Magnesium in PDB 5xn1: Hiv-1 Reverse Transcriptase Q151M:Dna:Entecavir-Triphosphate Ternary Complex
Protein crystallography data
The structure of Hiv-1 Reverse Transcriptase Q151M:Dna:Entecavir-Triphosphate Ternary Complex, PDB code: 5xn1
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)
|
47.02 /
2.45
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
284.707,
284.707,
95.793,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.8 /
22.7
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase Q151M:Dna:Entecavir-Triphosphate Ternary Complex
(pdb code 5xn1). 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:Entecavir-Triphosphate Ternary Complex, PDB code: 5xn1:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 5xn1
Go back to
Magnesium Binding Sites List in 5xn1
Magnesium binding site 1 out
of 2 in the Hiv-1 Reverse Transcriptase Q151M:Dna:Entecavir-Triphosphate 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:Entecavir-Triphosphate Ternary Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:32.1
occ:0.41
|
O1B
|
A:ET9601
|
1.8
|
47.7
|
1.0
|
O3G
|
A:ET9601
|
2.0
|
51.8
|
1.0
|
O
|
A:VAL111
|
2.0
|
49.2
|
1.0
|
OD1
|
A:ASP110
|
2.1
|
50.1
|
0.5
|
OD2
|
A:ASP185
|
2.1
|
50.6
|
1.0
|
O1A
|
A:ET9601
|
2.2
|
73.0
|
1.0
|
CG
|
A:ASP110
|
2.9
|
44.4
|
0.5
|
PB
|
A:ET9601
|
3.1
|
65.3
|
1.0
|
OD2
|
A:ASP110
|
3.2
|
43.8
|
0.5
|
C
|
A:VAL111
|
3.2
|
43.2
|
1.0
|
PG
|
A:ET9601
|
3.2
|
66.1
|
1.0
|
CG
|
A:ASP185
|
3.3
|
45.1
|
1.0
|
PA
|
A:ET9601
|
3.4
|
72.9
|
1.0
|
O3B
|
A:ET9601
|
3.6
|
70.5
|
1.0
|
O3A
|
A:ET9601
|
3.7
|
73.8
|
1.0
|
OD1
|
A:ASP185
|
3.9
|
41.6
|
1.0
|
O2G
|
A:ET9601
|
3.9
|
64.1
|
1.0
|
N
|
A:VAL111
|
4.0
|
39.9
|
1.0
|
C5'
|
A:ET9601
|
4.0
|
62.8
|
1.0
|
N
|
A:GLY112
|
4.1
|
39.2
|
1.0
|
CA
|
A:GLY112
|
4.1
|
44.5
|
1.0
|
CA
|
A:VAL111
|
4.2
|
42.4
|
1.0
|
O5'
|
A:ET9601
|
4.2
|
68.6
|
1.0
|
NZ
|
A:LYS220
|
4.3
|
67.5
|
1.0
|
O2B
|
A:ET9601
|
4.3
|
62.1
|
1.0
|
O1G
|
A:ET9601
|
4.3
|
66.9
|
1.0
|
CB
|
A:ASP110
|
4.3
|
43.6
|
0.5
|
CB
|
A:ASP110
|
4.3
|
43.8
|
0.5
|
CB
|
A:ASP185
|
4.4
|
41.8
|
1.0
|
N
|
A:ASP113
|
4.4
|
47.9
|
1.0
|
O2A
|
A:ET9601
|
4.5
|
73.8
|
1.0
|
C
|
A:GLY112
|
4.5
|
48.9
|
1.0
|
CB
|
A:ALA114
|
4.5
|
31.6
|
1.0
|
C
|
A:ASP110
|
4.5
|
42.9
|
1.0
|
N
|
A:ALA114
|
4.7
|
46.8
|
1.0
|
CD
|
A:LYS220
|
4.8
|
62.6
|
1.0
|
OD2
|
A:ASP110
|
4.8
|
41.2
|
0.5
|
CB
|
A:VAL111
|
4.8
|
42.7
|
1.0
|
CG
|
A:ASP110
|
4.8
|
42.6
|
0.5
|
CA
|
A:ASP110
|
4.9
|
42.6
|
0.5
|
CA
|
A:ASP110
|
5.0
|
42.6
|
0.5
|
CE
|
A:LYS220
|
5.0
|
66.8
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 5xn1
Go back to
Magnesium Binding Sites List in 5xn1
Magnesium binding site 2 out
of 2 in the Hiv-1 Reverse Transcriptase Q151M:Dna:Entecavir-Triphosphate 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:Entecavir-Triphosphate Ternary Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg602
b:54.8
occ:1.00
|
O
|
C:VAL111
|
1.9
|
83.7
|
1.0
|
O2G
|
C:ET9601
|
2.1
|
66.7
|
1.0
|
OD2
|
C:ASP110
|
2.2
|
83.6
|
1.0
|
O2B
|
C:ET9601
|
2.2
|
82.2
|
1.0
|
OD2
|
C:ASP185
|
2.4
|
61.4
|
1.0
|
O1A
|
C:ET9601
|
2.5
|
84.6
|
1.0
|
C
|
C:VAL111
|
3.0
|
73.9
|
1.0
|
CG
|
C:ASP110
|
3.3
|
76.7
|
1.0
|
PG
|
C:ET9601
|
3.4
|
77.9
|
1.0
|
CG
|
C:ASP185
|
3.5
|
57.2
|
1.0
|
PB
|
C:ET9601
|
3.5
|
81.0
|
1.0
|
PA
|
C:ET9601
|
3.8
|
83.4
|
1.0
|
N
|
C:VAL111
|
3.8
|
64.6
|
1.0
|
N
|
C:GLY112
|
3.9
|
71.3
|
1.0
|
CA
|
C:GLY112
|
3.9
|
68.9
|
1.0
|
O3B
|
C:ET9601
|
3.9
|
79.7
|
1.0
|
OD1
|
C:ASP185
|
4.0
|
56.6
|
1.0
|
CA
|
C:VAL111
|
4.0
|
66.5
|
1.0
|
O3A
|
C:ET9601
|
4.1
|
84.1
|
1.0
|
C
|
C:ASP110
|
4.1
|
64.9
|
1.0
|
CB
|
C:ASP110
|
4.1
|
69.0
|
1.0
|
OD1
|
C:ASP110
|
4.1
|
79.2
|
1.0
|
O3G
|
C:ET9601
|
4.2
|
79.6
|
1.0
|
O1G
|
C:ET9601
|
4.4
|
81.1
|
1.0
|
N
|
C:ASP113
|
4.4
|
65.1
|
1.0
|
C
|
C:GLY112
|
4.5
|
66.2
|
1.0
|
O
|
C:ASP110
|
4.5
|
67.7
|
1.0
|
C5'
|
C:ET9601
|
4.6
|
74.1
|
1.0
|
CB
|
C:ASP185
|
4.6
|
54.8
|
1.0
|
CA
|
C:ASP110
|
4.6
|
63.0
|
1.0
|
O1B
|
C:ET9601
|
4.7
|
79.5
|
1.0
|
O5'
|
C:ET9601
|
4.7
|
79.9
|
1.0
|
O2A
|
C:ET9601
|
4.7
|
86.5
|
1.0
|
CB
|
C:VAL111
|
4.7
|
61.6
|
1.0
|
CB
|
C:ALA114
|
4.9
|
52.5
|
1.0
|
N
|
C:ALA114
|
4.9
|
59.4
|
1.0
|
O
|
C:ASP185
|
5.0
|
51.9
|
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 22:09:42 2020
|