Cadmium in PDB 7oz2: Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A Transient P-Pocket
Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A Transient P-Pocket
Protein crystallography data
The structure of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A Transient P-Pocket, PDB code: 7oz2
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)
|
81.44 /
2.85
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
310.638,
62.07,
168.239,
90,
104.51,
90
|
R / Rfree (%)
|
21.7 /
25.7
|
Other elements in 7oz2:
The structure of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A 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 -
27;
Binding sites:
The binding sites of Cadmium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A Transient P-Pocket
(pdb code 7oz2). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 27 binding sites of Cadmium where determined in the
Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A Transient P-Pocket, PDB code: 7oz2:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cadmium binding site 1 out
of 27 in 7oz2
Go back to
Cadmium Binding Sites List in 7oz2
Cadmium binding site 1 out
of 27 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A 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 Showing A Transient P-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd601
b:48.5
occ:1.00
|
OD1
|
A:ASP443
|
2.3
|
62.4
|
1.0
|
OD2
|
A:ASP498
|
2.3
|
39.9
|
1.0
|
OD2
|
A:ASP443
|
2.3
|
49.3
|
1.0
|
OE2
|
A:GLU478
|
2.3
|
66.8
|
1.0
|
OD1
|
A:ASP498
|
2.3
|
49.7
|
1.0
|
OE1
|
A:GLU478
|
2.3
|
50.0
|
1.0
|
CG
|
A:ASP443
|
2.6
|
51.2
|
1.0
|
CG
|
A:ASP498
|
2.6
|
42.6
|
1.0
|
CD
|
A:GLU478
|
2.7
|
57.5
|
1.0
|
O
|
A:GLY444
|
4.1
|
48.5
|
1.0
|
CB
|
A:ASP443
|
4.1
|
34.4
|
1.0
|
CB
|
A:ASP498
|
4.1
|
37.3
|
1.0
|
CG
|
A:GLU478
|
4.2
|
42.3
|
1.0
|
N
|
A:GLY444
|
4.6
|
41.0
|
1.0
|
OP1
|
T:DT724
|
4.7
|
95.1
|
1.0
|
CA
|
A:ASP443
|
4.8
|
35.6
|
1.0
|
C
|
A:ASP498
|
4.9
|
39.1
|
1.0
|
CA
|
A:ASP498
|
5.0
|
39.4
|
1.0
|
O
|
A:ASP498
|
5.0
|
39.5
|
1.0
|
|
Cadmium binding site 2 out
of 27 in 7oz2
Go back to
Cadmium Binding Sites List in 7oz2
Cadmium binding site 2 out
of 27 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A 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 Showing A Transient P-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd602
b:66.1
occ:1.00
|
NE2
|
A:HIS539
|
2.3
|
64.9
|
1.0
|
OD2
|
A:ASP549
|
2.3
|
60.6
|
1.0
|
OD1
|
A:ASP549
|
2.3
|
64.1
|
1.0
|
CG
|
A:ASP549
|
2.6
|
53.8
|
1.0
|
CE1
|
A:HIS539
|
3.0
|
65.1
|
1.0
|
CD2
|
A:HIS539
|
3.3
|
57.2
|
1.0
|
OG
|
A:SER553
|
3.3
|
60.2
|
1.0
|
ND1
|
A:HIS539
|
4.1
|
58.0
|
1.0
|
CB
|
A:ASP549
|
4.2
|
38.9
|
1.0
|
CG
|
A:HIS539
|
4.3
|
53.9
