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

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

All present enzymatic activity of K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds- Dna and Complexed with Datp 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 Datp As the Incoming Nucleotide Substrate, PDB code: 3jyt 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) 48.86 / 3.30
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 169.720, 169.720, 155.410, 90.00, 90.00, 120.00
R / Rfree (%) 25.3 / 28.7

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 Datp As the Incoming Nucleotide Substrate (pdb code 3jyt). 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 Datp As the Incoming Nucleotide Substrate, PDB code: 3jyt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3jyt

Go back to Magnesium Binding Sites List in 3jyt
Magnesium binding site 1 out of 2 in the K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds- Dna and Complexed with Datp 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 Datp As the Incoming Nucleotide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg600

b:19.5
occ:1.00
O1G A:DTP700 2.4 82.6 1.0
O A:VAL111 2.4 58.2 1.0
OD2 A:ASP110 2.5 85.8 1.0
O2B A:DTP700 2.5 62.7 1.0
O1A A:DTP700 2.5 60.5 1.0
OD2 A:ASP185 2.8 35.8 1.0
PB A:DTP700 3.0 64.9 1.0
CG A:ASP110 3.0 81.5 1.0
O3A A:DTP700 3.1 60.0 1.0
PG A:DTP700 3.1 71.2 1.0
O3G A:DTP700 3.1 70.0 1.0
OD1 A:ASP110 3.2 90.7 1.0
PA A:DTP700 3.3 60.8 1.0
O3B A:DTP700 3.5 65.3 1.0
C A:VAL111 3.6 58.6 1.0
CG A:ASP185 4.0 51.9 1.0
NZ A:LYS219 4.1 97.2 1.0
O A:ASP110 4.1 61.6 1.0
CA A:GLY112 4.2 61.4 1.0
C A:ASP110 4.2 60.2 1.0
CB A:ASP110 4.3 71.0 1.0
N A:GLY112 4.3 57.4 1.0
OD1 A:ASP185 4.4 48.9 1.0
N A:VAL111 4.4 59.5 1.0
O2A A:DTP700 4.5 64.1 1.0
N A:ASP113 4.5 71.4 1.0
C5' A:DTP700 4.5 63.8 1.0
O5' A:DTP700 4.5 62.3 1.0
CA A:VAL111 4.6 58.9 1.0
O1B A:DTP700 4.6 58.1 1.0
O2G A:DTP700 4.7 77.5 1.0
C A:GLY112 4.7 67.1 1.0
CA A:ASP110 4.8 59.4 1.0
N A:ALA114 4.9 66.4 1.0
CB A:ALA114 5.0 66.6 1.0

Magnesium binding site 2 out of 2 in 3jyt

Go back to Magnesium Binding Sites List in 3jyt
Magnesium binding site 2 out of 2 in the K65R Mutant Hiv-1 Reverse Transcriptase Cross-Linked to Ds- Dna and Complexed with Datp 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 Datp As the Incoming Nucleotide Substrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:0.2
occ:1.00
OD2 A:ASP498 2.5 0.5 1.0
OD1 A:ASP498 2.5 1.0 1.0
OD1 A:ASP443 2.6 0.9 1.0
OD2 A:ASP443 2.6 0.8 1.0
CG A:ASP443 2.7 0.4 1.0
CG A:ASP498 2.9 0.5 1.0
OE1 A:GLU478 3.8 0.0 1.0
CB A:ASP443 3.9 0.7 1.0
CB A:ASP498 4.4 0.9 1.0
O A:GLY444 4.6 0.6 1.0
CB A:ALA538 4.7 0.7 1.0
OD1 A:ASP549 4.9 0.2 1.0
CA A:ASP443 4.9 0.6 1.0
N A:SER499 5.0 0.4 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: Mon Dec 14 08:20:57 2020

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