Cadmium in PDB 7oxq: Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 at the Transient P-Pocket.
Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 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 048 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 048 at the Transient P-Pocket., PDB code: 7oxq
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)
|
81.68 /
3.30
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
309.565,
61.9,
168.779,
90,
104.55,
90
|
R / Rfree (%)
|
26.2 /
29.6
|
Other elements in 7oxq:
The structure of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 at the Transient P-Pocket. also contains other interesting chemical elements:
Cadmium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
21;
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 048 at the Transient P-Pocket.
(pdb code 7oxq). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 21 binding sites of Cadmium where determined in the
Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 at the Transient P-Pocket., PDB code: 7oxq:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cadmium binding site 1 out
of 21 in 7oxq
Go back to
Cadmium Binding Sites List in 7oxq
Cadmium binding site 1 out
of 21 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 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 048 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd601
b:52.1
occ:1.00
|
OE2
|
A:GLU478
|
2.3
|
32.1
|
1.0
|
OD2
|
A:ASP443
|
2.3
|
62.4
|
1.0
|
OD1
|
A:ASP443
|
2.3
|
46.9
|
1.0
|
OD2
|
A:ASP498
|
2.3
|
35.5
|
1.0
|
CG
|
A:ASP443
|
2.6
|
48.2
|
1.0
|
CG
|
A:ASP498
|
3.0
|
28.1
|
1.0
|
OD1
|
A:ASP498
|
3.0
|
28.1
|
1.0
|
CD
|
A:GLU478
|
3.1
|
29.0
|
1.0
|
OE1
|
A:GLU478
|
3.2
|
33.3
|
1.0
|
O
|
A:GLY444
|
3.9
|
36.2
|
1.0
|
CB
|
A:ASP443
|
4.1
|
28.8
|
1.0
|
OD1
|
A:ASP549
|
4.4
|
75.5
|
1.0
|
CG
|
A:GLU478
|
4.4
|
27.1
|
1.0
|
CB
|
A:ASP498
|
4.4
|
22.1
|
1.0
|
N
|
A:GLY444
|
4.6
|
33.9
|
1.0
|
CB
|
A:ALA538
|
4.8
|
37.3
|
1.0
|
OP1
|
T:DT724
|
4.8
|
89.0
|
1.0
|
CA
|
A:ASP443
|
4.9
|
30.5
|
1.0
|
C
|
A:GLY444
|
5.0
|
34.1
|
1.0
|
|
Cadmium binding site 2 out
of 21 in 7oxq
Go back to
Cadmium Binding Sites List in 7oxq
Cadmium binding site 2 out
of 21 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 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 048 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd602
b:76.1
occ:1.00
|
NH1
|
A:ARG211
|
2.3
|
55.0
|
1.0
|
OE1
|
A:GLN174
|
2.3
|
68.9
|
1.0
|
ND1
|
A:HIS208
|
2.3
|
73.3
|
1.0
|
CE1
|
A:HIS208
|
2.7
|
72.9
|
1.0
|
CZ
|
A:ARG211
|
3.1
|
