Magnesium in PDB 6kdn: Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Dgtp Ternary Complex
Protein crystallography data
The structure of Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Dgtp Ternary Complex, PDB code: 6kdn
was solved by
Y.Yasutake,
S.I.Hattori,
N.Tamura,
K.Maeda,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.60 /
2.30
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
284.167,
284.167,
95.521,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.6 /
22.1
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y:Dna:Dgtp Ternary Complex
(pdb code 6kdn). 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 with Q151M/Y115F/F116Y:Dna:Dgtp Ternary Complex, PDB code: 6kdn:
Jump to Magnesium binding site number:
1;
2;
Magnesium binding site 1 out
of 2 in 6kdn
Go back to
Magnesium Binding Sites List in 6kdn
Magnesium binding site 1 out
of 2 in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y: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 with Q151M/Y115F/F116Y:Dna:Dgtp Ternary Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:49.3
occ:1.00
|
OD2
|
A:ASP185
|
2.1
|
62.2
|
1.0
|
O1B
|
A:DGT602
|
2.1
|
49.7
|
1.0
|
OD1
|
A:ASP110
|
2.1
|
73.7
|
1.0
|
O
|
A:VAL111
|
2.1
|
54.1
|
1.0
|
O2G
|
A:DGT602
|
2.1
|
51.8
|
1.0
|
O1A
|
A:DGT602
|
2.2
|
54.0
|
1.0
|
CG
|
A:ASP110
|
3.1
|
64.5
|
1.0
|
CG
|
A:ASP185
|
3.2
|
49.2
|
1.0
|
PB
|
A:DGT602
|
3.3
|
53.9
|
1.0
|
C
|
A:VAL111
|
3.3
|
48.6
|
1.0
|
PG
|
A:DGT602
|
3.4
|
55.9
|
1.0
|
PA
|
A:DGT602
|
3.4
|
54.5
|
1.0
|
OD2
|
A:ASP110
|
3.5
|
63.3
|
1.0
|
OD1
|
A:ASP185
|
3.6
|
49.4
|
1.0
|
O3A
|
A:DGT602
|
3.8
|
57.7
|
1.0
|
O3B
|
A:DGT602
|
3.8
|
58.1
|
1.0
|
C5'
|
A:DGT602
|
4.0
|
52.9
|
1.0
|
N
|
A:VAL111
|
4.1
|
43.5
|
1.0
|
O1G
|
A:DGT602
|
4.1
|
56.6
|
1.0
|
NZ
|
A:LYS220
|
4.1
|
77.4
|
1.0
|
N
|
A:GLY112
|
4.2
|
50.0
|
1.0
|
CA
|
A:GLY112
|
4.2
|
44.7
|
1.0
|
O5'
|
A:DGT602
|
4.2
|
55.9
|
1.0
|
CA
|
A:VAL111
|
4.3
|
43.5
|
1.0
|
CB
|
A:ASP110
|
4.4
|
53.2
|
1.0
|
N
|
A:ASP113
|
4.4
|
46.9
|
1.0
|
CB
|
A:ASP185
|
4.5
|
39.6
|
1.0
|
C
|
A:ASP110
|
4.5
|
42.7
|
1.0
|
O2B
|
A:DGT602
|
4.5
|
54.9
|
1.0
|
O3G
|
A:DGT602
|
4.5
|
64.8
|
1.0
|
CE
|
A:LYS220
|
4.5
|
81.0
|
1.0
|
O2A
|
A:DGT602
|
4.6
|
63.2
|
1.0
|
C
|
A:GLY112
|
4.6
|
47.7
