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Manganese in PDB 7aii: Hiv-1 Reverse Transcriptase Complex with Dna and L-Methionine Tenofovir with Bound Manganese

Enzymatic activity of Hiv-1 Reverse Transcriptase Complex with Dna and L-Methionine Tenofovir with Bound Manganese

All present enzymatic activity of Hiv-1 Reverse Transcriptase Complex with Dna and L-Methionine Tenofovir with Bound Manganese:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13; 3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Reverse Transcriptase Complex with Dna and L-Methionine Tenofovir with Bound Manganese, PDB code: 7aii was solved by W.Gu, S.E.Martinez, H.Nguyen, H.Xu, P.Herdewijn, S.De Jonghe, K.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.78 / 2.62
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.48, 132.67, 139.02, 90, 98.62, 90
R / Rfree (%) 22.3 / 25.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Hiv-1 Reverse Transcriptase Complex with Dna and L-Methionine Tenofovir with Bound Manganese (pdb code 7aii). 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 Complex with Dna and L-Methionine Tenofovir with Bound Manganese, PDB code: 7aii:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7aii

Go back to Manganese Binding Sites List in 7aii
Manganese binding site 1 out of 4 in the Hiv-1 Reverse Transcriptase Complex with Dna and L-Methionine Tenofovir with Bound Manganese


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 Complex with Dna and L-Methionine Tenofovir with Bound Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:92.9
occ:1.00
 O27 A:RFE603 1.9 87.1 1.0
OD2 A:ASP110 2.0 89.9 1.0
O A:VAL111 2.1 85.0 1.0
OD2 A:ASP185 2.1 87.3 1.0
CG A:ASP110 2.5 100.2 1.0
OD1 A:ASP110 2.6 108.9 1.0
P02 A:RFE603 3.0 94.7 1.0
C A:VAL111 3.1 86.7 1.0
CG A:ASP185 3.3 77.5 1.0
N18 A:RFE603 3.3 100.5 1.0
N A:VAL111 3.4 80.7 1.0
C03 A:RFE603 3.8 92.9 1.0
CA A:VAL111 3.8 79.5 1.0
OD1 A:ASP185 3.9 80.2 1.0
CB A:ASP110 3.9 69.0 1.0
N A:GLY112 4.1 78.7 1.0
C A:ASP110 4.2 87.7 1.0
CA A:GLY112 4.4 84.3 1.0
CB A:ASP185 4.4 71.9 1.0
O01 A:RFE603 4.4 84.1 1.0
CA A:ASP110 4.5 58.1 1.0
CB A:VAL111 4.5 75.5 1.0
C19 A:RFE603 4.7 98.3 1.0
N A:ASP113 4.7 79.1 1.0
CB A:ALA114 4.8 83.7 1.0
C A:GLY112 4.9 84.6 1.0

Manganese binding site 2 out of 4 in 7aii

Go back to Manganese Binding Sites List in 7aii
Manganese binding site 2 out of 4 in the Hiv-1 Reverse Transcriptase Complex with Dna and L-Methionine Tenofovir with Bound Manganese


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 Complex with Dna and L-Methionine Tenofovir with Bound Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:130.1
occ:1.00
 OD1 A:ASP443 2.0 60.2 1.0
O A:GLY444 2.7 68.2 1.0
CG A:ASP443 3.0 57.6 1.0
OE2 A:GLU478 3.0 73.0 1.0
OD2 A:ASP443 3.3 79.5 1.0
C A:GLY444 3.7 59.1 1.0
N A:GLY444 3.7 46.1 1.0
CD A:GLU478 3.9 58.9 1.0
CG A:GLU478 3.9 37.2 1.0
OD1 A:ASN498 3.9 64.8 1.0
ND2 A:ASN498 4.2 64.1 1.0
CA A:GLY444 4.3 46.8 1.0
CB A:ASP443 4.4 43.0 1.0
OD2 A:ASP549 4.5 101.9 1.0
CG A:ASN498 4.5 67.9 1.0
N A:ALA445 4.6 43.8 1.0
CA A:ASP443 4.7 55.6 1.0
C A:ASP443 4.7 41.2 1.0
OP1 T:DC723 4.7 115.1 1.0
CB A:ALA445 4.8 46.9 1.0
CA A:ALA445 4.8 50.7 1.0

