Cadmium in PDB 7oz5: Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.:
2.7.7.49;
2.7.7.7;
3.1.13.2;
3.1.26.13;
3.4.23.16;
Protein crystallography data
The structure of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket., PDB code: 7oz5
was solved by
S.E.Martinez,
A.K.Singh,
K.Das,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
150.13 /
3.37
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
310.747,
62.063,
169.292,
90,
104.93,
90
|
R / Rfree (%)
|
22.7 /
26.5
|
Cadmium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Cadmium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
(pdb code 7oz5). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 18 binding sites of Cadmium where determined in the
Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket., PDB code: 7oz5:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cadmium binding site 1 out
of 18 in 7oz5
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Cadmium Binding Sites List in 7oz5
Cadmium binding site 1 out
of 18 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd601
b:64.9
occ:1.00
|
OD1
|
A:ASP443
|
2.3
|
64.3
|
1.0
|
OD2
|
A:ASP498
|
2.3
|
60.0
|
1.0
|
OE2
|
A:GLU478
|
2.3
|
69.1
|
1.0
|
OD2
|
A:ASP443
|
2.9
|
74.4
|
1.0
|
CG
|
A:ASP498
|
2.9
|
63.6
|
1.0
|
CG
|
A:ASP443
|
2.9
|
68.7
|
1.0
|
OD1
|
A:ASP498
|
3.0
|
64.0
|
1.0
|
CD
|
A:GLU478
|
3.1
|
64.8
|
1.0
|
OE1
|
A:GLU478
|
3.3
|
67.2
|
1.0
|
O
|
A:GLY444
|
4.0
|
67.8
|
1.0
|
CB
|
A:ASP498
|
4.3
|
69.7
|
1.0
|
OP1
|
T:DT724
|
4.4
|
108.4
|
1.0
|
CB
|
A:ASP443
|
4.4
|
61.8
|
1.0
|
CG
|
A:GLU478
|
4.5
|
57.7
|
1.0
|
CB
|
A:ALA538
|
4.6
|
81.9
|
1.0
|
N
|
A:GLY444
|
4.8
|
61.0
|
1.0
|
|
Cadmium binding site 2 out
of 18 in 7oz5
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Cadmium Binding Sites List in 7oz5
Cadmium binding site 2 out
of 18 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd602
b:97.3
occ:1.00
|
ND1
|
A:HIS208
|
2.3
|
104.2
|
1.0
|
NH1
|
A:ARG211
|
2.8
|
111.6
|
1.0
|
CE1
|
A:HIS208
|
3.0
|
90.2
|
1.0
|
NH2
|
A:ARG211
|
3.1
|
106.0
|
1.0
|
CZ
|
A:ARG211
|
3.3
|
113.3
|
1.0
|
CG
|
A:HIS208
|
3.4
|
89.8
|
1.0
|
NE2
|
A:GLN174
|
3.6
|
86.3
|
1.0
|
OE1
|
A:GLN174
|
3.7
|
99.7
|
1.0
|
CB
|
A:HIS208
|
3.9
|
92.0
|
1.0
|
CD
|
A:GLN174
|
4.0
|
98.6
|
1.0
|
NE2
|
A:HIS208
|
4.1
|
83.1
|
1.0
|
CD2
|
A:HIS208
|
4.3
|
82.0
|
1.0
|
NE
|
A:ARG211
|
4.5
|
115.1
|
1.0
|
CA
|
A:HIS208
|
4.5
|
97.2
|
1.0
|
|
Cadmium binding site 3 out
of 18 in 7oz5
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Cadmium Binding Sites List in 7oz5
Cadmium binding site 3 out
of 18 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd603
b:136.8
occ:1.00
|
OD1
|
A:ASP549
|
2.3
|
100.3
|
1.0
|
NE2
|
A:HIS539
|
2.3
|
112.6
|
1.0
|
OD2
|
A:ASP549
|
2.3
|
101.5
|
1.0
|
CG
|
A:ASP549
|
2.6
|
97.0
|
1.0
|
CD2
|
