Cadmium in PDB 7oz2: Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A Transient P-Pocket

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase with A Double Stranded Dna Showing A Transient P-Pocket:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13; 3.4.23.16;

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

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:

Magnesium

(Mg)

1 atom

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 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 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 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 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 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 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 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 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 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 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

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.