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Manganese in PDB 7ahx: Hiv-1 Reverse Transcriptase Complex with Dna and D-Aspartate Tenofovir with Bound Manganese

Enzymatic activity of Hiv-1 Reverse Transcriptase Complex with Dna and D-Aspartate Tenofovir with Bound Manganese

All present enzymatic activity of Hiv-1 Reverse Transcriptase Complex with Dna and D-Aspartate 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 D-Aspartate Tenofovir with Bound Manganese, PDB code: 7ahx 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) 69.80 / 2.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.416, 132.371, 138.744, 90, 98.48, 90
R / Rfree (%) 21.4 / 25.4

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 7ahx

Go back to Manganese Binding Sites List in 7ahx
Manganese binding site 1 out of 4 in the Hiv-1 Reverse Transcriptase Complex with Dna and D-Aspartate 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 D-Aspartate Tenofovir with Bound Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:81.3
occ:1.00
 O27 A:REK603 1.8 76.9 1.0
O A:VAL111 2.0 88.6 1.0
OD2 A:ASP110 2.0 73.6 1.0
OD2 A:ASP185 2.0 78.3 1.0
CG A:ASP110 2.6 87.6 1.0
C A:VAL111 2.9 84.9 1.0
OD1 A:ASP110 2.9 98.1 1.0
N A:VAL111 3.2 77.0 1.0
CG A:ASP185 3.2 68.4 1.0
P02 A:REK603 3.3 85.5 1.0
CA A:VAL111 3.6 73.3 1.0
OD1 A:ASP185 3.9 64.6 1.0
N A:GLY112 3.9 78.8 1.0
CB A:ASP110 3.9 60.3 1.0
C12 A:REK603 4.1 73.8 1.0
C A:ASP110 4.1 82.1 1.0
CB A:VAL111 4.2 72.7 1.0
CA A:GLY112 4.2 82.9 1.0
N03 A:REK603 4.2 93.8 1.0
O01 A:REK603 4.2 86.1 1.0
CB A:ASP185 4.3 54.0 1.0
CA A:ASP110 4.4 57.5 1.0
CB A:ALA114 4.6 76.8 1.0
N A:ASP113 4.7 75.5 1.0
C A:GLY112 4.7 71.0 1.0
N A:ALA114 4.9 86.2 1.0

Manganese binding site 2 out of 4 in 7ahx

Go back to Manganese Binding Sites List in 7ahx
Manganese binding site 2 out of 4 in the Hiv-1 Reverse Transcriptase Complex with Dna and D-Aspartate 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 D-Aspartate Tenofovir with Bound Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:87.5
occ:1.00
 OD1 A:ASP443 2.0 52.0 1.0
OE2 A:GLU478 2.7 75.4 1.0
O A:GLY444 2.7 53.0 1.0
CG A:ASP443 2.9 52.8 1.0
OD2 A:ASP443 3.1 76.4 1.0
OD1 A:ASN498 3.6 55.9 1.0
CD A:GLU478 3.7 61.7 1.0
C A:GLY444 3.8 51.9 1.0
N A:GLY444 3.8 39.7 1.0
CG A:GLU478 4.0 35.5 1.0
ND2 A:ASN498 4.1 49.2 1.0
CG A:ASN498 4.3 56.2 1.0
CB A:ASP443 4.3 31.2 1.0
OD2 A:ASP549 4.4 100.6 1.0
CA A:GLY444 4.5 43.2 1.0
OP1 T:DC723 4.5 100.1 1.0
CA A:ASP443 4.7 45.8 1.0
C A:ASP443 4.8 36.1 1.0
N A:ALA445 4.8 43.7 1.0
OE1 A:GLU478 4.9 59.0 1.0
CB A:ALA445 5.0 35.2 1.0

Manganese binding site 3 out of 4 in 7ahx

Go back to Manganese Binding Sites List in 7ahx
Manganese binding site 3 out of 4 in the Hiv-1 Reverse Transcriptase Complex with Dna and D-Aspartate 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 D-Aspartate Tenofovir with Bound Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:124.7
occ:1.00
 OD2 C:ASP110 2.0 119.8 1.0
O27 C:REK603 2.0 117.3 1.0
OD2 C:ASP185 2.0 111.3 1.0
O C:VAL111 2.0 121.6 1.0
CG C:ASP110 2.2 125.8 1.0
OD1 C:ASP110 2.2 127.8 1.0
C C:VAL111 2.5 117.9 1.0
N C:VAL111 2.8 113.0 1.0
C C:ASP110 3.2 115.8 1.0
CG C:ASP185 3.2 108.1 1.0
CA C:VAL111 3.2 110.8 1.0
N C:GLY112 3.3 118.2 1.0
CB C:ASP110 3.4 115.8 1.0
P02 C:REK603 3.5 114.8 1.0
CA C:ASP110 3.7 110.7 1.0
CA C:GLY112 3.7 112.8 1.0
OD1 C:ASP185 3.8 107.5 1.0
O C:ASP110 3.8 124.9 1.0
CB C:VAL111 4.1 105.3 1.0
O01 C:REK603 4.1 117.5 1.0
CB C:ASP185 4.4 101.2 1.0
N03 C:REK603 4.4 112.7 1.0
C C:GLY112 4.5 105.7 1.0
C12 C:REK603 4.5 112.8 1.0
N C:ASP113 4.7 112.0 1.0
CB C:ALA114 4.9 109.4 1.0
CG1 C:VAL111 5.0 105.2 1.0

Manganese binding site 4 out of 4 in 7ahx

Go back to Manganese Binding Sites List in 7ahx
Manganese binding site 4 out of 4 in the Hiv-1 Reverse Transcriptase Complex with Dna and D-Aspartate 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 D-Aspartate Tenofovir with Bound Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn602

b:69.8
occ:1.00
 OD1 C:ASP443 2.1 50.0 1.0
OE2 C:GLU478 2.3 75.5 1.0
O C:GLY444 2.7 53.3 1.0
CG C:ASP443 3.1 40.1 1.0
OD2 C:ASP443 3.4 47.5 1.0
CD C:GLU478 3.4 68.6 1.0
C C:GLY444 3.6 46.1 1.0
N C:GLY444 3.8 38.3 1.0
OD1 C:ASN498 4.0 52.4 1.0
CG C:GLU478 4.0 35.6 1.0
ND2 C:ASN498 4.0 61.2 1.0
CA C:GLY444 4.3 34.5 1.0
CG C:ASN498 4.4 54.2 1.0
OE1 C:GLU478 4.4 54.0 1.0
CB C:ASP443 4.5 36.5 1.0
N C:ALA445 4.6 46.4 1.0
OD2 C:ASP549 4.6 66.6 1.0
OP1 E:DC723 4.7 99.7 1.0
C C:ASP443 4.8 36.4 1.0
CA C:ASP443 4.8 35.5 1.0
CA C:ALA445 4.8 41.0 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 08:03:58 2024

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