61.3
|
1.0
|
NH2
|
A:ARG211
|
3.2
|
67.1
|
1.0
|
CD
|
A:GLN174
|
3.4
|
64.2
|
1.0
|
CG
|
A:HIS208
|
3.5
|
64.0
|
1.0
|
NE2
|
A:HIS208
|
3.8
|
56.6
|
1.0
|
NE2
|
A:GLN174
|
3.8
|
67.2
|
1.0
|
CB
|
A:HIS208
|
4.2
|
65.9
|
1.0
|
CD2
|
A:HIS208
|
4.2
|
54.0
|
1.0
|
NE
|
A:ARG211
|
4.4
|
60.7
|
1.0
|
CG
|
A:GLN174
|
4.8
|
57.5
|
1.0
|
CA
|
A:PHE171
|
4.8
|
41.8
|
1.0
|
N
|
A:PHE171
|
4.9
|
40.8
|
1.0
|
CB
|
A:PHE171
|
4.9
|
45.9
|
1.0
|
CD2
|
A:PHE171
|
5.0
|
56.2
|
1.0
|
CA
|
A:HIS208
|
5.0
|
63.6
|
1.0
|
|
Cadmium binding site 3 out
of 21 in 7oxq
Go back to
Cadmium Binding Sites List in 7oxq
Cadmium binding site 3 out
of 21 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 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 048 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd603
b:100.0
occ:1.00
|
NE2
|
A:HIS539
|
2.3
|
67.3
|
1.0
|
OD1
|
A:ASP549
|
2.3
|
75.5
|
1.0
|
OD2
|
A:ASP549
|
2.3
|
69.2
|
1.0
|
CG
|
A:ASP549
|
2.6
|
68.3
|
1.0
|
CD2
|
A:HIS539
|
3.0
|
59.1
|
1.0
|
CE1
|
A:HIS539
|
3.2
|
66.8
|
1.0
|
OG
|
A:SER553
|
3.3
|
75.7
|
1.0
|
CG
|
A:HIS539
|
4.1
|
51.4
|
1.0
|
CB
|
A:ASP549
|
4.1
|
49.1
|
1.0
|
ND1
|
A:HIS539
|
4.2
|
59.1
|
1.0
|
O
|
A:ASP549
|
4.5
|
45.7
|
1.0
|
CB
|
A:SER553
|
4.5
|
61.3
|
1.0
|
CA
|
A:ASP549
|
4.8
|
47.8
|
1.0
|
C
|
A:ASP549
|
4.8
|
48.0
|
1.0
|
|
Cadmium binding site 4 out
of 21 in 7oxq
Go back to
Cadmium Binding Sites List in 7oxq
Cadmium binding site 4 out
of 21 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 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 048 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd501
b:102.8
occ:1.00
|
OE1
|
B:GLU413
|
3.0
|
45.8
|
1.0
|
NZ
|
B:LYS82
|
3.2
|
41.5
|
1.0
|
OE2
|
B:GLU413
|
3.4
|
31.9
|
1.0
|
CD
|
B:GLU413
|
3.6
|
35.1
|
1.0
|
OE1
|
B:GLU79
|
4.0
|
66.0
|
1.0
|
NH1
|
B:ARG78
|
4.1
|
31.3
|
1.0
|
CB
|
B:ARG78
|
4.2
|
38.9
|
1.0
|
CD
|
B:ARG78
|
4.2
|
26.8
|
1.0
|
CE
|
B:LYS82
|
4.2
|
37.0
|
1.0
|
CZ
|
B:ARG78
|
4.3
|
31.4
|
1.0
|
NE
|
B:ARG78
|
4.3
|
33.4
|
1.0
|
CG
|
B:ARG78
|
4.9
|
30.2
|
1.0
|
NH2
|
B:ARG78
|
5.0
|
22.6
|
1.0
|
|
Cadmium binding site 5 out
of 21 in 7oxq
Go back to
Cadmium Binding Sites List in 7oxq
Cadmium binding site 5 out
of 21 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 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 048 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd502
b:203.0
occ:1.00
|
OE1
|
B:GLU224
|
2.3
|
125.3
|
1.0
|
OE1
|
B:GLU233
|
2.3
|
124.7
|
1.0
|
NE2
|
B:HIS235
|
2.3
|
83.4
|
1.0
|
CD
|
B:GLU233
|
2.9
|
113.3
|
1.0
|
CD
|
B:GLU224
|
3.1
|
128.8
