49.5 1.0
N C:SER499 4.5 42.0 1.0
CB C:ASP443 4.5 40.0 1.0
O C:ASP498 4.6 56.3 1.0
C1 C:Y55603 4.6 92.1 1.0
CA C:ASP498 4.6 51.9 1.0
C4 C:Y55603 4.7 93.3 1.0
CA C:ASP443 4.8 45.1 1.0
CB C:SER499 4.8 43.1 1.0
CA C:SER499 4.9 44.6 1.0
N C:ASP498 5.0 61.0 1.0
O1 C:Y55603 5.0 91.7 1.0

Manganese binding site 4 out of 4 in 5uv5

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Manganese binding site 4 out of 4 in the Crystal Structure of A 2-Hydroxyisoquinoline-1,3-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 A 2-Hydroxyisoquinoline-1,3-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:75.2
occ:1.00
 O3 C:Y55603 2.1 91.9 1.0
OD1 C:ASP549 2.1 55.2 1.0
OD2 C:ASP443 2.2 43.2 1.0
O1 C:Y55603 2.6 91.7 1.0
N C:Y55603 3.0 91.9 1.0
CG C:ASP443 3.1 45.6 1.0
C1 C:Y55603 3.2 92.1 1.0
CG C:ASP549 3.2 58.0 1.0
OD1 C:ASP443 3.3 53.7 1.0
MN C:MN601 3.7 93.5 1.0
CB C:ASP549 3.8 56.7 1.0
OD2 C:ASP498 4.2 62.7 1.0
OD2 C:ASP549 4.2 55.7 1.0
C5 C:Y55603 4.2 93.3 1.0
NE2 C:HIS539 4.2 74.9 1.0
O C:GLY444 4.3 62.7 1.0
CA C:ASP549 4.4 54.4 1.0
OD1 C:ASP498 4.5 55.1 1.0
CB C:ASP443 4.5 40.0 1.0
C2 C:Y55603 4.5 96.3 1.0
CG C:ASP498 4.6 56.3 1.0
O2 C:Y55603 4.6 95.5 1.0
CE1 C:HIS539 4.8 78.3 1.0
CD2 C:HIS539 4.9 73.2 1.0

Reference:

K.A.Kirby, N.A.Myshakina, M.T.Christen, Y.L.Chen, H.A.Schmidt, A.D.Huber, Z.Xi, S.Kim, R.K.Rao, S.T.Kramer, Q.Yang, K.Singh, M.A.Parniak, Z.Wang, R.Ishima, S.G.Sarafianos. A 2-Hydroxyisoquinoline-1,3-Dione Active-Site Rnase H Inhibitor Binds in Multiple Modes to Hiv-1 Reverse Transcriptase. Antimicrob. Agents V. 61 2017CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 28760905
DOI: 10.1128/AAC.01351-17
Page generated: Sun Oct 6 03:05:48 2024

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