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: Mon Jan 25 15:36:48 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy