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Manganese in PDB 4qag: Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase

Enzymatic activity of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase

All present enzymatic activity of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13;

Protein crystallography data

The structure of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase, PDB code: 4qag was solved by D.M.Himmel, W.C.Ho, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.57 / 1.71
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 51.164, 51.164, 112.100, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 19

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase (pdb code 4qag). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase, PDB code: 4qag:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4qag

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Manganese binding site 1 out of 4 in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:46.8
occ:1.00
 O1 A:F95603 2.0 53.5 1.0
OD1 A:ASP549 2.1 53.8 1.0
O A:HOH711 2.2 42.3 1.0
OD1 A:ASP443 2.2 40.6 1.0
O A:HOH712 2.2 48.3 1.0
O2 A:F95603 2.2 48.5 1.0
C3 A:F95603 2.8 52.4 1.0
C4 A:F95603 2.9 52.2 1.0
CG A:ASP443 3.1 41.0 1.0
CG A:ASP549 3.2 52.9 1.0
OD2 A:ASP443 3.4 37.2 1.0
CB A:ASP549 3.6 50.2 1.0
MN A:MN602 3.7 42.1 1.0
OD2 A:ASP498 3.8 50.1 1.0
NE2 A:HIS539 4.1 64.8 1.0
C2 A:F95603 4.2 52.0 1.0
CA A:ASP549 4.2 46.6 1.0
C5 A:F95603 4.3 56.4 1.0
O A:GLY444 4.3 44.9 1.0
OD2 A:ASP549 4.3 59.7 1.0
CE1 A:HIS539 4.4 67.8 1.0
CB A:ASP443 4.6 34.3 1.0
O A:HOH731 4.6 53.7 1.0
O3 A:F95603 4.8 48.6 1.0
CG A:ASP498 4.9 40.2 1.0

Manganese binding site 2 out of 4 in 4qag

Go back to Manganese Binding Sites List in 4qag
Manganese binding site 2 out of 4 in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:42.1
occ:1.00
 OD1 A:ASP498 2.1 40.2 1.0
OE2 A:GLU478 2.1 46.5 1.0
OD2 A:ASP443 2.1 37.2 1.0
O1 A:F95603 2.1 53.5 1.0
OD2 A:ASP498 2.3 50.1 1.0
O3 A:F95603 2.5 48.6 1.0
CG A:ASP498 2.5 40.2 1.0
C3 A:F95603 3.0 52.4 1.0
CD A:GLU478 3.0 45.6 1.0
C2 A:F95603 3.1 52.0 1.0
CG A:ASP443 3.2 41.0 1.0
OE1 A:GLU478 3.2 46.3 1.0
C7 A:F95603 3.5 56.5 1.0
MN A:MN601 3.7 46.8 1.0
OD1 A:ASP443 3.7 40.6 1.0
O A:HOH701 3.7 37.6 1.0
O4 A:F95603 3.7 57.2 1.0
O A:HOH711 3.9 42.3 1.0
O A:HOH710 4.0 73.3 1.0
CB A:ASP498 4.1 39.4 1.0
O A:GLY444 4.2 44.9 1.0
C4 A:F95603 4.3 52.2 1.0
CG A:GLU478 4.4 40.7 1.0
CB A:ASP443 4.4 34.3 1.0
C1 A:F95603 4.5 57.8 1.0
N A:GLY444 4.5 34.5 1.0
O A:HOH712 4.5 48.3 1.0
CA A:ASP443 4.6 32.5 1.0
C A:ASP498 4.7 39.3 1.0
CA A:ASP498 4.8 36.7 1.0
O2 A:F95603 4.8 48.5 1.0
C8 A:F95603 4.8 59.6 1.0
O A:ASP498 4.9 42.9 1.0
N A:SER499 4.9 35.0 1.0