Manganese binding site 3 out of 4 in 7aii

Go back to Manganese Binding Sites List in 7aii
Manganese binding site 3 out of 4 in the Hiv-1 Reverse Transcriptase Complex with Dna and L-Methionine Tenofovir with Bound Manganese


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 Complex with Dna and L-Methionine Tenofovir with Bound Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:133.6
occ:1.00
 OD2 C:ASP185 2.0 110.5 1.0
OD2 C:ASP110 2.0 124.4 1.0
O C:VAL111 2.0 118.6 1.0
OD1 C:ASP110 2.1 132.5 1.0
CG C:ASP110 2.1 129.6 1.0
O27 C:RFE603 2.1 118.4 1.0
C C:VAL111 2.8 113.0 1.0
N C:VAL111 2.9 106.9 1.0
CG C:ASP185 3.1 108.0 1.0
P02 C:RFE603 3.2 118.0 1.0
N18 C:RFE603 3.2 120.8 1.0
C C:ASP110 3.3 114.2 1.0
CB C:ASP110 3.4 117.7 1.0
CA C:VAL111 3.4 106.1 1.0
CA C:ASP110 3.7 107.3 1.0
OD1 C:ASP185 3.8 105.6 1.0
N C:GLY112 3.9 109.0 1.0
O C:ASP110 3.9 121.9 1.0
CB C:VAL111 4.1 103.0 1.0
C03 C:RFE603 4.1 103.9 1.0
CB C:ASP185 4.2 102.2 1.0
CA C:GLY112 4.3 101.8 1.0
C19 C:RFE603 4.5 123.8 1.0
O01 C:RFE603 4.5 110.4 1.0
N C:ASP113 4.9 99.6 1.0
CB C:ALA114 4.9 110.0 1.0
C C:GLY112 4.9 95.8 1.0
C23 C:RFE603 5.0 127.6 1.0

Manganese binding site 4 out of 4 in 7aii

Go back to Manganese Binding Sites List in 7aii
Manganese binding site 4 out of 4 in the Hiv-1 Reverse Transcriptase Complex with Dna and L-Methionine Tenofovir with Bound Manganese


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 Complex with Dna and L-Methionine Tenofovir with Bound Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn602

b:85.6
occ:1.00
 OD1 C:ASP443 2.2 52.4 1.0
OE2 C:GLU478 2.4 86.7 1.0
O C:GLY444 2.6 59.0 1.0
CG C:ASP443 3.2 36.6 1.0
OD2 C:ASP443 3.5 52.3 1.0
CD C:GLU478 3.6 70.3 1.0
C C:GLY444 3.6 47.8 1.0
ND2 C:ASN498 3.8 75.5 1.0
N C:GLY444 3.8 38.5 1.0
CG C:GLU478 4.0 37.3 1.0
CA C:GLY444 4.3 37.4 1.0
OD1 C:ASN498 4.3 55.5 1.0
CG C:ASN498 4.5 52.8 1.0
N C:ALA445 4.5 49.1 1.0
CB C:ASP443 4.6 33.2 1.0
OD2 C:ASP549 4.6 64.2 1.0
OE1 C:GLU478 4.6 65.6 1.0
O C:HOH706 4.6 50.3 1.0
CA C:ALA445 4.7 49.9 1.0
C C:ASP443 4.8 33.6 1.0
OP1 E:DC723 4.8 116.1 1.0
CA C:ASP443 4.9 35.4 1.0
CB C:ALA445 5.0 43.4 1.0

Reference:

W.Gu, S.Martinez, H.Nguyen, H.Xu, P.Herdewijn, S.De Jonghe, K.Das. Tenofovir-Amino Acid Conjugates Act As Polymerase Substrates-Implications For Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33356231
DOI: 10.1021/ACS.JMEDCHEM.0C01747
Page generated: Sun Oct 6 08:04:01 2024

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