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Magnesium in PDB 1rtd: Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance

Enzymatic activity of Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance

All present enzymatic activity of Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance:
2.7.7.49;

Protein crystallography data

The structure of Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance, PDB code: 1rtd was solved by R.Chopra, H.Huang, G.L.Verdine, S.C.Harrison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.840, 150.700, 280.880, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 29.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance (pdb code 1rtd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance, PDB code: 1rtd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1rtd

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Magnesium binding site 1 out of 6 in the Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg600

b:10.0
occ:1.00
 OD1 A:ASP110 2.1 69.5 1.0
O1A A:TTP700 2.2 42.4 1.0
O A:VAL111 2.3 47.2 1.0
OD2 A:ASP185 2.4 38.5 1.0
O1G A:TTP700 2.4 35.7 1.0
O2B A:TTP700 2.4 28.5 1.0
C A:VAL111 3.1 43.8 1.0
CG A:ASP110 3.3 69.0 1.0
CG A:ASP185 3.4 35.9 1.0
PA A:TTP700 3.5 39.0 1.0
PG A:TTP700 3.6 34.2 1.0
MG A:MG601 3.6 10.0 1.0
PB A:TTP700 3.6 32.1 1.0
N A:VAL111 3.8 46.7 1.0
CA A:GLY112 3.8 46.9 1.0
N A:GLY112 3.8 43.1 1.0
O3B A:TTP700 3.8 34.1 1.0
OD1 A:ASP185 3.8 36.1 1.0
O3A A:TTP700 3.9 34.7 1.0
CA A:VAL111 4.1 43.0 1.0
OD2 A:ASP110 4.1 72.4 1.0
O3G A:TTP700 4.1 28.6 1.0
CB A:ASP110 4.2 62.0 1.0
C5' A:TTP700 4.3 32.2 1.0
C A:ASP110 4.3 49.8 1.0
O5' A:TTP700 4.5 36.1 1.0
C A:GLY112 4.5 49.0 1.0
CB A:ASP185 4.5 33.9 1.0
O2A A:TTP700 4.6 36.1 1.0
N A:ASP113 4.6 50.5 1.0
CA A:ASP110 4.7 52.1 1.0
O2G A:TTP700 4.8 32.5 1.0
CB A:ALA114 4.9 31.7 1.0
CB A:VAL111 4.9 39.1 1.0
O1B A:TTP700 4.9 32.1 1.0
N A:ALA114 5.0 38.8 1.0

Magnesium binding site 2 out of 6 in 1rtd

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Magnesium binding site 2 out of 6 in the Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:10.0
occ:1.00
 OD1 A:ASP185 2.1 36.1 1.0
OD1 A:ASP110 2.5 69.5 1.0
OD2 A:ASP110 2.7 72.4 1.0
CG A:ASP110 2.9 69.0 1.0
CG A:ASP185 2.9 35.9 1.0
O1A A:TTP700 3.0 42.4 1.0
OD2 A:ASP185 3.3 38.5 1.0
C3' F:DG22 3.4 41.6 1.0
MG A:MG600 3.6 10.0 1.0
N A:ASP186 3.7 36.4 1.0
CB A:ASP186 3.9 42.6 1.0
OD1 A:ASP186 3.9 50.8 1.0
C A:ASP185 3.9 37.7 1.0
CA A:ASP186 4.0 38.6 1.0
C4' F:DG22 4.1 42.8 1.0
PA A:TTP700 4.1 39.0 1.0
CB A:ASP185 4.1 33.9 1.0
CG A:ASP186 4.2 48.4 1.0
C5' F:DG22 4.3 43.0 1.0
CB A:ASP110 4.3 62.0 1.0
CA A:ASP185 4.4 36.9 1.0
O A:ASP185 4.4 37.6 1.0
O2A A:TTP700 4.4 36.1 1.0
C5' A:TTP700 4.4 32.2 1.0
N A:ASP185 4.5 37.8 1.0
C2' F:DG22 4.6 40.7 1.0
O5' A:TTP700 4.6 36.1 1.0
CA A:ASP110 4.7 52.1 1.0
O5' F:DG22 4.9 42.4 1.0
N A:VAL111 4.9 46.7 1.0

Magnesium binding site 3 out of 6 in 1rtd

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Magnesium binding site 3 out of 6 in the Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:23.5
occ:1.00
 OD2 A:ASP443 2.1 62.3 1.0
OD1 A:ASP549 2.5 76.6 1.0
MG A:MG605 2.7 79.9 1.0
CG A:ASP443 2.9 61.3 1.0
OD1 A:ASP443 3.0 61.9 1.0
OD2 A:ASP498 3.2 53.3 1.0
OP1 E:DA23 3.7 75.0 1.0
CG A:ASP549 3.8 74.0 1.0
CE1 A:HIS539 4.0 74.2 1.0
CG A:ASP498 4.1 54.3 1.0
OD1 A:ASP498 4.3 59.1 1.0
CB A:ASP443 4.4 57.0 1.0
CB A:ASP549 4.5 69.2 1.0
OD2 A:ASP549 4.7 73.6 1.0
ND1 A:HIS539 4.8 73.5 1.0
NE2 A:HIS539 5.0 77.4 1.0
CA A:ASP549 5.0 63.5 1.0

