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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:

Bromine (Br) 1 atom

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

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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

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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

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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

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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

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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 Dec 17 08:24:38 2021

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