|
1.0
|
CB
|
A:SER553
|
4.5
|
55.0
|
1.0
|
O
|
A:ASP549
|
4.7
|
53.1
|
1.0
|
CA
|
A:ASP549
|
5.0
|
45.0
|
1.0
|
|
Cadmium binding site 3 out
of 27 in 7oz2
Go back to
Cadmium Binding Sites List in 7oz2
Cadmium binding site 3 out
of 27 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A 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 Showing A Transient P-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd603
b:60.3
occ:1.00
|
OD1
|
A:ASP185
|
2.2
|
55.8
|
1.0
|
OD2
|
A:ASP110
|
2.3
|
67.5
|
1.0
|
O
|
A:HOH711
|
2.3
|
45.2
|
1.0
|
OD1
|
A:ASP186
|
2.3
|
55.6
|
1.0
|
OD2
|
A:ASP186
|
2.3
|
61.5
|
1.0
|
O3'
|
P:DC821
|
2.3
|
55.8
|
1.0
|
OP1
|
P:DG822
|
2.4
|
56.8
|
1.0
|
CG
|
A:ASP186
|
2.6
|
57.2
|
1.0
|
OD2
|
A:ASP185
|
2.7
|
49.4
|
1.0
|
CG
|
A:ASP185
|
2.8
|
50.4
|
1.0
|
P
|
P:DG822
|
2.9
|
53.0
|
1.0
|
CG
|
A:ASP110
|
3.3
|
61.9
|
1.0
|
C3'
|
P:DC821
|
3.6
|
53.5
|
1.0
|
CD
|
A:CD606
|
3.7
|
72.7
|
1.0
|
OD1
|
A:ASP110
|
3.7
|
63.9
|
1.0
|
OP2
|
P:DG822
|
3.9
|
57.5
|
1.0
|
C4'
|
P:DC821
|
3.9
|
47.8
|
1.0
|
C5'
|
P:DC821
|
4.0
|
46.0
|
1.0
|
CB
|
A:ASP186
|
4.0
|
49.2
|
1.0
|
O5'
|
P:DG822
|
4.1
|
47.3
|
1.0
|
N
|
A:ASP186
|
4.1
|
40.1
|
1.0
|
CB
|
A:ASP185
|
4.2
|
44.7
|
1.0
|
C
|
A:ASP185
|
4.3
|
45.2
|
1.0
|
C5'
|
P:DG822
|
4.3
|
54.4
|
1.0
|
O
|
A:HOH709
|
4.4
|
53.0
|
1.0
|
CA
|
A:ASP186
|
4.4
|
46.3
|
1.0
|
CB
|
A:ASP110
|
4.5
|
48.8
|
1.0
|
CA
|
A:ASP185
|
4.6
|
46.8
|
1.0
|
O
|
A:ASP185
|
4.7
|
51.9
|
1.0
|
C2'
|
P:DC821
|
4.7
|
54.7
|
1.0
|
N
|
A:ASP185
|
4.7
|
44.5
|
1.0
|
O5'
|
P:DC821
|
4.7
|
47.5
|
1.0
|
CA
|
A:ASP110
|
4.9
|
43.3
|
1.0
|
|
Cadmium binding site 4 out
of 27 in 7oz2
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Cadmium Binding Sites List in 7oz2
Cadmium binding site 4 out
of 27 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A 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 Showing A Transient P-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd604
b:97.1
occ:1.00
|
OD2
|
A:ASP123
|
2.3
|
82.0
|
1.0
|
OD2
|
A:ASP121
|
2.3
|
58.2
|
1.0
|
OD1
|
A:ASP121
|
2.3
|
56.6
|
1.0
|
CG
|
A:ASP121
|
2.6
|
46.0
|
1.0
|
CG
|
A:ASP123
|
3.4
|
71.2
|
1.0
|
CB
|
A:ASP123
|
3.8
|
58.7
|
1.0
|
CB
|
A:ASP121
|
4.1
|
35.4
|
1.0
|
CA
|
A:PRO9
|
4.1
|
36.0
|
1.0
|
O
|
A:VAL10
|
4.1
|
44.5
|
1.0
|
N
|
A:VAL10
|
4.2
|
40.8
|
1.0
|
O
|
A:HOH728
|
4.2
|
30.3
|
1.0
|
CB
|
A:PRO9
|
4.4
|
38.3
|
1.0
|
OD1
|
A:ASP123
|
4.5
|
72.7
|
1.0
|
N
|
A:ASP123
|
4.5
|
45.3
|
1.0
|
O
|
A:HOH746
|
4.6
|
48.9
|
1.0
|
CE
|
A:LYS11
|
4.6
|
61.3
|
1.0
|
C
|
A:PRO9
|
4.7
|
43.7
|
1.0
|
CA
|
A:ASP123
|
4.7
|
51.0
|
1.0
|
CD
|
A:LYS11
|
5.0
|
71.2
|
1.0
|
|
Cadmium binding site 5 out
of 27 in 7oz2
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Cadmium Binding Sites List in 7oz2
