Cadmium in PDB 8pvt: Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev)

The structure of Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev), PDB code: 8pvt 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)	43.59 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	60.846, 60.846, 187.469, 90, 90, 90
R / Rfree (%)	20.5 / 25.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Cadmium atom in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev) (pdb code 8pvt). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 23 binding sites of Cadmium where determined in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev), PDB code: 8pvt:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 23 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev)


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 (Sad 7 Kev) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:64.8 occ:1.00 O A:HOH323 2.8 47.5 1.0 NE2 A:HIS87 2.8 48.5 1.0 O A:HOH318 2.8 58.3 1.0 O A:HOH324 2.8 46.9 1.0 CD2 A:HIS87 3.6 26.8 1.0 CE1 A:HIS87 3.8 33.6 1.0 CG A:HIS87 4.8 24.9 1.0 ND1 A:HIS87 4.9 37.3 1.0

Cadmium binding site 2 out of 23 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev)


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 (Sad 7 Kev) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:59.1 occ:1.00 NE2 A:HIS15 2.8 47.8 1.0 O A:ALA33 2.8 45.0 1.0 CD2 A:HIS15 3.7 40.4 1.0 CE1 A:HIS15 3.8 38.5 1.0 C A:ALA33 4.0 48.1 1.0 O B:LYS24 4.0 51.9 1.0 O B:SER22 4.3 51.6 1.0 N B:LYS24 4.5 60.4 1.0 CA A:LEU34 4.6 44.3 1.0 N A:LEU34 4.8 42.3 1.0 OG B:SER22 4.8 47.1 1.0 O A:HOH316 4.8 48.7 1.0 CG A:HIS15 4.9 43.5 1.0 ND1 A:HIS15 4.9 46.9 1.0 C B:SER22 4.9 47.5 1.0 CA A:ALA33 4.9 49.8 1.0 C B:LYS24 4.9 51.5 1.0 CA B:GLY23 5.0 39.4 1.0

Cadmium binding site 3 out of 23 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev)


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 (Sad 7 Kev) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:57.1 occ:1.00 NE2 A:HIS106 2.7 41.9 1.0 OE2 A:GLU102 2.7 43.9 1.0 OD1 A:ASP11 2.7 46.9 1.0 OE1 A:GLU105 2.8 38.1 1.0 O A:GLU102 2.9 37.0 1.0 OD2 A:ASP11 3.1 47.6 1.0 CG A:ASP11 3.3 46.2 1.0 CD A:GLU102 3.5 49.6 1.0 CE1 A:HIS106 3.6 39.4 1.0 CD2 A:HIS106 3.6 31.5 1.0 CD A:CD207 3.7 67.6 1.0 C A:GLU102 4.0 40.5 1.0 CD A:GLU105 4.0 38.9 1.0 CG A:GLU102 4.0 49.2 1.0 CA A:GLU102 4.4 31.7 1.0 OE1 A:GLU102 4.4 49.9 1.0 CB A:GLU105 4.5 34.6 1.0 ND1 A:HIS106 4.7 43.7 1.0 CG A:HIS106 4.7 41.6 1.0 OE2 A:GLU105 4.7 49.7 1.0 CB A:GLU102 4.8 31.2 1.0 CB A:ASP11 4.8 35.5 1.0 CG A:GLU105 4.9 43.6 1.0

Cadmium binding site 4 out of 23 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev)


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 (Sad 7 Kev) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:36.8 occ:1.00 NE2 A:HIS79 2.6 38.8 1.0 OE2 A:GLU83 2.7 30.6 1.0 ND1 A:HIS98 2.7 31.4 1.0 O A:HOH321 2.8 37.5 1.0 O A:HOH314 2.8 12.9 1.0 CD A:GLU83 3.3 38.9 1.0 CD2 A:HIS79 3.4 22.1 1.0 OE1 A:GLU83 3.5 41.2 1.0 O A:HOH309 3.5 43.9 1.0 CG A:HIS98 3.5 30.7 1.0 CB A:HIS98 3.6 27.9 1.0 CE1 A:HIS79 3.7 36.5 1.0 CE1 A:HIS98 3.7 43.0 1.0 CD A:CD205 3.9 34.7 1.0 CA A:HIS98 4.1 30.7 1.0 CG A:GLU83 4.6 36.7 1.0 CG A:HIS79 4.7 34.9 1.0 CD2 A:HIS98 4.7 39.6 1.0 ND1 A:HIS79 4.8 37.0 1.0 NE2 A:HIS98 4.8 39.6 1.0 NE2 B:GLN60 4.9 70.3 1.0

Cadmium binding site 5 out of 23 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev)


