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Magnesium in PDB 5txn: Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp

Enzymatic activity of Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp

All present enzymatic activity of Structure of Q151M Mutant 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 Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp, PDB code: 5txn 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) 33.38 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.039, 133.634, 139.206, 90.00, 97.88, 90.00
R / Rfree (%) 19.6 / 22.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp (pdb code 5txn). 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 Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp, PDB code: 5txn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5txn

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Magnesium binding site 1 out of 4 in the Structure of Q151M Mutant 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 Q151M Mutant 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:95.9
occ:1.00
 OD1 A:ASP110 2.1 0.1 1.0
O2B A:DTP603 2.1 0.8 1.0
OD2 A:ASP185 2.3 1.0 1.0
O A:VAL111 2.3 0.3 1.0
O2G A:DTP603 2.4 0.3 1.0
O1A A:DTP603 2.4 0.0 1.0
CG A:ASP110 2.7 0.6 1.0
OD2 A:ASP110 2.9 0.0 1.0
O3G A:DTP603 3.2 1.0 1.0
PG A:DTP603 3.2 0.7 1.0
PB A:DTP603 3.4 0.5 1.0
C A:VAL111 3.5 0.5 1.0
CG A:ASP185 3.5 89.8 1.0
PA A:DTP603 3.7 0.8 1.0
O3B A:DTP603 3.8 0.1 1.0
N A:VAL111 4.0 96.9 1.0
O3A A:DTP603 4.0 0.7 1.0
CB A:ASP110 4.1 98.8 1.0
OD1 A:ASP185 4.2 88.1 1.0
CA A:VAL111 4.3 96.2 1.0
C5' A:DTP603 4.4 0.3 1.0
N A:GLY112 4.5 0.8 1.0
CB A:ASP185 4.5 81.9 1.0
O1B A:DTP603 4.5 1.0 1.0
O1G A:DTP603 4.6 0.7 1.0
C A:ASP110 4.6 98.7 1.0
O5' A:DTP603 4.6 0.7 1.0
CA A:GLY112 4.6 98.9 1.0
N A:ASP113 4.7 0.4 1.0
O2A A:DTP603 4.7 0.9 1.0
CA A:ASP110 4.8 92.3 1.0
CB A:ALA114 4.8 0.2 1.0
CB A:VAL111 4.9 88.5 1.0
C A:GLY112 4.9 99.7 1.0
N A:ALA114 4.9 0.5 1.0

Magnesium binding site 2 out of 4 in 5txn

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Magnesium binding site 2 out of 4 in the Structure of Q151M Mutant 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 Q151M Mutant 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:85.0
occ:1.00
 OD2 A:ASP443 2.3 72.3 1.0
O A:HOH713 2.4 67.5 1.0
OD1 A:ASP443 2.4 66.8 1.0
CG A:ASP443 2.7 59.5 1.0
OD1 A:ASN498 3.6 53.8 1.0
O A:GLY444 3.8 64.0 1.0
OD2 A:ASP549 3.8 71.0 1.0
ND2 A:ASN498 3.9 72.8 1.0
CG A:ASN498 4.2 58.8 1.0
CB A:ASP443 4.2 46.5 1.0
OP1 T:DC723 4.3 0.8 1.0
N A:GLY444 4.6 50.2 1.0
C A:GLY444 4.7 48.3 1.0
OE2 A:GLU478 4.8 78.9 1.0
CG A:ASP549 4.8 70.5 1.0

Magnesium binding site 3 out of 4 in 5txn

Go back to Magnesium Binding Sites List in 5txn
Magnesium binding site 3 out of 4 in the Structure of Q151M Mutant 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 Q151M Mutant 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:80.8
occ:1.00
 O C:VAL111 2.0 0.7 1.0
O2B C:DTP601 2.1 1.0 1.0
OD1 C:ASP110 2.2 0.9 1.0
O1A C:DTP601 2.3 93.8 1.0
OD2 C:ASP185 2.3 94.2 1.0
O2G C:DTP601 2.5 0.3 1.0
O3G C:DTP601 3.1 0.7 1.0
PG C:DTP601 3.2 0.9 1.0
C C:VAL111 3.2 0.6 1.0
PB C:DTP601 3.3 0.5 1.0
CG C:ASP110 3.3 0.3 1.0
CG C:ASP185 3.6 89.0 1.0
PA C:DTP601 3.6 0.8 1.0
O3B C:DTP601 3.7 0.1 1.0
OD2 C:ASP110 3.7 0.7 1.0
O3A C:DTP601 3.8 0.5 1.0
N C:VAL111 4.1 0.0 1.0
N C:GLY112 4.1 0.3 1.0
CA C:GLY112 4.1 99.8 1.0
CA C:VAL111 4.2 99.8 1.0
N C:ASP113 4.2 97.6 1.0
C5' C:DTP601 4.2 96.2 1.0
CB C:ALA114 4.3 94.5 1.0
NZ C:LYS220 4.3 0.6 1.0
OD1 C:ASP185 4.3 88.9 1.0
C C:GLY112 4.4 0.5 1.0
N C:ALA114 4.4 0.8 1.0
O5' C:DTP601 4.4 0.9 1.0
O1B C:DTP601 4.5 0.4 1.0
O1G C:DTP601 4.6 0.7 1.0
CB C:ASP185 4.6 88.4 1.0
CB C:ASP110 4.6 0.2 1.0
O2A C:DTP601 4.7 1.0 1.0
C C:ASP110 4.7 0.3 1.0
CB C:VAL111 4.7 88.8 1.0
CA C:ALA114 4.9 0.9 1.0

Magnesium binding site 4 out of 4 in 5txn

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Magnesium binding site 4 out of 4 in the Structure of Q151M Mutant 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 Q151M Mutant 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:96.2
occ:1.00
 OD1 C:ASP443 2.0 60.3 1.0
OD2 C:ASP443 2.1 60.7 1.0
O C:HOH712 2.2 47.1 1.0
CG C:ASP443 2.3 53.8 1.0
O C:HOH731 2.4 61.3 1.0
ND2 C:ASN498 3.4 59.9 1.0
O C:GLY444 3.5 55.8 1.0
OD2 C:ASP549 3.6 58.7 1.0
OD1 C:ASN498 3.7 64.5 1.0
CB C:ASP443 3.9 42.0 1.0
CG C:ASN498 3.9 50.8 1.0
N C:GLY444 4.3 44.2 1.0
O C:HOH702 4.4 51.6 1.0
C C:GLY444 4.5 48.2 1.0
CA C:ASP443 4.7 40.0 1.0
OE2 C:GLU478 4.7 79.0 1.0
CG C:ASP549 4.8 56.6 1.0
C C:ASP443 5.0 39.0 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 05:04:08 2024

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