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Manganese in PDB 3k2p: Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site

Enzymatic activity of Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site

All present enzymatic activity of Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site:
3.1.26.4;

Protein crystallography data

The structure of Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site, PDB code: 3k2p was solved by T.A.Pauly, D.M.Himmel, K.Maegley, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.28 / 2.04
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 51.143, 51.143, 112.435, 90.00, 90.00, 120.00
R / Rfree (%) 22.6 / 24.1

Manganese Binding Sites:

The binding sites of Manganese atom in the Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site (pdb code 3k2p). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site, PDB code: 3k2p:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3k2p

Go back to Manganese Binding Sites List in 3k2p
Manganese binding site 1 out of 4 in the Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site


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 Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn901

b:30.0
occ:1.00
 OE2 A:GLU478 1.8 28.3 1.0
O1 A:JTH1001 2.0 27.1 1.0
OD1 A:ASP498 2.1 28.9 1.0
O7 A:JTH1001 2.2 29.8 1.0
OD1 A:ASP443 2.3 25.6 1.0
C1 A:JTH1001 2.9 31.6 1.0
CD A:GLU478 3.0 25.1 1.0
CG A:ASP498 3.0 29.7 1.0
C7 A:JTH1001 3.0 31.9 1.0
OD2 A:ASP498 3.2 28.7 1.0
CG A:ASP443 3.3 26.9 1.0
OE1 A:GLU478 3.5 28.7 1.0
OD2 A:ASP443 3.7 28.1 1.0
MN A:MN902 3.7 33.7 1.0
O A:HOH1 3.8 21.4 1.0
O A:GLY444 4.1 29.0 1.0
O A:HOH159 4.1 35.4 1.0
O A:HOH217 4.2 34.3 1.0
CG A:GLU478 4.2 20.8 1.0
C2 A:JTH1001 4.2 30.4 1.0
C6 A:JTH1001 4.3 32.1 1.0
CB A:ASP498 4.5 25.4 1.0
N A:GLY444 4.6 27.4 1.0
CB A:ASP443 4.6 23.6 1.0
O2 A:JTH1001 4.7 33.6 1.0
CA A:ASP443 4.8 24.7 1.0
C A:ASP498 4.8 25.9 1.0
O A:ASP498 4.9 26.7 1.0

Manganese binding site 2 out of 4 in 3k2p

Go back to Manganese Binding Sites List in 3k2p
Manganese binding site 2 out of 4 in the Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site


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 Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn902

b:33.7
occ:1.00
 OD2 A:ASP549 2.2 29.0 1.0
O2 A:JTH1001 2.2 33.6 1.0
OD2 A:ASP443 2.2 28.1 1.0
O1 A:JTH1001 2.3 27.1 1.0
C2 A:JTH1001 3.0 30.4 1.0
C1 A:JTH1001 3.0 31.6 1.0
CG A:ASP549 3.2 32.0 1.0
CG A:ASP443 3.2 26.9 1.0
NH2 A:ARG557 3.3 63.6 1.0
OD1 A:ASP443 3.5 25.6 1.0
CB A:ASP549 3.6 31.8 1.0
MN A:MN901 3.7 30.0 1.0
NE2 A:HIS539 3.9 36.3 1.0
CA A:ASP549 4.1 32.5 1.0
OD2 A:ASP498 4.1 28.7 1.0
O A:GLY444 4.2 29.0 1.0
C3 A:JTH1001 4.2 36.5 1.0
C7 A:JTH1001 4.3 31.9 1.0
OD1 A:ASP549 4.3 36.7 1.0
CZ A:ARG557 4.3 63.0 1.0
CE1 A:HIS539 4.4 37.1 1.0
O A:HOH131 4.5 35.1 1.0
NH1 A:ARG557 4.5 61.8 1.0
CB A:ASP443 4.6 23.6 1.0
O7 A:JTH1001 4.7 29.8 1.0
CD2 A:HIS539 4.8 36.1 1.0
O A:ASP549 4.9 35.0 1.0
C A:ASP549 4.9 34.0 1.0
O A:HOH126 4.9 44.0 1.0
CG A:ASP498 5.0 29.7 1.0