A:HIS539
|
2.9
|
101.5
|
1.0
|
CE1
|
A:HIS539
|
3.2
|
105.5
|
1.0
|
OG
|
A:SER553
|
3.5
|
109.2
|
1.0
|
CG
|
A:HIS539
|
3.9
|
87.4
|
1.0
|
ND1
|
A:HIS539
|
4.1
|
94.9
|
1.0
|
CB
|
A:ASP549
|
4.1
|
87.1
|
1.0
|
CB
|
A:SER553
|
4.6
|
105.5
|
1.0
|
O
|
A:ASP549
|
4.7
|
89.2
|
1.0
|
CA
|
A:ASP549
|
4.9
|
85.3
|
1.0
|
|
Cadmium binding site 4 out
of 18 in 7oz5
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Cadmium Binding Sites List in 7oz5
Cadmium binding site 4 out
of 18 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd501
b:103.3
occ:1.00
|
OE1
|
B:GLU297
|
2.3
|
113.3
|
1.0
|
OE2
|
B:GLU297
|
2.3
|
110.1
|
1.0
|
CD
|
B:GLU297
|
2.6
|
112.5
|
1.0
|
CG
|
B:GLU297
|
4.2
|
97.2
|
1.0
|
CB
|
B:GLU297
|
5.0
|
95.0
|
1.0
|
|
Cadmium binding site 5 out
of 18 in 7oz5
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Cadmium Binding Sites List in 7oz5
Cadmium binding site 5 out
of 18 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd502
b:159.7
occ:1.00
|
ND1
|
B:HIS208
|
2.6
|
105.3
|
1.0
|
CE1
|
B:HIS208
|
3.2
|
116.3
|
1.0
|
CG
|
B:HIS208
|
3.7
|
111.1
|
1.0
|
CB
|
B:HIS208
|
4.2
|
108.5
|
1.0
|
NH1
|
B:ARG211
|
4.3
|
131.6
|
1.0
|
NE2
|
B:HIS208
|
4.4
|
120.4
|
1.0
|
CD2
|
B:HIS208
|
4.7
|
114.5
|
1.0
|
CA
|
B:HIS208
|
4.9
|
104.6
|
1.0
|
|
Cadmium binding site 6 out
of 18 in 7oz5
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Cadmium Binding Sites List in 7oz5
Cadmium binding site 6 out
of 18 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd503
b:169.1
occ:1.00
|
OE1
|
B:GLU233
|
2.3
|
140.3
|
1.0
|
OE1
|
B:GLU224
|
2.3
|
147.0
|
1.0
|
NE2
|
B:HIS235
|
2.3
|
119.5
|
1.0
|
OE2
|
B:GLU224
|
2.3
|
128.6
|
1.0
|
OE2
|
B:GLU233
|
2.3
|
137.9
|
1.0
|
CD
|
B:GLU233
|
2.5
|
136.7
|
1.0
|
CD
|
B:GLU224
|
2.6
|
141.1
|
1.0
|
CD2
|
B:HIS235
|
3.3
|
112.8
|
1.0
|
CE1
|
B:HIS235
|
3.3
|
113.8
|
1.0
|
CG
|
B:GLU233
|
3.8
|
122.9
|
1.0
|
CG
|
B:GLU224
|
4.1
|
145.9
|
1.0
|
ND1
|
B:HIS235
|
4.4
|
98.8
|
1.0
|
CG
|
B:HIS235
|
4.4
|
99.1
|
1.0
|
CB
|
B:GLU233
|
4.5
|
115.0
|
1.0
|
O
|
B:GLU233
|
4.5
|
124.7
|
1.0
|
NH2
|
B:ARG199
|
4.6
|
120.6
|
1.0
|
CB
|
B:GLU224
|
5.0
|
143.7
|
1.0
|
|
Cadmium binding site 7 out
of 18 in 7oz5
Go back to
Cadmium Binding Sites List in 7oz5
Cadmium binding site 7 out
of 18 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Cd801
b:187.0
occ:1.00
|
N7
|
T:DG708
|
3.4
|
91.6
|
1.0
|
N4
|
T:DC709
|
3.6
|
82.5
|
1.0
|
C8
|
T:DG708
|
3.9
|
83.9
|
1.0
|
C5
|
T:DC709
|
3.9
|
87.1
|
1.0
|
C4
|
T:DC709
|
4.2
|
84.8
|
1.0
|
C5
|
T:DG708
|
4.3
|
87.3
|
1.0
|
O6
|
T:DG708
|
4.8
|
96.5
|
1.0
|
C6
|
T:DG708
|
4.8
|
91.6
|
1.0
|
N9
|
T:DG708
|
4.9
|
77.6
|
1.0
|
OP2
|
T:DG708
|
5.0
|
84.8
|
1.0
|
|
Cadmium binding site 8 out
of 18 in 7oz5
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Cadmium Binding Sites List in 7oz5