Cadmium binding site 5 out
of 27 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A 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 Showing A Transient P-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd605
b:129.4
occ:1.00
|
ND1
|
A:HIS208
|
2.9
|
56.4
|
1.0
|
CE1
|
A:HIS208
|
3.6
|
51.3
|
1.0
|
NH1
|
A:ARG211
|
3.7
|
76.7
|
1.0
|
CG
|
A:HIS208
|
3.8
|
44.2
|
1.0
|
OE1
|
A:GLN174
|
3.9
|
74.1
|
1.0
|
CB
|
A:HIS208
|
4.1
|
43.6
|
1.0
|
NE2
|
A:GLN174
|
4.2
|
84.0
|
1.0
|
CD
|
A:GLN174
|
4.4
|
79.9
|
1.0
|
NE2
|
A:HIS208
|
4.5
|
44.2
|
1.0
|
CD2
|
A:HIS208
|
4.6
|
41.1
|
1.0
|
CZ
|
A:ARG211
|
4.9
|
68.7
|
1.0
|
CA
|
A:HIS208
|
4.9
|
47.7
|
1.0
|
CD1
|
A:PHE171
|
5.0
|
42.2
|
1.0
|
|
Cadmium binding site 6 out
of 27 in 7oz2
Go back to
Cadmium Binding Sites List in 7oz2
Cadmium binding site 6 out
of 27 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A 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 Showing A Transient P-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd606
b:72.7
occ:1.00
|
OP1
|
P:DG822
|
2.3
|
56.8
|
1.0
|
O
|
A:VAL111
|
2.3
|
59.9
|
1.0
|
OD1
|
A:ASP110
|
2.3
|
63.9
|
1.0
|
OD2
|
A:ASP185
|
2.3
|
49.4
|
1.0
|
O3
|
A:SO4608
|
2.6
|
49.9
|
1.0
|
CG
|
A:ASP110
|
3.3
|
61.9
|
1.0
|
CG
|
A:ASP185
|
3.4
|
50.4
|
1.0
|
C
|
A:VAL111
|
3.4
|
44.9
|
1.0
|
OD2
|
A:ASP110
|
3.6
|
67.5
|
1.0
|
CD
|
A:CD603
|
3.7
|
60.3
|
1.0
|
P
|
P:DG822
|
3.7
|
53.0
|
1.0
|
S
|
A:SO4608
|
3.9
|
71.1
|
1.0
|
OD1
|
A:ASP185
|
4.0
|
55.8
|
1.0
|
C5'
|
P:DG822
|
4.1
|
54.4
|
1.0
|
O5'
|
P:DG822
|
4.2
|
47.3
|
1.0
|
N
|
A:VAL111
|
4.2
|
41.5
|
1.0
|
CA
|
A:GLY112
|
4.3
|
40.5
|
1.0
|
N
|
A:GLY112
|
4.3
|
38.2
|
1.0
|
CA
|
A:VAL111
|
4.4
|
39.6
|
1.0
|
O4
|
A:SO4608
|
4.4
|
71.4
|
1.0
|
CB
|
A:ASP185
|
4.4
|
44.7
|
1.0
|
O2
|
A:SO4608
|
4.4
|
75.2
|
1.0
|
N
|
A:ASP113
|
4.6
|
47.8
|
1.0
|
O3'
|
P:DC821
|
4.6
|
55.8
|
1.0
|
CB
|
A:ASP110
|
4.6
|
48.8
|
1.0
|
C
|
A:ASP110
|
4.6
|
42.3
|
1.0
|
OP2
|
P:DG822
|
4.7
|
57.5
|
1.0
|
C
|
A:GLY112
|
4.8
|
45.5
|
1.0
|
CB
|
A:ALA114
|
4.8
|
49.2
|
1.0
|
O1
|
A:SO4608
|
4.9
|
66.7
|
1.0
|
NZ
|
A:LYS220
|
4.9
|
74.3
|
1.0
|
O
|
A:HOH711
|
4.9
|
45.2
|
1.0
|
N
|
A:ALA114
|
4.9
|
52.8
|
1.0
|
|
Cadmium binding site 7 out
of 27 in 7oz2
Go back to
Cadmium Binding Sites List in 7oz2
Cadmium binding site 7 out
of 27 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A 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 Showing A Transient P-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd607
b:116.1
occ:1.00
|
NE2
|
A:HIS235
|
2.6
|
69.7
|
1.0
|
NE2
|
A:HIS315
|
2.8
|
72.7
|
1.0
|
CD2
|
A:HIS235
|
3.5
|
67.5
|
1.0
|
CE1
|
A:HIS235
|
3.6
|
73.4
|
1.0
|
CE1
|
A:HIS315