|
1.0
|
CD2
|
B:HIS235
|
3.2
|
74.6
|
1.0
|
OE2
|
B:GLU224
|
3.2
|
133.5
|
1.0
|
CE1
|
B:HIS235
|
3.3
|
82.5
|
1.0
|
OE2
|
B:GLU233
|
3.6
|
105.6
|
1.0
|
CG
|
B:GLU233
|
3.7
|
91.4
|
1.0
|
CB
|
B:GLU233
|
4.0
|
88.1
|
1.0
|
O
|
B:GLU233
|
4.1
|
69.0
|
1.0
|
CG
|
B:HIS235
|
4.4
|
65.9
|
1.0
|
ND1
|
B:HIS235
|
4.4
|
67.4
|
1.0
|
CG
|
B:GLU224
|
4.5
|
123.1
|
1.0
|
NH2
|
B:ARG199
|
4.5
|
95.0
|
1.0
|
C
|
B:GLU233
|
4.8
|
69.1
|
1.0
|
CB
|
B:GLU224
|
5.0
|
124.0
|
1.0
|
|
Cadmium binding site 6 out
of 21 in 7oxq
Go back to
Cadmium Binding Sites List in 7oxq
Cadmium binding site 6 out
of 21 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 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 048 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd503
b:143.2
occ:1.00
|
O
|
B:LYS249
|
2.3
|
78.3
|
1.0
|
NE1
|
B:TRP252
|
2.3
|
69.3
|
1.0
|
CE2
|
B:TRP252
|
3.0
|
60.8
|
1.0
|
CZ2
|
B:TRP252
|
3.1
|
51.5
|
1.0
|
N
|
B:LYS249
|
3.3
|
64.7
|
1.0
|
C
|
B:LYS249
|
3.3
|
69.2
|
1.0
|
CD1
|
B:TRP252
|
3.5
|
55.3
|
1.0
|
CA
|
B:LYS249
|
3.8
|
61.3
|
1.0
|
C
|
B:GLU248
|
4.3
|
64.0
|
1.0
|
CD2
|
B:TRP252
|
4.3
|
50.5
|
1.0
|
NH2
|
B:ARG307
|
4.3
|
47.9
|
1.0
|
CD2
|
B:LEU303
|
4.4
|
40.3
|
1.0
|
CA
|
B:GLU248
|
4.4
|
53.8
|
1.0
|
CH2
|
B:TRP252
|
4.5
|
43.2
|
1.0
|
CB
|
B:LYS249
|
4.5
|
57.4
|
1.0
|
N
|
B:ASP250
|
4.5
|
62.9
|
1.0
|
CG
|
B:TRP252
|
4.5
|
45.6
|
1.0
|
O
|
B:PRO247
|
4.7
|
55.7
|
1.0
|
CD1
|
B:LEU295
|
4.8
|
52.0
|
1.0
|
NH1
|
B:ARG307
|
4.9
|
48.2
|
1.0
|
CA
|
B:ASP250
|
4.9
|
49.8
|
1.0
|
|
Cadmium binding site 7 out
of 21 in 7oxq
Go back to
Cadmium Binding Sites List in 7oxq
Cadmium binding site 7 out
of 21 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 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 048 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Cd801
b:157.7
occ:1.00
|
N4
|
T:DC709
|
3.0
|
42.4
|
1.0
|
N7
|
T:DG708
|
3.4
|
40.7
|
1.0
|
C5
|
T:DC709
|
3.7
|
39.6
|
1.0
|
C4
|
T:DC709
|
3.7
|
32.4
|
1.0
|
C5
|
T:DG708
|
4.0
|
36.7
|
1.0
|
O6
|
T:DG708
|
4.1
|
36.4
|
1.0
|
C8
|
T:DG708
|
4.2
|
36.4
|
1.0
|
C6
|
T:DG708
|
4.3
|
36.7
|
1.0
|
O6
|
P:DG819
|
4.9
|
45.3
|
1.0
|
C6
|
T:DC709
|
4.9
|
33.0
|
1.0
|
N3
|
T:DC709
|
5.0
|
27.5
|
1.0
|
|
Cadmium binding site 8 out
of 21 in 7oxq
Go back to
Cadmium Binding Sites List in 7oxq
Cadmium binding site 8 out
of 21 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 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 048 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Cd802
b:154.1
occ:1.00
|
N7
|
T:DG720
|
2.8
|
81.5
|
1.0
|
C8
