Magnesium in PDB 5txn: Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp
Enzymatic activity of Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp
All present enzymatic activity of Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp:
2.7.7.49;
2.7.7.7;
Protein crystallography data
The structure of Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp, PDB code: 5txn
was solved by
K.Das,
S.M.Martinez,
E.Arnold,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.38 /
2.55
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.039,
133.634,
139.206,
90.00,
97.88,
90.00
|
R / Rfree (%)
|
19.6 /
22.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp
(pdb code 5txn). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp, PDB code: 5txn:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5txn
Go back to
Magnesium Binding Sites List in 5txn
Magnesium binding site 1 out
of 4 in the Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:95.9
occ:1.00
|
OD1
|
A:ASP110
|
2.1
|
0.1
|
1.0
|
O2B
|
A:DTP603
|
2.1
|
0.8
|
1.0
|
OD2
|
A:ASP185
|
2.3
|
1.0
|
1.0
|
O
|
A:VAL111
|
2.3
|
0.3
|
1.0
|
O2G
|
A:DTP603
|
2.4
|
0.3
|
1.0
|
O1A
|
A:DTP603
|
2.4
|
0.0
|
1.0
|
CG
|
A:ASP110
|
2.7
|
0.6
|
1.0
|
OD2
|
A:ASP110
|
2.9
|
0.0
|
1.0
|
O3G
|
A:DTP603
|
3.2
|
1.0
|
1.0
|
PG
|
A:DTP603
|
3.2
|
0.7
|
1.0
|
PB
|
A:DTP603
|
3.4
|
0.5
|
1.0
|
C
|
A:VAL111
|
3.5
|
0.5
|
1.0
|
CG
|
A:ASP185
|
3.5
|
89.8
|
1.0
|
PA
|
A:DTP603
|
3.7
|
0.8
|
1.0
|
O3B
|
A:DTP603
|
3.8
|
0.1
|
1.0
|
N
|
A:VAL111
|
4.0
|
96.9
|
1.0
|
O3A
|
A:DTP603
|
4.0
|
0.7
|
1.0
|
CB
|
A:ASP110
|
4.1
|
98.8
|
1.0
|
OD1
|
A:ASP185
|
4.2
|
88.1
|
1.0
|
CA
|
A:VAL111
|
4.3
|
96.2
|
1.0
|
C5'
|
A:DTP603
|
4.4
|
0.3
|
1.0
|
N
|
A:GLY112
|
4.5
|
0.8
|
1.0
|
CB
|
A:ASP185
|
4.5
|
81.9
|
1.0
|
O1B
|
A:DTP603
|
4.5
|
1.0
|
1.0
|
O1G
|
A:DTP603
|
4.6
|
0.7
|
1.0
|
C
|
A:ASP110
|
4.6
|
98.7
|
1.0
|
O5'
|
A:DTP603
|
4.6
|
0.7
|
1.0
|
CA
|
A:GLY112
|
4.6
|
98.9
|
1.0
|
N
|
A:ASP113
|
4.7
|
0.4
|
1.0
|
O2A
|
A:DTP603
|
4.7
|
0.9
|
1.0
|
CA
|
A:ASP110
|
4.8
|
92.3
|
1.0
|
CB
|
A:ALA114
|
4.8
|
0.2
|
1.0
|
CB
|
A:VAL111
|
4.9
|
88.5
|
1.0
|
C
|
A:GLY112
|
4.9
|
99.7
|
1.0
|
N
|
A:ALA114
|
4.9
|
0.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5txn
Go back to
Magnesium Binding Sites List in 5txn
Magnesium binding site 2 out
of 4 in the Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg602
b:85.0
occ:1.00
|
OD2
|
A:ASP443
|
2.3
|
72.3
|
1.0
|
O
|
A:HOH713
|
2.4
|
67.5
|
1.0
|
OD1
|
A:ASP443
|
2.4
|
66.8
|
1.0
|
CG
|
A:ASP443
|
2.7
|
59.5
|
1.0
|
OD1
|
A:ASN498
|
3.6
|
53.8
|
1.0
|
O
|
A:GLY444
|
3.8
|
64.0
|
1.0
|
OD2
|
A:ASP549
|
3.8
|
71.0
|
1.0
|
ND2
|
A:ASN498
|
3.9
|
72.8
|
1.0
|
CG
|
A:ASN498
|
4.2
|
58.8
|
1.0
|
CB
|
A:ASP443
|
4.2
|
46.5
|
1.0
|
OP1
|
T:DC723
|
4.3
|
0.8
|
1.0
|
N
|
A:GLY444
|
4.6
|
50.2
|
1.0
|
C
|
A:GLY444
|
4.7
|
48.3
|
1.0
|
OE2
|
A:GLU478
|
4.8
|
78.9
