Magnesium in PDB 5xn2: Hiv-1 Reverse Transcriptase Q151M:Dna:Dgtp Ternary Complex
Protein crystallography data
The structure of Hiv-1 Reverse Transcriptase Q151M:Dna:Dgtp Ternary Complex, PDB code: 5xn2
was solved by
Y.Yasutake,
N.Tamura,
H.Hayashi,
K.Maeda,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.90 /
2.38
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
285.694,
285.694,
96.325,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.9 /
22.3
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase Q151M:Dna:Dgtp Ternary Complex
(pdb code 5xn2). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the
Hiv-1 Reverse Transcriptase Q151M:Dna:Dgtp Ternary Complex, PDB code: 5xn2:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 5xn2
Go back to
Magnesium Binding Sites List in 5xn2
Magnesium binding site 1 out
of 2 in the Hiv-1 Reverse Transcriptase Q151M:Dna:Dgtp Ternary Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Hiv-1 Reverse Transcriptase Q151M:Dna:Dgtp Ternary Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:59.9
occ:1.00
|
OD1
|
A:ASP110
|
2.1
|
65.0
|
0.6
|
O2B
|
A:DGT602
|
2.1
|
65.8
|
1.0
|
O
|
A:VAL111
|
2.1
|
71.5
|
1.0
|
O3G
|
A:DGT602
|
2.1
|
71.4
|
1.0
|
O1A
|
A:DGT602
|
2.2
|
72.6
|
1.0
|
OD2
|
A:ASP185
|
2.2
|
60.0
|
1.0
|
CG
|
A:ASP110
|
3.2
|
56.5
|
0.6
|
PB
|
A:DGT602
|
3.2
|
73.3
|
1.0
|
C
|
A:VAL111
|
3.3
|
57.1
|
1.0
|
PG
|
A:DGT602
|
3.3
|
77.5
|
1.0
|
CG
|
A:ASP185
|
3.4
|
54.9
|
1.0
|
PA
|
A:DGT602
|
3.4
|
76.9
|
1.0
|
OD2
|
A:ASP110
|
3.7
|
57.8
|
0.6
|
O3B
|
A:DGT602
|
3.7
|
80.7
|
1.0
|
O3A
|
A:DGT602
|
3.7
|
78.1
|
1.0
|
O2G
|
A:DGT602
|
3.9
|
76.6
|
1.0
|
OD1
|
A:ASP185
|
3.9
|
53.4
|
1.0
|
NZ
|
A:LYS220
|
4.0
|
97.3
|
1.0
|
N
|
A:VAL111
|
4.0
|
51.5
|
1.0
|
C5'
|
A:DGT602
|
4.1
|
72.0
|
1.0
|
N
|
A:GLY112
|
4.2
|
53.9
|
1.0
|
CA
|
A:GLY112
|
4.2
|
58.4
|
1.0
|
CA
|
A:VAL111
|
4.2
|
52.2
|
1.0
|
O5'
|
A:DGT602
|
4.3
|
75.9
|
1.0
|
N
|
A:ASP113
|
4.4
|
51.8
|
1.0
|
CB
|
A:ASP110
|
4.4
|
54.3
|
0.4
|
CB
|
A:ASP110
|
4.4
|
54.1
|
0.6
|
O1B
|
A:DGT602
|
4.5
|
69.7
|
1.0
|
O1G
|
A:DGT602
|
4.5
|
81.8
|
1.0
|
O2A
|
A:DGT602
|
4.5
|
85.4
|
1.0
|
CB
|
A:ASP185
|
4.6
|
50.3
|
1.0
|
C
|
A:GLY112
|
4.6
|
59.2
|
1.0
|
C
|
A:ASP110