|
3.6
|
71.9
|
1.0
|
OE1
|
A:GLU233
|
3.7
|
72.0
|
1.0
|
CD2
|
A:HIS315
|
3.9
|
67.3
|
1.0
|
CG2
|
A:THR240
|
4.1
|
52.9
|
1.0
|
CE
|
A:LYS238
|
4.4
|
78.9
|
1.0
|
ND1
|
A:HIS235
|
4.6
|
70.9
|
1.0
|
CG
|
A:HIS235
|
4.7
|
63.4
|
1.0
|
ND1
|
A:HIS315
|
4.8
|
79.6
|
1.0
|
NZ
|
A:LYS238
|
4.8
|
82.8
|
1.0
|
CD
|
A:GLU233
|
4.9
|
73.5
|
1.0
|
CB
|
A:THR240
|
5.0
|
59.0
|
1.0
|
CG
|
A:HIS315
|
5.0
|
73.9
|
1.0
|
|
Cadmium binding site 8 out
of 27 in 7oz2
Go back to
Cadmium Binding Sites List in 7oz2
Cadmium binding site 8 out
of 27 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A 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 Showing A Transient P-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd501
b:66.9
occ:1.00
|
O
|
B:HOH603
|
2.3
|
45.3
|
1.0
|
OE1
|
B:GLU297
|
2.3
|
76.1
|
1.0
|
OE2
|
B:GLU297
|
2.3
|
77.2
|
1.0
|
CD
|
B:GLU297
|
2.6
|
74.5
|
1.0
|
CG
|
B:GLU297
|
4.2
|
60.9
|
1.0
|
CB
|
B:GLU297
|
5.0
|
48.2
|
1.0
|
|
Cadmium binding site 9 out
of 27 in 7oz2
Go back to
Cadmium Binding Sites List in 7oz2
Cadmium binding site 9 out
of 27 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A 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 Showing A Transient P-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd502
b:89.9
occ:1.00
|
OE2
|
B:GLU312
|
2.3
|
74.8
|
1.0
|
OE2
|
B:GLU308
|
2.3
|
67.8
|
1.0
|
CD
|
B:GLU312
|
3.1
|
82.2
|
1.0
|
OE1
|
B:GLU312
|
3.2
|
80.8
|
1.0
|
CD
|
B:GLU308
|
3.3
|
66.9
|
1.0
|
CG
|
B:GLU308
|
4.1
|
66.7
|
1.0
|
OE1
|
B:GLU308
|
4.2
|
61.6
|
1.0
|
CG
|
B:GLU312
|
4.5
|
77.0
|
1.0
|
OE2
|
B:GLU305
|
4.8
|
61.6
|
1.0
|
|
Cadmium binding site 10 out
of 27 in 7oz2
Go back to
Cadmium Binding Sites List in 7oz2
Cadmium binding site 10 out
of 27 in the Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A 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 Showing A Transient P-Pocket within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd503
b:58.0
occ:1.00
|
OE2
|
B:GLU233
|
2.3
|
62.5
|
1.0
|
NE2
|
B:HIS235
|
2.3
|
42.0
|
1.0
|
OE1
|
B:GLU224
|
2.3
|
55.5
|
1.0
|
OE2
|
B:GLU224
|
2.3
|
51.6
|
1.0
|
CD
|
B:GLU224
|
2.6
|
54.4
|
1.0
|
CD
|
B:GLU233
|
3.1
|
53.0
|
1.0
|
CD2
|
B:HIS235
|
3.2
|
51.8
|
1.0
|
CE1
|
B:HIS235
|
3.4
|
58.4
|
1.0
|
CG
|
B:GLU233
|
3.7
|
42.8
|
1.0
|
OE1
|
B:GLU233
|
4.0
|
63.9
|
1.0
|
O
|
B:GLU233
|
4.0
|
54.4
|
1.0
|
CG
|
B:GLU224
|
4.1
|
59.3
|
1.0
|
CB
|
B:GLU233
|
4.1
|
48.8
|
1.0
|
CG
|
B:HIS235
|
4.4
|
49.9
|
1.0
|
NH2
|
B:ARG199
|
4.4
|
65.0
|
1.0
|
ND1
|
B:HIS235
|
4.4
|
53.5
|
1.0
|
C
|
B:GLU233
|
4.7
|
54.0
|
1.0
|
CB
|
B:GLU224
|
4.8
|
63.2
|
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 20:04:42 2024
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