|
1.0
|
CG
|
A:ASP549
|
4.8
|
70.5
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5txn
Go back to
Magnesium Binding Sites List in 5txn
Magnesium binding site 3 out
of 4 in the Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg602
b:80.8
occ:1.00
|
O
|
C:VAL111
|
2.0
|
0.7
|
1.0
|
O2B
|
C:DTP601
|
2.1
|
1.0
|
1.0
|
OD1
|
C:ASP110
|
2.2
|
0.9
|
1.0
|
O1A
|
C:DTP601
|
2.3
|
93.8
|
1.0
|
OD2
|
C:ASP185
|
2.3
|
94.2
|
1.0
|
O2G
|
C:DTP601
|
2.5
|
0.3
|
1.0
|
O3G
|
C:DTP601
|
3.1
|
0.7
|
1.0
|
PG
|
C:DTP601
|
3.2
|
0.9
|
1.0
|
C
|
C:VAL111
|
3.2
|
0.6
|
1.0
|
PB
|
C:DTP601
|
3.3
|
0.5
|
1.0
|
CG
|
C:ASP110
|
3.3
|
0.3
|
1.0
|
CG
|
C:ASP185
|
3.6
|
89.0
|
1.0
|
PA
|
C:DTP601
|
3.6
|
0.8
|
1.0
|
O3B
|
C:DTP601
|
3.7
|
0.1
|
1.0
|
OD2
|
C:ASP110
|
3.7
|
0.7
|
1.0
|
O3A
|
C:DTP601
|
3.8
|
0.5
|
1.0
|
N
|
C:VAL111
|
4.1
|
0.0
|
1.0
|
N
|
C:GLY112
|
4.1
|
0.3
|
1.0
|
CA
|
C:GLY112
|
4.1
|
99.8
|
1.0
|
CA
|
C:VAL111
|
4.2
|
99.8
|
1.0
|
N
|
C:ASP113
|
4.2
|
97.6
|
1.0
|
C5'
|
C:DTP601
|
4.2
|
96.2
|
1.0
|
CB
|
C:ALA114
|
4.3
|
94.5
|
1.0
|
NZ
|
C:LYS220
|
4.3
|
0.6
|
1.0
|
OD1
|
C:ASP185
|
4.3
|
88.9
|
1.0
|
C
|
C:GLY112
|
4.4
|
0.5
|
1.0
|
N
|
C:ALA114
|
4.4
|
0.8
|
1.0
|
O5'
|
C:DTP601
|
4.4
|
0.9
|
1.0
|
O1B
|
C:DTP601
|
4.5
|
0.4
|
1.0
|
O1G
|
C:DTP601
|
4.6
|
0.7
|
1.0
|
CB
|
C:ASP185
|
4.6
|
88.4
|
1.0
|
CB
|
C:ASP110
|
4.6
|
0.2
|
1.0
|
O2A
|
C:DTP601
|
4.7
|
1.0
|
1.0
|
C
|
C:ASP110
|
4.7
|
0.3
|
1.0
|
CB
|
C:VAL111
|
4.7
|
88.8
|
1.0
|
CA
|
C:ALA114
|
4.9
|
0.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5txn
Go back to
Magnesium Binding Sites List in 5txn
Magnesium binding site 4 out
of 4 in the Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp
 Mono view
 Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Q151M Mutant Hiv-1 Reverse Transcriptase (Rt) Ternary Complex with A Double Stranded Dna and An Incoming Datp within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg603
b:96.2
occ:1.00
|
OD1
|
C:ASP443
|
2.0
|
60.3
|
1.0
|
OD2
|
C:ASP443
|
2.1
|
60.7
|
1.0
|
O
|
C:HOH712
|
2.2
|
47.1
|
1.0
|
CG
|
C:ASP443
|
2.3
|
53.8
|
1.0
|
O
|
C:HOH731
|
2.4
|
61.3
|
1.0
|
ND2
|
C:ASN498
|
3.4
|
59.9
|
1.0
|
O
|
C:GLY444
|
3.5
|
55.8
|
1.0
|
OD2
|
C:ASP549
|
3.6
|
58.7
|
1.0
|
OD1
|
C:ASN498
|
3.7
|
64.5
|
1.0
|
CB
|
C:ASP443
|
3.9
|
42.0
|
1.0
|
CG
|
C:ASN498
|
3.9
|
50.8
|
1.0
|
N
|
C:GLY444
|
4.3
|
44.2
|
1.0
|
O
|
C:HOH702
|
4.4
|
51.6
|
1.0
|
C
|
C:GLY444
|
4.5
|
48.2
|
1.0
|
CA
|
C:ASP443
|
4.7
|
40.0
|
1.0
|
OE2
|
C:GLU478
|
4.7
|
79.0
|
1.0
|
CG
|
C:ASP549
|
4.8
|
56.6
|
1.0
|
C
|
C:ASP443
|
5.0
|
39.0
|
1.0
|
|
Reference:
K.Das,
S.E.Martinez,
E.Arnold.
Structural Insights Into Hiv Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance. Antimicrob. Agents V. 61 2017CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 28396546
DOI: 10.1128/AAC.00224-17
Page generated: Mon Sep 30 05:04:08 2024
|