Cadmium in PDB 8pvz: Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium

The structure of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium, PDB code: 8pvz was solved by C.Mota, D.De Sanctis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.60 / 2.00
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.785, 60.785, 187.681, 90, 90, 90
R / Rfree (%)	18.6 / 22

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Cadmium atom in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (pdb code 8pvz). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 24 binding sites of Cadmium where determined in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium, PDB code: 8pvz:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 24 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:34.1 occ:1.00 ND1 A:HIS98 2.5 34.1 1.0 OE2 A:GLU83 2.5 32.4 1.0 NE2 A:HIS79 2.5 29.0 1.0 O A:HOH351 2.6 33.4 1.0 O A:HOH352 2.6 36.9 1.0 O A:HOH348 2.7 27.6 1.0 CD A:GLU83 3.2 35.1 1.0 CD2 A:HIS79 3.3 29.9 1.0 CG A:HIS98 3.4 35.8 1.0 CE1 A:HIS98 3.4 40.1 1.0 OE1 A:GLU83 3.5 30.5 1.0 CE1 A:HIS79 3.5 37.0 1.0 CB A:HIS98 3.6 35.5 1.0 CD A:CD202 4.0 34.6 1.0 CA A:HIS98 4.1 35.0 1.0 CG A:GLU83 4.4 27.1 1.0 O B:HOH319 4.5 52.9 1.0 CG A:HIS79 4.5 32.1 1.0 NE2 A:HIS98 4.6 35.4 1.0 CD2 A:HIS98 4.6 40.4 1.0 ND1 A:HIS79 4.6 32.0 1.0 CE1 A:HIS128 4.9 34.4 1.0

Cadmium binding site 2 out of 24 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:34.6 occ:1.00 OD2 A:ASP126 2.4 32.5 1.0 ND1 A:HIS128 2.5 30.8 1.0 OD2 A:ASP130 2.5 34.1 1.0 OE1 A:GLU83 2.5 30.5 1.0 O A:HOH348 2.6 27.6 1.0 CG A:ASP126 3.0 30.6 1.0 OD1 A:ASP126 3.0 30.6 1.0 CE1 A:HIS128 3.3 34.4 1.0 CG A:ASP130 3.5 38.0 1.0 CD A:GLU83 3.5 35.1 1.0 CG A:HIS128 3.5 34.9 1.0 OE2 A:GLU83 3.8 32.4 1.0 O A:HOH351 3.8 33.4 1.0 CB A:ASP130 3.8 31.4 1.0 CB A:HIS128 3.8 34.7 1.0 CD A:CD201 4.0 34.1 1.0 CB A:ASP126 4.3 28.9 1.0 NE2 A:HIS128 4.5 38.1 1.0 OD1 A:ASP130 4.6 32.5 1.0 CD2 A:HIS128 4.6 33.8 1.0 N A:HIS128 4.6 32.6 1.0 NE A:ARG80 4.7 31.2 1.0 CG A:GLU83 4.8 27.1 1.0 CA A:HIS128 4.8 36.2 1.0 CG A:ARG80 4.9 28.5 1.0 CB A:GLU83 4.9 24.8 1.0 CD A:ARG80 5.0 25.4 1.0

Cadmium binding site 3 out of 24 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:45.6 occ:0.82 O A:HOH301 2.2 26.9 1.0 OE2 A:GLU105 2.4 39.8 1.0 NE2 A:HIS106 2.5 36.0 1.0 OD1 A:ASP11 2.6 36.2 1.0 OE2 A:GLU102 2.7 46.9 1.0 O A:GLU102 3.0 41.3 1.0 CD A:GLU105 3.3 38.1 1.0 CD A:GLU102 3.3 49.2 1.0 CD2 A:HIS106 3.3 39.5 1.0 CG A:ASP11 3.3 37.8 1.0 OD2 A:ASP11 3.4 46.8 1.0 CE1 A:HIS106 3.5 41.9 1.0 CD A:CD208 3.6 49.4 0.6 CG A:GLU102 3.6 46.9 1.0 CG A:GLU105 3.7 35.7 1.0 C A:GLU102 4.0 39.2 1.0 OE1 A:GLU102 4.2 46.7 1.0 OE1 A:GLU105 4.2 36.9 1.0 CA A:GLU102 4.3 37.5 1.0 CG A:HIS106 4.5 41.1 1.0 ND1 A:HIS106 4.5 43.8 1.0 CB A:GLU102 4.6 42.2 1.0 CB A:ASP11 4.8 35.9 1.0

Cadmium binding site 4 out of 24 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:42.7 occ:0.80 O B:HOH354 2.5 43.7 1.0 NE2 A:HIS15 2.5 42.2 1.0 O A:ALA33 2.5 43.5 1.0 O A:HOH353 2.6 47.0 1.0 O B:HOH306 2.6 45.2 1.0 CD2 A:HIS15 3.2 39.3 1.0 C A:ALA33 3.7 48.5 1.0 CE1 A:HIS15 3.7 40.4 1.0 CA A:LEU34 4.2 48.3 1.0 O B:SER22 4.2 38.5 1.0 O B:LYS24 4.2 45.9 1.0 N A:LEU34 4.3 44.4 1.0 CG A:HIS15 4.5 39.7 1.0 OG B:SER22 4.5 45.1 1.0 ND1 A:HIS15 4.7 43.3 1.0 CA A:ALA33 4.7 44.1 1.0 O A:HOH343 4.7 52.8 1.0 N B:LYS24 4.8 42.2 1.0 C A:LEU34 4.8 52.5 1.0 CB A:ALA33 4.9 41.4 1.0 C B:SER22 4.9 41.5 1.0