Manganese binding site 3 out of 4 in 4qag

Go back to Manganese Binding Sites List in 4qag
Manganese binding site 3 out of 4 in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:49.9
occ:1.00
 OD1 B:ASP549 2.1 53.0 1.0
O1 B:F95603 2.1 53.5 1.0
OD1 B:ASP443 2.2 45.0 1.0
O B:HOH717 2.2 58.2 1.0
O B:HOH705 2.2 50.1 1.0
O2 B:F95603 2.2 52.1 1.0
C3 B:F95603 2.9 58.6 1.0
C4 B:F95603 2.9 54.1 1.0
CG B:ASP443 3.2 47.2 1.0
CG B:ASP549 3.2 56.9 1.0
OD2 B:ASP443 3.4 42.3 1.0
MN B:MN602 3.6 45.3 1.0
CB B:ASP549 3.7 47.9 1.0
OD2 B:ASP498 3.9 47.8 1.0
O B:HOH718 3.9 85.9 1.0
NE2 B:HIS539 4.1 58.7 1.0
CA B:ASP549 4.2 49.5 1.0
C2 B:F95603 4.2 56.8 1.0
C5 B:F95603 4.2 59.9 1.0
OD2 B:ASP549 4.3 62.3 1.0
O B:GLY444 4.3 46.6 1.0
OG B:SER553 4.5 69.4 1.0
CB B:ASP443 4.5 39.4 1.0
CE1 B:HIS539 4.6 62.9 1.0
O B:HOH701 4.8 57.3 1.0
O3 B:F95603 4.8 55.1 1.0
CG B:ASP498 5.0 37.5 1.0
O B:ASP549 5.0 55.2 1.0
CD2 B:HIS539 5.0 62.7 1.0

Manganese binding site 4 out of 4 in 4qag

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Manganese binding site 4 out of 4 in the Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn602

b:45.3
occ:1.00
 O1 B:F95603 2.0 53.5 1.0
OD1 B:ASP498 2.1 42.9 1.0
OD2 B:ASP443 2.1 42.3 1.0
OE1 B:GLU478 2.1 43.3 1.0
OD2 B:ASP498 2.3 47.8 1.0
CG B:ASP498 2.5 37.5 1.0
O3 B:F95603 2.5 55.1 1.0
C3 B:F95603 2.9 58.6 1.0
CD B:GLU478 3.1 45.2 1.0
CG B:ASP443 3.1 47.2 1.0
C2 B:F95603 3.1 56.8 1.0
OE2 B:GLU478 3.3 45.4 1.0
OD1 B:ASP443 3.5 45.0 1.0
MN B:MN601 3.6 49.9 1.0
C7 B:F95603 3.6 55.4 1.0
O B:HOH705 3.7 50.1 1.0
O B:HOH704 3.8 41.0 1.0
O4 B:F95603 3.9 53.2 1.0
CB B:ASP498 4.0 40.8 1.0
C4 B:F95603 4.2 54.1 1.0
O B:GLY444 4.2 46.6 1.0
CB B:ASP443 4.3 39.4 1.0
C1 B:F95603 4.5 62.1 1.0
CG B:GLU478 4.5 39.4 1.0
N B:GLY444 4.5 38.6 1.0
O B:HOH717 4.6 58.2 1.0
CA B:ASP443 4.7 40.6 1.0
O2 B:F95603 4.7 52.1 1.0
C B:ASP498 4.8 41.1 1.0
CA B:ASP498 4.8 41.2 1.0
C8 B:F95603 4.9 60.3 1.0
O B:ASP498 4.9 42.8 1.0

Reference:

D.M.Himmel, N.S.Myshakina, T.Ilina, A.Van Ry, W.C.Ho, M.A.Parniak, E.Arnold. Structure of A Dihydroxycoumarin Active-Site Inhibitor in Complex with the Rnase H Domain of Hiv-1 Reverse Transcriptase and Structure-Activity Analysis of Inhibitor Analogs. J.Mol.Biol. V. 426 2617 2014.
ISSN: ISSN 0022-2836
PubMed: 24840303
DOI: 10.1016/J.JMB.2014.05.006
Page generated: Sat Oct 5 20:58:56 2024

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