|
T:DG720
|
3.6
|
75.6
|
1.0
|
C8
|
T:DG719
|
3.8
|
73.3
|
1.0
|
N7
|
T:DG719
|
3.9
|
73.5
|
1.0
|
C5
|
T:DG720
|
4.0
|
76.3
|
1.0
|
O6
|
T:DG720
|
4.3
|
72.8
|
1.0
|
O6
|
T:DG721
|
4.5
|
57.9
|
1.0
|
C6
|
T:DG720
|
4.6
|
69.5
|
1.0
|
N9
|
T:DG719
|
4.6
|
73.1
|
1.0
|
C5
|
T:DG719
|
4.7
|
71.8
|
1.0
|
C2'
|
T:DG719
|
4.8
|
78.6
|
1.0
|
N9
|
T:DG720
|
4.9
|
69.2
|
1.0
|
|
Cadmium binding site 9 out
of 21 in 7oxq
Go back to
Cadmium Binding Sites List in 7oxq
Cadmium binding site 9 out
of 21 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 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 048 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Cd901
b:103.1
occ:1.00
|
N7
|
P:DG815
|
2.3
|
80.0
|
1.0
|
C5
|
P:DG815
|
3.2
|
65.5
|
1.0
|
O6
|
P:DG815
|
3.2
|
64.6
|
1.0
|
C8
|
P:DG815
|
3.3
|
80.8
|
1.0
|
C6
|
P:DG815
|
3.6
|
62.2
|
1.0
|
C6
|
P:DC814
|
3.6
|
78.3
|
1.0
|
C5
|
P:DC814
|
3.7
|
74.4
|
1.0
|
C2'
|
P:DC814
|
4.1
|
86.0
|
1.0
|
N1
|
P:DC814
|
4.1
|
78.1
|
1.0
|
C4
|
P:DC814
|
4.3
|
71.0
|
1.0
|
C4
|
P:DG815
|
4.4
|
62.6
|
1.0
|
N9
|
P:DG815
|
4.5
|
75.2
|
1.0
|
C2
|
P:DC814
|
4.6
|
66.1
|
1.0
|
O6
|
P:DG816
|
4.6
|
47.9
|
1.0
|
N7
|
P:DG816
|
4.6
|
52.7
|
1.0
|
N3
|
P:DC814
|
4.7
|
64.0
|
1.0
|
C1'
|
P:DC814
|
4.7
|
80.9
|
1.0
|
N1
|
P:DG815
|
4.9
|
58.3
|
1.0
|
N4
|
P:DC814
|
4.9
|
69.7
|
1.0
|
|
Cadmium binding site 10 out
of 21 in 7oxq
Go back to
Cadmium Binding Sites List in 7oxq
Cadmium binding site 10 out
of 21 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna in Complex with Fragment 048 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 048 at the Transient P-Pocket. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cd602
b:40.1
occ:1.00
|
OE2
|
C:GLU478
|
2.3
|
27.3
|
1.0
|
OD2
|
C:ASP498
|
2.3
|
32.6
|
1.0
|
OD1
|
C:ASP443
|
2.3
|
42.0
|
1.0
|
OD1
|
C:ASP498
|
2.3
|
31.6
|
1.0
|
CG
|
C:ASP498
|
2.6
|
32.3
|
1.0
|
CD
|
C:GLU478
|
3.0
|
29.8
|
1.0
|
OE1
|
C:GLU478
|
3.0
|
32.9
|
1.0
|
CG
|
C:ASP443
|
3.2
|
40.3
|
1.0
|
OD2
|
C:ASP443
|
3.5
|
44.6
|
1.0
|
CB
|
C:ASP498
|
4.1
|
32.1
|
1.0
|
OP1
|
E:DA722
|
4.2
|
81.3
|
1.0
|
CB
|
C:ALA538
|
4.2
|
48.1
|
1.0
|
O
|
C:GLY444
|
4.3
|
44.3
|
1.0
|
CG
|
C:GLU478
|
4.4
|
34.8
|
1.0
|
CB
|
C:ASP443
|
4.6
|
34.4
|
1.0
|
OD1
|
C:ASP549
|
4.6
|
68.0
|
1.0
|
N
|
C:GLY444
|
4.7
|
35.9
|
1.0
|
C
|
C:ASP498
|
4.8
|
29.4
|
1.0
|
O
|
C:ASP498
|
4.9
|
31.0
|
1.0
|
CA
|
C:ASP443
|
4.9
|
34.6
|
1.0
|
CA
|
C:ASP498
|
4.9
|
25.2
|
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 20:04:27 2024
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