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

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

All present enzymatic activity of Structure of 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 Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Ddatp, PDB code: 5txm 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) 46.05 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.337, 133.946, 139.399, 90.00, 97.71, 90.00
R / Rfree (%) 18.4 / 22.3

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 Ddatp (pdb code 5txm). 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 Ddatp, PDB code: 5txm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5txm

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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 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 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
 O2B A:DDS603 2.0 0.3 1.0
OD1 A:ASP110 2.0 0.2 1.0
OD1 A:ASP185 2.2 0.2 1.0
O A:VAL111 2.2 0.6 1.0
O2A A:DDS603 2.4 0.4 1.0
O2G A:DDS603 2.4 0.5 1.0
CG A:ASP185 3.0 0.0 1.0
CG A:ASP110 3.1 0.9 1.0
PB A:DDS603 3.1 0.3 1.0
PG A:DDS603 3.3 0.6 1.0
PA A:DDS603 3.4 0.2 1.0
OD2 A:ASP110 3.4 0.9 1.0
C A:VAL111 3.4 0.1 1.0
OD2 A:ASP185 3.6 1.0 1.0
O3B A:DDS603 3.6 0.6 1.0
O3G A:DDS603 3.6 0.2 1.0
O3A A:DDS603 3.6 1.0 1.0
O5' A:DDS603 3.8 0.3 1.0
CB A:ASP185 4.1 88.4 1.0
N A:VAL111 4.1 92.1 1.0
O1B A:DDS603 4.3 0.1 1.0
CA A:VAL111 4.4 93.1 1.0
N A:GLY112 4.4 99.1 1.0
CB A:ASP110 4.4 97.0 1.0
CA A:GLY112 4.4 94.2 1.0
C A:ASP110 4.4 97.6 1.0
O1G A:DDS603 4.6 0.8 1.0
O1A A:DDS603 4.7 0.1 1.0
CB A:ALA114 4.8 0.7 1.0
CA A:ASP110 4.8 87.5 1.0
N A:ASP113 4.8 0.7 1.0
C5' A:DDS603 4.8 98.2 1.0
O A:ASP110 4.9 0.9 1.0
CB A:VAL111 5.0 84.3 1.0

Magnesium binding site 2 out of 4 in 5txm

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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 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 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:0.9
occ:1.00
 OD2 A:ASP443 2.0 0.2 1.0
O A:HOH717 2.1 68.8 1.0
O T:HOH902 2.1 86.7 1.0
OD2 A:ASP549 2.4 83.0 1.0
OD1 A:ASP443 2.5 84.7 1.0
CG A:ASP443 2.6 85.7 1.0
CG A:ASP549 3.6 72.4 1.0
O A:GLY444 3.9 71.1 1.0
CB A:ASP443 4.0 65.8 1.0
CB A:ASP549 4.1 60.4 1.0
ND2 A:ASN498 4.2 54.9 1.0
OD1 A:ASN498 4.4 50.6 1.0
CA A:ASP549 4.5 68.0 1.0
CG2 A:VAL552 4.6 38.2 1.0
OD1 A:ASP549 4.6 75.5 1.0
N A:GLY444 4.6 53.0 1.0
C A:GLY444 4.7 59.5 1.0
CG A:ASN498 4.7 52.3 1.0
OP1 T:DC723 4.8 0.9 1.0

Magnesium binding site 3 out of 4 in 5txm

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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 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 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 1.8 0.0 1.0
O2B C:DDS601 2.0 0.7 1.0
OD1 C:ASP185 2.1 0.4 1.0
O2G C:DDS601 2.1 0.6 1.0
OD1 C:ASP110 2.2 0.8 1.0
O1A C:DDS601 2.3 0.6 1.0
C C:VAL111 2.9 0.7 1.0
PB C:DDS601 3.2 0.6 1.0
PA C:DDS601 3.2 0.0 1.0
CG C:ASP185 3.3 0.3 1.0
CG C:ASP110 3.3 0.5 1.0
PG C:DDS601 3.4 1.0 1.0
O5' C:DDS601 3.5 95.2 1.0
O3A C:DDS601 3.6 1.0 1.0
O3B C:DDS601 3.7 0.1 1.0
OD2 C:ASP110 3.7 0.4 1.0
N C:GLY112 3.8 0.4 1.0
CA C:GLY112 3.8 0.1 1.0
CA C:VAL111 3.9 0.1 1.0
N C:VAL111 4.0 97.3 1.0
OD2 C:ASP185 4.0 98.8 1.0
O1G C:DDS601 4.3 0.4 1.0
N C:ASP113 4.3 0.6 1.0
CB C:ASP185 4.3 89.5 1.0
CB C:ALA114 4.4 0.1 1.0
CB C:VAL111 4.4 99.5 1.0
O1B C:DDS601 4.4 0.8 1.0
C C:GLY112 4.4 0.0 1.0
C C:ASP110 4.4 100.0 1.0
O3G C:DDS601 4.5 1.0 1.0
N C:ALA114 4.5 0.2 1.0
O2A C:DDS601 4.6 0.7 1.0
CB C:ASP110 4.6 0.4 1.0
C5' C:DDS601 4.7 86.1 1.0
O C:ASP110 4.9 1.0 1.0
CG1 C:VAL111 5.0 97.8 1.0

Magnesium binding site 4 out of 4 in 5txm

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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 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 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:0.4
occ:1.00
 O C:HOH736 2.1 86.0 1.0
OD2 C:ASP443 2.1 75.3 1.0
OD2 C:ASP549 2.3 77.3 1.0
CG C:ASP443 2.9 60.7 1.0
OD1 C:ASP443 3.0 52.7 1.0
CG C:ASP549 3.5 66.7 1.0
OD1 C:ASN498 3.9 78.7 1.0
O C:GLY444 4.1 64.8 1.0
ND2 C:ASN498 4.2 62.5 1.0
CB C:ASP549 4.3 62.5 1.0
CB C:ASP443 4.4 52.3 1.0
OD1 C:ASP549 4.4 65.8 1.0
CG C:ASN498 4.4 47.4 1.0
OP1 E:DC723 4.6 0.2 1.0
CA C:ASP549 4.8 65.8 1.0
NE2 C:HIS539 4.8 82.4 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 21:13:15 2020

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