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
Go back to
Magnesium Binding Sites List in 1rtd
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
Go back to
Magnesium Binding Sites List in 1rtd
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
Go back to
Magnesium Binding Sites List in 1rtd
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
Go back to
Magnesium Binding Sites List in 1rtd
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
Go back to
Magnesium Binding Sites List in 1rtd
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
Go back to
Magnesium Binding Sites List in 1rtd
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: Tue Aug 13 13:07:07 2024
|