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

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

All present enzymatic activity of Hiv-1 Reverse Transcriptase Complex with Dna and L-Glutamate 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-Glutamate Tenofovir with Bound Manganese, PDB code: 7aif 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) 80.14 / 2.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.651, 132.702, 138.77, 90, 98.65, 90
R / Rfree (%) 21.8 / 24.9

Manganese Binding Sites:

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

Manganese binding site 1 out of 4 in 7aif

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

b:83.9
occ:1.00
 OD2 A:ASP110 2.0 93.3 1.0
O28 A:RE5603 2.0 94.0 1.0
O A:VAL111 2.0 91.8 1.0
OD2 A:ASP185 2.0 89.3 1.0
CG A:ASP110 2.8 99.3 1.0
C A:VAL111 3.0 90.3 1.0
P02 A:RE5603 3.1 85.2 1.0
OD1 A:ASP110 3.1 108.8 1.0
CG A:ASP185 3.3 73.4 1.0
N A:VAL111 3.4 79.7 1.0
N03 A:RE5603 3.4 96.6 1.0
CA A:VAL111 3.8 73.5 1.0
C13 A:RE5603 3.8 85.3 1.0
OD1 A:ASP185 4.0 75.1 1.0
N A:GLY112 4.0 85.5 1.0
CB A:ASP110 4.1 61.4 1.0
CA A:GLY112 4.3 83.1 1.0
CB A:ASP185 4.3 66.6 1.0
C A:ASP110 4.4 90.7 1.0
CB A:VAL111 4.4 77.4 1.0
O01 A:RE5603 4.5 86.4 1.0
CA A:ASP110 4.6 74.0 1.0
N A:ASP113 4.7 75.7 1.0
CB A:ALA114 4.8 83.9 1.0
C04 A:RE5603 4.8 97.9 1.0
C A:GLY112 4.8 74.3 1.0
N A:ALA114 5.0 85.3 1.0

Manganese binding site 2 out of 4 in 7aif

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

b:155.9
occ:1.00
 OD1 A:ASP443 2.2 69.0 1.0
O A:GLY444 2.8 79.3 1.0
OE2 A:GLU478 3.1 97.3 1.0
CG A:ASP443 3.1 61.0 1.0
OD2 A:ASP443 3.3 78.8 1.0
ND2 A:ASN498 3.7 71.0 1.0
C A:GLY444 3.9 58.4 1.0
N A:GLY444 3.9 56.1 1.0
CD A:GLU478 4.0 76.9 1.0
OD1 A:ASN498 4.2 70.9 1.0
CG A:GLU478 4.2 45.2 1.0
OD2 A:ASP549 4.3 114.5 1.0
CG A:ASN498 4.4 67.2 1.0
CB A:ASP443 4.5 46.0 1.0
CA A:GLY444 4.6 46.5 1.0
OP1 T:DC723 4.6 106.6 1.0
CG A:ASP549 4.7 120.2 1.0
OD1 A:ASP549 4.7 123.3 1.0
O A:HOH718 4.8 46.1 1.0
N A:ALA445 4.8 50.0 1.0
CB A:ALA445 4.8 42.0 1.0
CA A:ASP443 4.8 48.6 1.0
C A:ASP443 4.9 46.1 1.0
CA A:ALA445 5.0 49.2 1.0

Manganese binding site 3 out of 4 in 7aif

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

b:133.3
occ:1.00
 O C:VAL111 2.0 126.0 1.0
OD2 C:ASP185 2.1 112.1 1.0
OD2 C:ASP110 2.1 128.1 1.0
O28 C:RE5603 2.1 128.5 1.0
CG C:ASP110 2.7 132.4 1.0
N03 C:RE5603 2.8 126.8 1.0
P02 C:RE5603 2.8 122.0 1.0
OD1 C:ASP110 2.9 137.2 1.0
C C:VAL111 3.0 120.3 1.0
CG C:ASP185 3.3 113.8 1.0
N C:VAL111 3.6 112.1 1.0
C13 C:RE5603 3.6 111.5 1.0
CA C:VAL111 3.8 114.6 1.0
C C:ASP110 3.9 120.1 1.0
N C:GLY112 3.9 118.3 1.0
OD1 C:ASP185 3.9 116.3 1.0
CB C:ASP110 4.0 122.4 1.0
CA C:GLY112 4.0 116.1 1.0
C04 C:RE5603 4.2 130.5 1.0
O01 C:RE5603 4.3 118.4 1.0
O C:ASP110 4.3 133.7 1.0
CA C:ASP110 4.4 116.9 1.0
CB C:ASP185 4.4 105.6 1.0
N C:ASP113 4.5 109.1 1.0
CB C:VAL111 4.6 109.3 1.0
C C:GLY112 4.6 111.5 1.0
CB C:ALA114 4.8 109.5 1.0
C08 C:RE5603 4.8 133.1 1.0
O14 C:RE5603 4.8 113.7 1.0
N C:ALA114 4.9 117.1 1.0

Manganese binding site 4 out of 4 in 7aif

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

b:85.8
occ:1.00
 OD1 C:ASP443 2.3 52.0 1.0
O C:GLY444 2.8 64.7 1.0
OE2 C:GLU478 3.1 88.1 1.0
CG C:ASP443 3.3 44.7 1.0
OD2 C:ASP443 3.6 59.0 1.0
C C:GLY444 3.7 50.7 1.0
OD1 C:ASN498 3.8 61.2 1.0
N C:GLY444 3.9 38.9 1.0
CD C:GLU478 3.9 71.6 1.0
CG C:GLU478 4.0 48.5 1.0
ND2 C:ASN498 4.1 69.9 1.0
CG C:ASN498 4.4 67.9 1.0
CA C:GLY444 4.4 47.4 1.0
CB C:ASP443 4.6 35.8 1.0
N C:ALA445 4.6 50.1 1.0
OP1 E:DC723 4.7 103.2 1.0
OD2 C:ASP549 4.8 75.5 1.0
CA C:ALA445 4.9 46.1 1.0
C C:ASP443 4.9 37.7 1.0
CA C:ASP443 4.9 35.7 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 08:04:00 2024

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