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Magnesium in PDB 3jsm: K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds-Dna and Complexed with Tenofovir-Diphosphate As the Incoming Nucleotide Substrate

Enzymatic activity of K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds-Dna and Complexed with Tenofovir-Diphosphate As the Incoming Nucleotide Substrate

All present enzymatic activity of K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds-Dna and Complexed with Tenofovir-Diphosphate As the Incoming Nucleotide Substrate:
2.7.7.49;

Protein crystallography data

The structure of K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds-Dna and Complexed with Tenofovir-Diphosphate As the Incoming Nucleotide Substrate, PDB code: 3jsm was solved by K.Das, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.17 / 3.00
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 170.310, 170.310, 155.440, 90.00, 90.00, 120.00
R / Rfree (%) 25.2 / 28.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds-Dna and Complexed with Tenofovir-Diphosphate As the Incoming Nucleotide Substrate (pdb code 3jsm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds-Dna and Complexed with Tenofovir-Diphosphate As the Incoming Nucleotide Substrate, PDB code: 3jsm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3jsm

Go back to Magnesium Binding Sites List in 3jsm
Magnesium binding site 1 out of 2 in the K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds-Dna and Complexed with Tenofovir-Diphosphate As the Incoming Nucleotide Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds-Dna and Complexed with Tenofovir-Diphosphate As the Incoming Nucleotide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg600

b:33.8
occ:1.00
O A:VAL111 2.2 46.4 1.0
OD2 A:ASP185 2.3 41.5 1.0
O2B A:TNV823 2.3 45.4 1.0
O1G A:TNV823 2.3 57.6 1.0
OD1 A:ASP110 2.3 64.0 1.0
O1A A:TNV823 2.4 54.8 1.0
PG A:TNV823 3.2 61.4 1.0
CG A:ASP110 3.2 63.4 1.0
PB A:TNV823 3.3 55.0 1.0
C A:VAL111 3.4 46.3 1.0
O3G A:TNV823 3.4 62.7 1.0
OD2 A:ASP110 3.4 75.8 1.0
PA A:TNV823 3.5 49.3 1.0
CG A:ASP185 3.5 37.2 1.0
O3B A:TNV823 3.6 57.2 1.0
O3A A:TNV823 3.6 40.3 1.0
C9' A:TNV823 4.1 48.9 1.0
CA A:GLY112 4.2 45.8 1.0
OD1 A:ASP185 4.2 27.9 1.0
N A:GLY112 4.2 45.9 1.0
N A:VAL111 4.2 48.3 1.0
CA A:VAL111 4.4 46.7 1.0
C A:ASP110 4.4 48.3 1.0
CB A:ASP185 4.5 37.0 1.0
O2G A:TNV823 4.6 58.2 1.0
O A:ASP110 4.6 48.1 1.0
CB A:ASP110 4.6 52.6 1.0
NZ A:LYS219 4.6 64.9 1.0
CB A:ALA114 4.6 38.0 1.0
N A:ASP113 4.7 49.2 1.0
O1B A:TNV823 4.7 49.7 1.0
C A:GLY112 4.8 45.6 1.0
N A:ALA114 4.8 47.2 1.0
O2A A:TNV823 4.8 50.4 1.0
CA A:ASP110 5.0 46.7 1.0

Magnesium binding site 2 out of 2 in 3jsm

Go back to Magnesium Binding Sites List in 3jsm
Magnesium binding site 2 out of 2 in the K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds-Dna and Complexed with Tenofovir-Diphosphate As the Incoming Nucleotide Substrate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds-Dna and Complexed with Tenofovir-Diphosphate As the Incoming Nucleotide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:75.8
occ:1.00
O A:HOH561 2.3 51.6 1.0
OD2 A:ASP498 2.4 99.7 1.0
OD2 A:ASP443 2.5 93.0 1.0
OD1 A:ASP498 2.6 0.6 1.0
OD1 A:ASP443 2.6 99.8 1.0
CG A:ASP443 2.7 96.0 1.0
CG A:ASP498 2.8 0.5 1.0
OE1 A:GLU478 3.5 0.7 1.0
CB A:ASP443 3.9 96.2 1.0
CB A:ASP498 4.3 0.8 1.0
O A:GLY444 4.4 99.0 1.0
CA A:ASP443 4.5 98.7 1.0
N A:GLY444 4.7 97.2 1.0
N A:SER499 4.7 0.8 1.0
CD A:GLU478 4.8 0.9 1.0
CB A:ALA538 4.9 0.4 1.0
OD1 A:ASP549 4.9 0.9 1.0
CB A:SER499 4.9 0.2 1.0
C A:ASP498 5.0 0.8 1.0

Reference:

K.Das, R.P.Bandwar, K.L.White, J.Y.Feng, S.G.Sarafianos, S.Tuske, X.Tu, A.D.Clark, P.L.Boyer, X.Hou, B.L.Gaffney, R.A.Jones, M.D.Miller, S.H.Hughes, E.Arnold. Structural Basis For the Role of the K65R Mutation in Hiv-1 Reverse Transcriptase Polymerization, Excision Antagonism, and Tenofovir Resistance. J.Biol.Chem. V. 284 35092 2009.
ISSN: ISSN 0021-9258
PubMed: 19812032
DOI: 10.1074/JBC.M109.022525
Page generated: Sun Aug 10 23:19:43 2025

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