|
4.6
|
54.9
|
1.0
|
CD
|
A:LYS220
|
4.7
|
86.6
|
1.0
|
CB
|
A:ALA114
|
4.7
|
36.9
|
1.0
|
N
|
A:ALA114
|
4.7
|
52.0
|
1.0
|
CB
|
A:VAL111
|
4.9
|
50.5
|
1.0
|
CE
|
A:LYS220
|
4.9
|
91.2
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 5xn2
Go back to
Magnesium Binding Sites List in 5xn2
Magnesium binding site 2 out
of 2 in the Hiv-1 Reverse Transcriptase Q151M:Dna:Dgtp Ternary Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Hiv-1 Reverse Transcriptase Q151M:Dna:Dgtp Ternary Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:60.1
occ:1.00
|
O
|
C:VAL111
|
2.0
|
81.5
|
1.0
|
OD2
|
C:ASP110
|
2.1
|
89.5
|
1.0
|
O1B
|
C:DGT602
|
2.3
|
74.6
|
1.0
|
OD2
|
C:ASP185
|
2.4
|
72.6
|
1.0
|
O1A
|
C:DGT602
|
2.4
|
85.1
|
1.0
|
O2G
|
C:DGT602
|
2.5
|
82.1
|
1.0
|
CG
|
C:ASP110
|
3.2
|
82.3
|
1.0
|
C
|
C:VAL111
|
3.2
|
68.8
|
1.0
|
PB
|
C:DGT602
|
3.4
|
80.2
|
1.0
|
CG
|
C:ASP185
|
3.5
|
67.2
|
1.0
|
PG
|
C:DGT602
|
3.6
|
91.0
|
1.0
|
PA
|
C:DGT602
|
3.7
|
84.3
|
1.0
|
O3A
|
C:DGT602
|
3.8
|
89.6
|
1.0
|
OD1
|
C:ASP110
|
3.8
|
84.0
|
1.0
|
O3B
|
C:DGT602
|
3.9
|
86.0
|
1.0
|
N
|
C:VAL111
|
3.9
|
67.0
|
1.0
|
OD1
|
C:ASP185
|
4.0
|
65.8
|
1.0
|
N
|
C:GLY112
|
4.1
|
69.1
|
1.0
|
CA
|
C:VAL111
|
4.1
|
66.5
|
1.0
|
CA
|
C:GLY112
|
4.2
|
68.3
|
1.0
|
CB
|
C:ASP110
|
4.2
|
73.6
|
1.0
|
O3G
|
C:DGT602
|
4.2
|
95.8
|
1.0
|
C
|
C:ASP110
|
4.3
|
66.3
|
1.0
|
C5'
|
C:DGT602
|
4.4
|
74.9
|
1.0
|
N
|
C:ASP113
|
4.5
|
75.1
|
1.0
|
O5'
|
C:DGT602
|
4.6
|
78.5
|
1.0
|
CB
|
C:ASP185
|
4.7
|
65.8
|
1.0
|
C
|
C:GLY112
|
4.7
|
70.7
|
1.0
|
O2B
|
C:DGT602
|
4.7
|
78.2
|
1.0
|
O2A
|
C:DGT602
|
4.7
|
92.1
|
1.0
|
O
|
C:ASP110
|
4.8
|
69.4
|
1.0
|
CA
|
C:ASP110
|
4.8
|
62.5
|
1.0
|
CB
|
C:VAL111
|
4.8
|
63.6
|
1.0
|
O1G
|
C:DGT602
|
4.8
|
97.7
|
1.0
|
N
|
C:ALA114
|
4.9
|
64.8
|
1.0
|
CB
|
C:ALA114
|
5.0
|
55.3
|
1.0
|
|
Reference:
Y.Yasutake,
S.I.Hattori,
H.Hayashi,
K.Matsuda,
N.Tamura,
S.Kohgo,
K.Maeda,
H.Mitsuya.
Hiv-1 with Hbv-Associated Q151M Substitution in Rt Becomes Highly Susceptible to Entecavir: Structural Insights Into Hbv-Rt Inhibition By Entecavir. Sci Rep V. 8 1624 2018.
ISSN: ESSN 2045-2322
PubMed: 29374261
DOI: 10.1038/S41598-018-19602-9
Page generated: Mon Dec 14 22:09:44 2020
|