|
1.0
|
CB
|
A:ALA114
|
4.6
|
30.3
|
1.0
|
N
|
A:ALA114
|
4.7
|
44.1
|
1.0
|
CB
|
A:VAL111
|
4.9
|
42.8
|
1.0
|
O
|
A:ASP110
|
4.9
|
51.8
|
1.0
|
CA
|
A:ASP110
|
4.9
|
40.0
|
1.0
|
|
Magnesium binding site 2 out
of 2 in 6kdn
Go back to
Magnesium Binding Sites List in 6kdn
Magnesium binding site 2 out
of 2 in the Hiv-1 Reverse Transcriptase with Q151M/Y115F/F116Y: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 with Q151M/Y115F/F116Y:Dna:Dgtp Ternary Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:56.4
occ:1.00
|
O1B
|
C:DGT602
|
2.1
|
63.6
|
1.0
|
O
|
C:VAL111
|
2.1
|
69.7
|
1.0
|
OD2
|
C:ASP185
|
2.1
|
70.2
|
1.0
|
OD2
|
C:ASP110
|
2.1
|
87.8
|
1.0
|
O1A
|
C:DGT602
|
2.3
|
67.0
|
1.0
|
O1G
|
C:DGT602
|
2.4
|
70.5
|
1.0
|
CG
|
C:ASP185
|
3.3
|
56.2
|
1.0
|
PB
|
C:DGT602
|
3.3
|
70.3
|
1.0
|
CG
|
C:ASP110
|
3.3
|
81.5
|
1.0
|
C
|
C:VAL111
|
3.3
|
60.3
|
1.0
|
PA
|
C:DGT602
|
3.5
|
67.5
|
1.0
|
PG
|
C:DGT602
|
3.5
|
73.6
|
1.0
|
OD1
|
C:ASP185
|
3.8
|
54.2
|
1.0
|
O3B
|
C:DGT602
|
3.8
|
73.3
|
1.0
|
O3A
|
C:DGT602
|
3.8
|
75.8
|
1.0
|
OD1
|
C:ASP110
|
4.0
|
82.2
|
1.0
|
C5'
|
C:DGT602
|
4.1
|
56.9
|
1.0
|
O3G
|
C:DGT602
|
4.1
|
75.6
|
1.0
|
CA
|
C:GLY112
|
4.1
|
60.2
|
1.0
|
N
|
C:GLY112
|
4.2
|
64.0
|
1.0
|
N
|
C:VAL111
|
4.2
|
54.3
|
1.0
|
N
|
C:ASP113
|
4.3
|
64.7
|
1.0
|
CA
|
C:VAL111
|
4.3
|
57.1
|
1.0
|
O5'
|
C:DGT602
|
4.4
|
62.9
|
1.0
|
CB
|
C:ASP110
|
4.4
|
70.9
|
1.0
|
NZ
|
C:LYS220
|
4.5
|
77.8
|
1.0
|
CB
|
C:ASP185
|
4.5
|
46.1
|
1.0
|
C
|
C:ASP110
|
4.5
|
56.0
|
1.0
|
CD
|
C:LYS220
|
4.5
|
77.1
|
1.0
|
C
|
C:GLY112
|
4.5
|
59.4
|
1.0
|
O2B
|
C:DGT602
|
4.5
|
64.4
|
1.0
|
N
|
C:ALA114
|
4.6
|
49.6
|
1.0
|
CB
|
C:ALA114
|
4.6
|
44.5
|
1.0
|
O2A
|
C:DGT602
|
4.7
|
75.3
|
1.0
|
O2G
|
C:DGT602
|
4.8
|
81.6
|
1.0
|
O
|
C:HOH791
|
4.8
|
66.7
|
1.0
|
O
|
C:ASP110
|
4.9
|
57.6
|
1.0
|
CA
|
C:ASP110
|
4.9
|
58.1
|
1.0
|
CB
|
C:VAL111
|
5.0
|
52.4
|
1.0
|
|
Reference:
Y.Yasutake,
S.I.Hattori,
N.Tamura,
K.Matsuda,
S.Kohgo,
K.Maeda,
H.Mitsuya.
Structural Features in Common of Hbv and Hiv-1 Resistance Against Chirally-Distinct Nucleoside Analogues Entecavir and Lamivudine. Sci Rep V. 10 3021 2020.
ISSN: ESSN 2045-2322
PubMed: 32080249
DOI: 10.1038/S41598-020-59775-W
Page generated: Mon Dec 14 23:05:36 2020
|