Magnesium binding site 4 out of 6 in 1rtd

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Magnesium binding site 4 out of 6 in the Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:48.3
occ:1.00
 O1A C:TTP705 1.9 91.7 1.0
O1G C:TTP705 2.2 99.0 1.0
O C:VAL111 2.5 83.1 1.0
OD2 C:ASP185 2.5 89.0 1.0
O2B C:TTP705 2.6 97.4 1.0
OD1 C:ASP110 2.9 92.2 1.0
MG C:MG604 2.9 0.0 1.0
PG C:TTP705 3.3 98.9 1.0
PA C:TTP705 3.3 93.1 1.0
C C:VAL111 3.4 81.4 1.0
O3B C:TTP705 3.5 99.0 1.0
PB C:TTP705 3.5 98.2 1.0
CG C:ASP185 3.6 85.7 1.0
CA C:GLY112 3.8 88.1 1.0
O3A C:TTP705 3.9 96.0 1.0
O3G C:TTP705 3.9 0.1 1.0
N C:GLY112 4.0 83.7 1.0
C5' C:TTP705 4.0 81.5 1.0
CG C:ASP110 4.1 90.9 1.0
OD1 C:ASP185 4.1 87.5 1.0
O5' C:TTP705 4.1 88.0 1.0
N C:ASP113 4.1 92.9 1.0
C C:GLY112 4.2 91.4 1.0
O2A C:TTP705 4.3 93.1 1.0
N C:VAL111 4.4 76.7 1.0
N C:ALA114 4.5 80.5 1.0
CB C:ALA114 4.5 77.6 1.0
CA C:VAL111 4.6 77.6 1.0
O2G C:TTP705 4.6 97.9 1.0
CB C:ASP185 4.8 80.9 1.0
OD2 C:ASP110 4.8 90.3 1.0
O1B C:TTP705 4.9 96.8 1.0
CB C:ASP110 5.0 88.5 1.0

Magnesium binding site 5 out of 6 in 1rtd

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Magnesium binding site 5 out of 6 in the Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg604

b:0.0
occ:1.00
 O1A C:TTP705 2.2 91.7 1.0
OD1 C:ASP110 2.7 92.2 1.0
OD1 C:ASP185 2.8 87.5 1.0
MG C:MG603 2.9 48.3 1.0
PA C:TTP705 3.0 93.1 1.0
O5' C:TTP705 3.0 88.0 1.0
OD2 C:ASP185 3.1 89.0 1.0
C5' C:TTP705 3.3 81.5 1.0
CG C:ASP185 3.3 85.7 1.0
O2A C:TTP705 3.4 93.1 1.0
OD2 C:ASP110 3.5 90.3 1.0
CG C:ASP110 3.5 90.9 1.0
C3' H:DG22 3.6 80.0 1.0
C2' H:DG22 4.3 80.4 1.0
O2B C:TTP705 4.4 97.4 1.0
O3A C:TTP705 4.5 96.0 1.0
O1G C:TTP705 4.5 99.0 1.0
C4' H:DG22 4.7 80.5 1.0
C4' C:TTP705 4.7 75.4 1.0
O C:VAL111 4.8 83.1 1.0
CB C:ASP185 4.8 80.9 1.0
CB C:ASP110 5.0 88.5 1.0

Magnesium binding site 6 out of 6 in 1rtd

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Magnesium binding site 6 out of 6 in the Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Nucleoside Analog Drug Resistance within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:79.9
occ:1.00
 MG A:MG602 2.7 23.5 1.0
OD1 A:ASP549 2.8 76.6 1.0
CG A:ASP549 3.8 74.0 1.0
OP1 E:DA23 3.9 75.0 1.0
CB A:ALA445 3.9 52.6 1.0
OD1 A:ASP443 4.2 61.9 1.0
OD2 A:ASP443 4.2 62.3 1.0
OD2 A:ASP549 4.2 73.6 1.0
CG A:ASP443 4.5 61.3 1.0
CE1 A:HIS539 4.6 74.2 1.0
CG2 A:VAL552 4.7 44.0 1.0
O A:ASP549 4.7 63.9 1.0
OG A:SER553 4.7 59.2 1.0
CB A:ASP549 4.9 69.2 1.0
CA A:ASP549 5.0 63.5 1.0
CA A:ALA445 5.0 54.1 1.0

Reference:

H.Huang, R.Chopra, G.L.Verdine, S.C.Harrison. Structure of A Covalently Trapped Catalytic Complex of Hiv-1 Reverse Transcriptase: Implications For Drug Resistance. Science V. 282 1669 1998.
ISSN: ISSN 0036-8075
PubMed: 9831551
DOI: 10.1126/SCIENCE.282.5394.1669
Page generated: Mon Dec 14 06:43:04 2020

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