Cadmium binding site 5 out of 24 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:36.1 occ:0.89 NE2 A:HIS78 2.3 29.2 1.0 OE1 A:GLU110 2.5 39.8 1.0 O A:HOH304 2.5 41.8 1.0 OE1 A:GLU113 2.5 40.8 1.0 OE2 A:GLU74 2.6 59.5 1.0 OE2 A:GLU110 2.6 39.4 1.0 CD A:GLU74 2.6 51.8 1.0 CD A:GLU110 2.8 41.5 1.0 OE1 A:GLU74 3.0 55.9 1.0 CG A:GLU74 3.2 42.2 1.0 CE1 A:HIS78 3.2 38.9 1.0 CD A:GLU113 3.3 35.9 1.0 CD2 A:HIS78 3.3 34.8 1.0 OE2 A:GLU113 3.4 37.8 1.0 CG A:GLU110 4.3 39.2 1.0 ND1 A:HIS78 4.4 41.9 1.0 O A:HOH315 4.4 42.5 1.0 CG A:HIS78 4.4 31.5 1.0 O A:HOH356 4.6 42.2 1.0 CG A:GLU113 4.6 32.8 1.0 CB A:GLU74 4.7 37.2 1.0 O A:HOH308 4.7 44.2 1.0 CA A:GLU110 4.8 40.1 1.0 CB A:GLU113 4.9 30.5 1.0 CB A:GLU110 5.0 42.8 1.0

Cadmium binding site 6 out of 24 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:58.0 occ:0.91 O A:HOH347 2.5 56.9 1.0 NE2 A:HIS87 2.6 39.5 1.0 O A:HOH357 2.7 61.3 1.0 O A:HOH350 2.7 58.6 1.0 CD2 A:HIS87 3.3 40.9 1.0 CE1 A:HIS87 3.7 45.8 1.0 CG A:HIS87 4.6 35.0 1.0 ND1 A:HIS87 4.7 38.0 1.0

Cadmium binding site 7 out of 24 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:48.0 occ:0.93 ND1 A:HIS125 2.5 35.5 1.0 O A:HOH355 2.6 49.2 1.0 O A:HOH349 2.7 34.7 1.0 O A:HOH358 2.8 51.6 1.0 CE1 A:HIS125 3.5 38.4 1.0 CG A:HIS125 3.5 33.6 1.0 CB A:HIS125 3.7 33.2 1.0 CB A:THR124 4.4 30.8 1.0 N A:HIS125 4.5 28.7 1.0 NE2 A:HIS125 4.6 39.2 1.0 CD2 A:HIS125 4.7 37.8 1.0 CA A:HIS125 4.7 30.1 1.0 OG1 A:THR124 4.9 41.0 1.0

Cadmium binding site 8 out of 24 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:49.4 occ:0.60 NZ A:LYS14 2.5 48.9 1.0 OE2 A:GLU105 2.5 39.8 1.0 OE1 A:GLU102 2.6 46.7 1.0 OE2 A:GLU102 2.6 46.9 1.0 CE A:LYS14 2.8 46.7 1.0 CD A:GLU102 2.9 49.2 1.0 OE1 A:GLU105 2.9 36.9 1.0 CD A:GLU105 3.1 38.1 1.0 CD A:LYS14 3.1 46.0 1.0 CD A:CD203 3.6 45.6 0.8 ND1 A:HIS79 3.9 32.0 1.0 OD1 A:ASP11 3.9 36.2 1.0 CE1 A:HIS79 4.2 37.0 1.0 CG A:GLU102 4.3 46.9 1.0 CG A:GLU105 4.6 35.7 1.0 O B:SER22 4.6 38.5 1.0 CG A:LYS14 4.7 42.7 1.0 CA A:GLU102 4.7 37.5 1.0 CG A:HIS79 4.8 32.1 1.0 CB A:GLU102 4.8 42.2 1.0

Cadmium binding site 9 out of 24 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd209 b:126.5 occ:0.59 OE2 A:GLU50 2.7 93.1 1.0 NH2 A:ARG46 3.0 83.1 1.0 OE1 A:GLU50 3.1 87.2 1.0 CD A:GLU50 3.3 88.8 1.0 CZ A:ARG46 4.2 88.1 1.0 NE A:ARG46 4.5 82.2 1.0 CG A:GLU50 4.7 76.7 1.0

Cadmium binding site 10 out of 24 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd210 b:93.3 occ:0.58 OD2 A:ASP95 2.7 58.5 1.0 OD1 A:ASP95 2.7 47.7 1.0 CG A:ASP95 3.1 50.6 1.0 OE2 A:GLU96 4.1 53.4 1.0 O A:HOH332 4.2 47.0 1.0 CB A:ASP95 4.6 45.2 1.0 CB A:PRO93 4.6 41.1 1.0 CG A:GLU96 4.7 46.6 1.0 CD A:GLU96 4.9 52.5 1.0 CG A:PRO93 5.0 43.6 1.0

C.Mota, M.Webster, M.Saidi, U.Kapp, C.Zubieta, G.Giachin, J.A.Manso, D.De Sanctis. Metal Ion Activation and Dna Recognition By the Deinococcus Radiodurans Manganese Sensor DR2539. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 38652591
DOI: 10.1111/FEBS.17140