Manganese binding site 3 out of 4 in 3k2p

Go back to Manganese Binding Sites List in 3k2p
Manganese binding site 3 out of 4 in the Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn901

b:31.4
occ:1.00
 OE2 B:GLU478 1.9 20.7 1.0
OD1 B:ASP498 2.1 22.3 1.0
O7 B:JTH1001 2.3 34.4 1.0
O1 B:JTH1001 2.3 40.0 1.0
OD1 B:ASP443 2.4 29.4 1.0
CD B:GLU478 2.9 29.0 1.0
CG B:ASP498 3.0 26.3 1.0
C7 B:JTH1001 3.1 38.3 1.0
C1 B:JTH1001 3.1 36.5 1.0
OD2 B:ASP498 3.2 28.9 1.0
OE1 B:GLU478 3.4 23.9 1.0
CG B:ASP443 3.4 34.6 1.0
OD2 B:ASP443 3.7 26.6 1.0
MN B:MN902 3.8 32.5 1.0
O B:HOH132 4.1 34.2 1.0
O B:GLY444 4.1 26.1 1.0
CG B:GLU478 4.3 28.3 1.0
C6 B:JTH1001 4.4 39.7 1.0
CB B:ASP498 4.4 27.2 1.0
C2 B:JTH1001 4.4 39.4 1.0
N B:GLY444 4.6 27.5 1.0
CB B:ASP443 4.7 27.9 1.0
C B:ASP498 4.7 27.2 1.0
N B:SER499 4.9 26.5 1.0
O B:ASP498 4.9 28.3 1.0
CA B:ASP443 4.9 28.6 1.0
CB B:ALA538 4.9 32.7 1.0
CA B:ASP498 5.0 28.6 1.0
O2 B:JTH1001 5.0 31.0 1.0

Manganese binding site 4 out of 4 in 3k2p

Go back to Manganese Binding Sites List in 3k2p
Manganese binding site 4 out of 4 in the Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hiv-1 Reverse Transcriptase Isolated Rnaseh Domain with the Inhibitor Beta-Thujaplicinol Bound at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn902

b:32.5
occ:1.00
 O1 B:JTH1001 2.2 40.0 1.0
OD2 B:ASP549 2.2 20.6 1.0
OD2 B:ASP443 2.2 26.6 1.0
O2 B:JTH1001 2.5 31.0 1.0
C1 B:JTH1001 3.1 36.5 1.0
CG B:ASP549 3.2 31.5 1.0
C2 B:JTH1001 3.2 39.4 1.0
CG B:ASP443 3.2 34.6 1.0
CB B:ASP549 3.6 26.1 1.0
OD1 B:ASP443 3.6 29.4 1.0
NH2 B:ARG557 3.6 72.5 1.0
MN B:MN901 3.8 31.4 1.0
NE2 B:HIS539 3.8 33.7 1.0
CA B:ASP549 4.1 27.2 1.0
O B:GLY444 4.1 26.1 1.0
OD2 B:ASP498 4.2 28.9 1.0
OD1 B:ASP549 4.2 38.2 1.0
O B:HOH2 4.3 26.7 1.0
C7 B:JTH1001 4.3 38.3 1.0
CE1 B:HIS539 4.3 29.5 1.0
C3 B:JTH1001 4.5 42.4 1.0
CB B:ASP443 4.5 27.9 1.0
CD2 B:HIS539 4.7 34.7 1.0
O7 B:JTH1001 4.7 34.4 1.0
CZ B:ARG557 4.9 75.1 1.0
CB B:ALA538 5.0 32.7 1.0

Reference:

D.M.Himmel, K.A.Maegley, T.A.Pauly, J.D.Bauman, K.Das, C.Dharia, A.D.Clark, K.Ryan, M.J.Hickey, R.A.Love, S.H.Hughes, S.Bergqvist, E.Arnold. Structure of Hiv-1 Reverse Transcriptase with the Inhibitor Beta-Thujaplicinol Bound at the Rnase H Active Site. Structure V. 17 1625 2009.
ISSN: ISSN 0969-2126
PubMed: 20004166
DOI: 10.1016/J.STR.2009.09.016
Page generated: Tue Dec 15 04:11:12 2020

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