Cadmium binding site 8 out
of 18 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Cd802
b:173.4
occ:1.00
|
N7
|
T:DG720
|
2.3
|
116.9
|
1.0
|
C5
|
T:DG720
|
3.2
|
113.0
|
1.0
|
O6
|
T:DG720
|
3.3
|
113.1
|
1.0
|
C8
|
T:DG720
|
3.3
|
109.6
|
1.0
|
N7
|
T:DG719
|
3.5
|
107.8
|
1.0
|
C8
|
T:DG719
|
3.5
|
111.1
|
1.0
|
C6
|
T:DG720
|
3.6
|
109.7
|
1.0
|
C5
|
T:DG719
|
4.2
|
107.2
|
1.0
|
N9
|
T:DG719
|
4.2
|
110.4
|
1.0
|
C4
|
T:DG720
|
4.4
|
109.6
|
1.0
|
N9
|
T:DG720
|
4.5
|
106.8
|
1.0
|
O6
|
T:DG721
|
4.6
|
119.0
|
1.0
|
C4
|
T:DG719
|
4.6
|
105.3
|
1.0
|
C2'
|
T:DG719
|
4.6
|
109.2
|
1.0
|
C6
|
T:DG719
|
5.0
|
106.7
|
1.0
|
N1
|
T:DG720
|
5.0
|
102.0
|
1.0
|
|
Cadmium binding site 9 out
of 18 in 7oz5
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Cadmium Binding Sites List in 7oz5
Cadmium binding site 9 out
of 18 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Cd901
b:130.9
occ:1.00
|
N7
|
P:DG815
|
2.3
|
106.6
|
1.0
|
C5
|
P:DG815
|
3.2
|
99.4
|
1.0
|
C8
|
P:DG815
|
3.3
|
102.8
|
1.0
|
O6
|
P:DG815
|
3.3
|
93.7
|
1.0
|
C6
|
P:DG815
|
3.6
|
93.7
|
1.0
|
C6
|
P:DC814
|
3.7
|
106.9
|
1.0
|
C5
|
P:DC814
|
3.8
|
108.3
|
1.0
|
C2'
|
P:DC814
|
4.3
|
105.2
|
1.0
|
N1
|
P:DC814
|
4.4
|
103.0
|
1.0
|
C4
|
P:DG815
|
4.4
|
98.3
|
1.0
|
N9
|
P:DG815
|
4.5
|
98.3
|
1.0
|
C4
|
P:DC814
|
4.5
|
101.7
|
1.0
|
O6
|
P:DG816
|
4.8
|
92.8
|
1.0
|
N7
|
P:DG816
|
4.8
|
90.1
|
1.0
|
C1'
|
P:DC814
|
4.9
|
99.6
|
1.0
|
N1
|
P:DG815
|
5.0
|
94.7
|
1.0
|
|
Cadmium binding site 10 out
of 18 in 7oz5
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Cadmium Binding Sites List in 7oz5
Cadmium binding site 10 out
of 18 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 10 of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 166 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cd601
b:77.0
occ:1.00
|
OE2
|
C:GLU478
|
2.3
|
66.2
|
1.0
|
OD2
|
C:ASP498
|
2.3
|
71.7
|
1.0
|
OD1
|
C:ASP443
|
2.3
|
82.8
|
1.0
|
OD2
|
C:ASP443
|
2.3
|
88.1
|
1.0
|
OD1
|
C:ASP498
|
2.3
|
68.9
|
1.0
|
CG
|
C:ASP443
|
2.6
|
79.1
|
1.0
|
CG
|
C:ASP498
|
2.6
|
67.4
|
1.0
|
CD
|
C:GLU478
|
3.2
|
73.5
|
1.0
|
OE1
|
C:GLU478
|
3.4
|
69.1
|
1.0
|
CB
|
C:ASP443
|
4.1
|
64.6
|
1.0
|
CB
|
C:ASP498
|
4.2
|
54.1
|
1.0
|
O
|
C:GLY444
|
4.2
|
78.3
|
1.0
|
OP1
|
E:DA722
|
4.3
|
134.4
|
1.0
|
OD1
|
C:ASP549
|
4.6
|
117.4
|
1.0
|
CG
|
C:GLU478
|
4.6
|
80.1
|
1.0
|
N
|
C:GLY444
|
4.7
|
75.8
|
1.0
|
CB
|
C:ALA538
|
4.7
|
69.4
|
1.0
|
CA
|
C:ASP443
|
4.8
|
68.8
|
1.0
|
C
|
C:ASP498
|
4.9
|
63.8
|
1.0
|
|
Reference:
A.K.Singh,
S.E.Martinez,
W.Gu,
H.Nguyen,
D.Schols,
P.Herdewijn,
S.De Jonghe,
K.Das.
Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 at the Transient P-Pocket. To Be Published.
Page generated: Fri Jul 19 20:05:31 2024
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