Magnesium in PDB 5txl: Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp

Enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp

All present enzymatic activity of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp:
2.7.7.49; 2.7.7.7;

Protein crystallography data

The structure of Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp, PDB code: 5txl 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) 48.08 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.380, 133.846, 139.340, 90.00, 97.30, 90.00
R / Rfree (%) 19.3 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp (pdb code 5txl). 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 Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp, PDB code: 5txl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5txl

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Magnesium binding site 1 out of 4 in the Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp


Mono view


Stereo pair view

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

b:0.3
occ:1.00
 OD1 A:ASP185 2.1 0.9 1.0
O2G A:DTP603 2.1 0.7 1.0
OD1 A:ASP110 2.1 1.0 1.0
O A:VAL111 2.2 99.1 1.0
O1A A:DTP603 2.2 83.0 1.0
O2B A:DTP603 2.2 0.3 1.0
CG A:ASP110 2.9 0.1 1.0
OD2 A:ASP110 3.1 0.4 1.0
PB A:DTP603 3.3 0.7 1.0
CG A:ASP185 3.3 89.3 1.0
PG A:DTP603 3.3 0.4 1.0
PA A:DTP603 3.4 99.2 1.0
C A:VAL111 3.4 96.8 1.0
O3A A:DTP603 3.5 0.1 1.0
O3B A:DTP603 3.7 0.7 1.0
O3G A:DTP603 3.9 0.7 1.0
OD2 A:ASP185 4.0 93.5 1.0
N A:VAL111 4.2 92.0 1.0
CB A:ASP110 4.3 97.8 1.0
N A:GLY112 4.3 97.3 1.0
CA A:GLY112 4.3 95.9 1.0
C5' A:DTP603 4.3 97.5 1.0
CA A:VAL111 4.4 88.0 1.0
CB A:ASP185 4.4 81.4 1.0
O5' A:DTP603 4.4 95.5 1.0
O2A A:DTP603 4.4 0.6 1.0
O1G A:DTP603 4.5 0.5 1.0
C A:ASP110 4.5 99.1 1.0
O1B A:DTP603 4.5 0.5 1.0
N A:ASP113 4.8 0.1 1.0
CA A:ASP110 4.9 95.6 1.0
CB A:ALA114 4.9 0.0 1.0
C A:GLY112 5.0 0.1 1.0
CB A:VAL111 5.0 82.8 1.0

Magnesium binding site 2 out of 4 in 5txl

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Magnesium binding site 2 out of 4 in the Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp


Mono view


Stereo pair view

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

b:88.6
occ:1.00
 O A:HOH715 2.1 66.0 1.0
O T:HOH902 2.1 99.2 1.0
OD2 A:ASP443 2.2 85.2 1.0
OD2 A:ASP549 2.2 75.3 1.0
CG A:ASP443 3.1 69.8 1.0
OD1 A:ASP443 3.3 66.7 1.0
CG A:ASP549 3.4 69.3 1.0
CB A:ASP549 4.0 54.0 1.0
CA A:ASP549 4.3 72.0 1.0
O A:GLY444 4.4 55.6 1.0
OD1 A:ASP549 4.4 74.5 1.0
CB A:ASP443 4.5 55.2 1.0
CG2 A:VAL552 4.5 45.2 1.0
ND2 A:ASN498 4.6 63.6 1.0
OP1 T:DC723 4.7 0.6 1.0
NE2 A:HIS539 4.7 80.3 1.0
OD1 A:ASN498 4.8 55.5 1.0
O A:ASP549 4.8 64.6 1.0
CB A:ALA445 5.0 41.1 1.0

Magnesium binding site 3 out of 4 in 5txl

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Magnesium binding site 3 out of 4 in the Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp


Mono view


Stereo pair view

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

b:96.3
occ:1.00
 O C:VAL111 1.8 0.5 1.0
O1A C:DTP601 2.0 87.1 1.0
OD1 C:ASP110 2.1 0.6 1.0
OD1 C:ASP185 2.1 99.8 1.0
O2B C:DTP601 2.1 90.2 1.0
O2G C:DTP601 2.4 0.3 1.0
C C:VAL111 3.0 0.3 1.0
CG C:ASP110 3.2 0.5 1.0
PB C:DTP601 3.2 0.2 1.0
PA C:DTP601 3.3 89.4 1.0
CG C:ASP185 3.3 88.7 1.0
PG C:DTP601 3.4 1.0 1.0
OD2 C:ASP110 3.5 0.0 1.0
O3A C:DTP601 3.6 0.5 1.0
O3B C:DTP601 3.7 0.2 1.0
O3G C:DTP601 3.8 0.0 1.0
N C:GLY112 3.9 0.5 1.0
CA C:GLY112 4.0 0.1 1.0
OD2 C:ASP185 4.0 95.9 1.0
N C:VAL111 4.0 93.1 1.0
CA C:VAL111 4.0 90.0 1.0
C5' C:DTP601 4.2 84.6 1.0
O5' C:DTP601 4.3 80.3 1.0
O2A C:DTP601 4.3 95.1 1.0
CB C:ASP185 4.4 82.9 1.0
C C:ASP110 4.4 93.5 1.0
N C:ASP113 4.4 0.5 1.0
O1B C:DTP601 4.5 97.7 1.0
CB C:ASP110 4.5 96.3 1.0
C C:GLY112 4.6 0.8 1.0
CB C:VAL111 4.6 79.0 1.0
CB C:ALA114 4.6 0.4 1.0
O1G C:DTP601 4.7 0.3 1.0
NZ C:LYS220 4.7 98.0 1.0
N C:ALA114 4.7 0.5 1.0
O C:ASP110 4.9 95.5 1.0
CA C:ASP110 5.0 90.3 1.0

Magnesium binding site 4 out of 4 in 5txl

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Magnesium binding site 4 out of 4 in the Structure of Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp


Mono view


Stereo pair view

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

b:1.0
occ:1.00
 O C:HOH721 2.1 66.5 1.0
O C:HOH750 2.1 68.3 1.0
OD1 C:ASP443 2.1 55.5 1.0
OD2 C:ASP443 2.1 67.8 1.0
CG C:ASP443 2.4 59.6 1.0
OD2 C:ASP549 3.5 67.3 1.0
OD1 C:ASN498 3.5 79.4 1.0
O C:GLY444 3.5 60.4 1.0
ND2 C:ASN498 3.7 61.8 1.0
CB C:ASP443 3.9 48.0 1.0
CG C:ASN498 4.0 54.9 1.0
N C:GLY444 4.3 44.3 1.0
C C:GLY444 4.5 48.6 1.0
O C:HOH725 4.5 53.7 1.0
CG C:ASP549 4.6 66.2 1.0
CA C:ASP443 4.8 45.6 1.0
OE2 C:GLU478 4.8 94.2 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 Dec 14 21:13:14 2020

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