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Magnesium in PDB 5txp: Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp

Enzymatic activity of Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp

All present enzymatic activity of Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp:
2.7.7.49; 2.7.7.7;

Protein crystallography data

The structure of Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp, PDB code: 5txp was solved by K.Das, S.M.Martinez, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.62 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.945, 133.273, 139.062, 90.00, 97.59, 90.00
R / Rfree (%) 19.6 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp (pdb code 5txp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp, PDB code: 5txp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5txp

Go back to Magnesium Binding Sites List in 5txp
Magnesium binding site 1 out of 4 in the Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:0.1
occ:1.00
 OD1 A:ASP110 2.1 0.8 1.0
O2B A:DDS603 2.2 0.8 1.0
O2G A:DDS603 2.2 0.7 1.0
OD2 A:ASP185 2.2 0.0 1.0
O A:VAL111 2.2 0.8 1.0
O2A A:DDS603 2.4 0.7 1.0
CG A:ASP110 2.7 0.0 1.0
OD2 A:ASP110 2.8 1.0 1.0
CG A:ASP185 3.2 0.0 1.0
C A:VAL111 3.4 0.3 1.0
PA A:DDS603 3.5 0.5 1.0
PB A:DDS603 3.5 0.7 1.0
PG A:DDS603 3.5 0.5 1.0
O5' A:DDS603 3.7 0.1 1.0
OD1 A:ASP185 3.9 0.7 1.0
N A:VAL111 4.0 0.4 1.0
O3A A:DDS603 4.0 0.7 1.0
CB A:ASP110 4.0 0.5 1.0
O3B A:DDS603 4.0 0.2 1.0
O3G A:DDS603 4.1 0.3 1.0
CB A:ASP185 4.1 80.4 1.0
CA A:VAL111 4.3 0.5 1.0
C A:ASP110 4.3 0.6 1.0
N A:GLY112 4.4 0.1 1.0
CA A:ASP110 4.6 97.9 1.0
CA A:GLY112 4.6 0.6 1.0
O1B A:DDS603 4.6 0.5 1.0
O1G A:DDS603 4.7 0.8 1.0
OD2 A:ASP186 4.7 0.1 1.0
O1A A:DDS603 4.8 0.2 1.0
C5' A:DDS603 4.8 0.8 1.0
CB A:VAL111 4.8 94.5 1.0
O A:ASP110 4.9 0.1 1.0
CB A:ALA114 4.9 0.3 1.0

Magnesium binding site 2 out of 4 in 5txp

Go back to Magnesium Binding Sites List in 5txp
Magnesium binding site 2 out of 4 in the Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:0.3
occ:1.00
 O A:HOH710 2.1 63.0 1.0
OD2 A:ASP443 2.1 89.8 1.0
O T:HOH902 2.1 1.0 1.0
OD1 A:ASP443 2.1 87.1 1.0
CG A:ASP443 2.4 74.2 1.0
O A:GLY444 3.6 75.6 1.0
OD2 A:ASP549 3.6 68.9 1.0
OD1 A:ASN498 3.6 59.1 1.0
ND2 A:ASN498 3.8 66.1 1.0
CB A:ASP443 3.9 50.8 1.0
CG A:ASN498 4.2 53.1 1.0
OP1 T:DC723 4.3 0.5 1.0
N A:GLY444 4.3 61.8 1.0
C A:GLY444 4.5 56.9 1.0
CG A:ASP549 4.7 61.8 1.0
CA A:ASP443 4.7 47.4 1.0
OE2 A:GLU478 4.9 90.2 1.0
CB A:ASP549 4.9 46.5 1.0

Magnesium binding site 3 out of 4 in 5txp

Go back to Magnesium Binding Sites List in 5txp
Magnesium binding site 3 out of 4 in the Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:0.9
occ:1.00
 O C:VAL111 1.9 0.7 1.0
OD2 C:ASP185 2.1 0.3 1.0
O1A C:DDS601 2.2 0.2 1.0
O2B C:DDS601 2.3 0.1 1.0
O2G C:DDS601 2.3 0.5 1.0
OD1 C:ASP110 2.4 0.6 1.0
C C:VAL111 3.1 0.6 1.0
CG C:ASP185 3.2 88.1 1.0
PA C:DDS601 3.3 0.4 1.0
CG C:ASP110 3.4 0.6 1.0
PB C:DDS601 3.6 0.2 1.0
O5' C:DDS601 3.6 0.3 1.0
PG C:DDS601 3.7 0.2 1.0
OD2 C:ASP110 3.8 0.6 1.0
O3A C:DDS601 4.0 0.8 1.0
CB C:ASP185 4.0 84.4 1.0
N C:GLY112 4.0 0.2 1.0
CA C:VAL111 4.0 0.7 1.0
N C:VAL111 4.0 0.3 1.0
OD1 C:ASP185 4.1 91.3 1.0
CA C:GLY112 4.1 0.8 1.0
O3B C:DDS601 4.2 0.2 1.0
CB C:ALA114 4.2 0.4 1.0
N C:ASP113 4.5 0.1 1.0
O1G C:DDS601 4.5 0.8 1.0
CB C:VAL111 4.5 94.4 1.0
N C:ALA114 4.5 0.4 1.0
C C:ASP110 4.6 0.2 1.0
O2A C:DDS601 4.6 0.4 1.0
C C:GLY112 4.6 0.2 1.0
O1B C:DDS601 4.7 0.4 1.0
CB C:ASP110 4.7 0.2 1.0
O3G C:DDS601 4.7 0.1 1.0
NZ C:LYS220 4.8 0.7 1.0
C5' C:DDS601 4.8 0.9 1.0

Magnesium binding site 4 out of 4 in 5txp

Go back to Magnesium Binding Sites List in 5txp
Magnesium binding site 4 out of 4 in the Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Q151M Complex (A62V, V75I, F77L, F116Y, Q151M) Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:0.2
occ:1.00
 O C:HOH722 2.1 77.9 1.0
O C:HOH703 2.1 95.1 1.0
OD1 C:ASP443 2.1 64.3 1.0
OD2 C:ASP443 2.1 67.5 1.0
CG C:ASP443 2.4 63.4 1.0
O C:GLY444 3.1 88.4 1.0
OD2 C:ASP549 3.6 69.3 1.0
CB C:ASP443 3.9 53.5 1.0
N C:GLY444 4.0 56.6 1.0
C C:GLY444 4.0 60.5 1.0
OD1 C:ASN498 4.0 74.3 1.0
ND2 C:ASN498 4.0 64.4 1.0
CG C:ASN498 4.5 52.3 1.0
OE2 C:GLU478 4.5 87.1 1.0
CA C:ASP443 4.6 48.6 1.0
CA C:GLY444 4.6 56.8 1.0
C C:ASP443 4.8 48.9 1.0
CG C:ASP549 4.8 60.7 1.0
N C:ALA445 4.9 54.2 1.0
CB C:ALA445 4.9 38.3 1.0
CG2 C:VAL552 4.9 74.3 1.0

Reference:

K.Das, S.E.Martinez, E.Arnold. Structural Insights Into Hiv Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance. Antimicrob. Agents V. 61 2017CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 28396546
DOI: 10.1128/AAC.00224-17
Page generated: Mon Sep 30 05:04:15 2024

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