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 (Sad 7 Kev) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:34.7 occ:1.00 OE1 A:GLU83 2.7 41.2 1.0 OD2 A:ASP126 2.7 30.4 1.0 OD2 A:ASP130 2.7 44.7 1.0 O A:HOH314 2.7 12.9 1.0 ND1 A:HIS128 2.7 30.6 1.0 OD1 A:ASP126 3.1 36.8 1.0 CG A:ASP126 3.2 30.9 1.0 CD A:GLU83 3.5 38.9 1.0 O A:HOH321 3.5 37.5 1.0 OE2 A:GLU83 3.6 30.6 1.0 CG A:ASP130 3.6 34.2 1.0 CG A:HIS128 3.7 40.0 1.0 CE1 A:HIS128 3.7 30.3 1.0 CB A:ASP130 3.8 23.9 1.0 CB A:HIS128 3.8 28.9 1.0 CD A:CD204 3.9 36.8 1.0 CB A:ASP126 4.5 25.2 1.0 NE A:ARG80 4.6 35.7 1.0 CG A:ARG80 4.7 36.8 1.0 N A:HIS128 4.8 34.1 1.0 CG A:GLU83 4.8 36.7 1.0 NE2 A:HIS128 4.8 30.6 1.0 OD1 A:ASP130 4.8 52.1 1.0 CD2 A:HIS128 4.8 29.9 1.0 CA A:HIS128 4.9 34.0 1.0 CD A:ARG80 4.9 25.5 1.0 CB A:GLU83 5.0 26.4 1.0

Cadmium binding site 6 out of 23 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev)


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 (Sad 7 Kev) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:41.0 occ:1.00 NE2 A:HIS78 2.6 24.8 1.0 OE1 A:GLU110 2.7 32.0 1.0 O A:HOH302 2.7 32.8 1.0 OE1 A:GLU113 2.7 40.2 1.0 OE2 A:GLU110 2.7 47.2 1.0 OE2 A:GLU74 2.8 47.9 1.0 CD A:GLU110 3.1 42.1 1.0 CD A:GLU74 3.2 40.8 1.0 CG A:GLU74 3.3 39.3 1.0 CD A:GLU113 3.4 37.0 1.0 OE2 A:GLU113 3.5 44.3 1.0 CE1 A:HIS78 3.5 31.0 1.0 CD2 A:HIS78 3.7 26.9 1.0 O A:HOH308 3.8 44.1 1.0 OE1 A:GLU74 4.2 63.6 1.0 O A:HOH303 4.3 51.1 1.0 O A:HOH305 4.5 34.1 1.0 O A:HOH326 4.5 42.1 1.0 CG A:GLU110 4.5 33.0 1.0 ND1 A:HIS78 4.7 37.7 1.0 CG A:GLU113 4.7 32.0 1.0 CG A:HIS78 4.8 27.2 1.0 CB A:GLU74 4.8 37.5 1.0 CA A:GLU110 5.0 30.1 1.0

Cadmium binding site 7 out of 23 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev)


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 (Sad 7 Kev) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:67.6 occ:1.00 OE2 A:GLU105 2.7 49.7 1.0 OE2 A:GLU102 2.7 43.9 1.0 NZ A:LYS14 2.7 44.2 1.0 OE1 A:GLU105 2.8 38.1 1.0 OE1 A:GLU102 2.8 49.9 1.0 CD A:GLU102 3.1 49.6 1.0 CD A:GLU105 3.1 38.9 1.0 CD A:LYS14 3.3 44.7 1.0 CE A:LYS14 3.4 61.4 1.0 OD1 A:ASP11 3.6 46.9 1.0 CD A:CD203 3.7 57.1 1.0 ND1 A:HIS79 4.0 37.0 1.0 CE1 A:HIS79 4.3 36.5 1.0 O B:SER22 4.5 51.6 1.0 CG A:GLU102 4.5 49.2 1.0 CG A:GLU105 4.6 43.6 1.0 CG A:LYS14 4.7 43.2 1.0 CG A:ASP11 4.8 46.2 1.0 O A:HOH309 4.8 43.9 1.0 CG A:HIS79 4.9 34.9 1.0 CA A:GLU102 4.9 31.7 1.0

Cadmium binding site 8 out of 23 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev)


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 (Sad 7 Kev) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:54.8 occ:1.00 O A:HOH327 2.7 35.2 1.0 ND1 A:HIS125 2.8 43.1 1.0 O A:HOH322 2.9 48.9 1.0 O A:HOH325 2.9 28.0 1.0 CG A:HIS125 3.6 36.0 1.0 CB A:HIS125 3.7 33.7 1.0 OG1 A:THR124 3.8 52.8 1.0 CE1 A:HIS125 3.8 34.9 1.0 N A:HIS125 4.4 29.2 1.0 CA A:HIS125 4.7 31.5 1.0 CD2 A:HIS125 4.8 42.6 1.0 NE2 A:HIS125 4.9 41.0 1.0

Cadmium binding site 9 out of 23 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev)


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 (Sad 7 Kev) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd209 b:148.4 occ:1.00 OE2 A:GLU50 2.4 103.8 1.0 OE1 A:GLU50 2.7 98.4 1.0 CD A:GLU50 2.9 95.0 1.0 CG A:GLU50 4.3 76.1 1.0 CB A:GLU50 4.9 70.5 1.0

Cadmium binding site 10 out of 23 in the Manganese-Dependent Transcriptional Repressor DR2539 Complexed with Cadmium (Sad 7 Kev)


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 (Sad 7 Kev) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd210 b:122.1 occ:1.00 OD2 A:ASP95 2.8 63.0 1.0 OD1 A:ASP95 3.2 51.2 1.0 CG A:ASP95 3.3 56.7 1.0 OE2 A:GLU96 4.7 49.5 1.0 CB A:ASP95 4.8 40.1 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