Cadmium in PDB 4p5n: Structure of CNAG_02591 From Cryptococcus Neoformans

The structure of Structure of CNAG_02591 From Cryptococcus Neoformans, PDB code: 4p5n was solved by U.A.Ramagopal, E.E.Mcclelland, R.Toro, A.Casadevall, S.C.Almo, New Yorkstructural Genomics Research Consortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.51 / 1.49
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	31.775, 34.686, 38.253, 73.93, 72.85, 79.46
R / Rfree (%)	13.7 / 18

The binding sites of Cadmium atom in the Structure of CNAG_02591 From Cryptococcus Neoformans (pdb code 4p5n). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Structure of CNAG_02591 From Cryptococcus Neoformans, PDB code: 4p5n:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in the Structure of CNAG_02591 From Cryptococcus Neoformans


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of CNAG_02591 From Cryptococcus Neoformans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:9.2 occ:0.40 CD A:CD101 0.0 9.2 0.4 CD A:CD101 1.1 16.3 0.4 NE2 A:HIS66 2.1 14.3 1.0 O A:HOH216 2.2 14.4 0.4 O A:HOH203 2.3 26.4 0.8 OG1 A:THR22 2.4 15.0 1.0 O A:HOH248 2.5 13.7 0.4 O A:HOH246 2.5 4.1 0.4 O A:HOH246 2.6 8.2 0.4 CE1 A:HIS66 3.0 12.7 1.0 CD2 A:HIS66 3.1 12.2 1.0 CB A:THR22 3.5 10.8 1.0 CG2 A:THR22 3.7 11.3 1.0 ND1 A:HIS66 4.2 11.4 1.0 CG A:HIS66 4.2 11.0 1.0 O A:PRO23 4.2 11.9 1.0 O4 A:SO4103 4.3 19.4 0.8 O2 A:SO4103 4.4 20.1 0.8 CA A:THR22 4.8 8.9 1.0 O A:THR70 4.9 18.5 1.0 C A:THR22 4.9 8.2 1.0 OG1 A:THR70 5.0 15.5 1.0

Cadmium binding site 2 out of 9 in the Structure of CNAG_02591 From Cryptococcus Neoformans


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of CNAG_02591 From Cryptococcus Neoformans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:16.3 occ:0.40 CD A:CD101 0.0 16.3 0.4 CD A:CD101 1.1 9.2 0.4 O A:HOH248 1.7 13.7 0.4 O A:HOH246 2.2 8.2 0.4 O A:HOH203 2.2 26.4 0.8 O A:HOH246 2.2 4.1 0.4 NE2 A:HIS66 2.6 14.3 1.0 O A:HOH216 2.8 14.4 0.4 CD2 A:HIS66 3.4 12.2 1.0 OG1 A:THR22 3.5 15.0 1.0 CE1 A:HIS66 3.7 12.7 1.0 O4 A:SO4103 4.0 19.4 0.8 CG2 A:THR22 4.4 11.3 1.0 O2 A:SO4103 4.4 20.1 0.8 CB A:THR22 4.5 10.8 1.0 O A:PRO23 4.5 11.9 1.0 O A:HOH260 4.6 16.4 1.0 CG A:HIS66 4.6 11.0 1.0 ND1 A:HIS66 4.7 11.4 1.0 O B:HOH265 4.9 19.2 1.0 O A:HOH272 4.9 32.2 1.0 S A:SO4103 4.9 16.9 0.8 O B:HOH255 5.0 34.0 1.0

Cadmium binding site 3 out of 9 in the Structure of CNAG_02591 From Cryptococcus Neoformans


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of CNAG_02591 From Cryptococcus Neoformans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd102 b:23.3 occ:0.50 CD A:CD102 0.0 23.3 0.5 OE1 A:GLU42 2.5 33.4 1.0 OD1 A:ASP35 2.6 27.3 1.0 OD2 A:ASP35 2.7 31.9 1.0 CD A:CD102 2.8 22.8 0.4 CG A:ASP35 3.0 24.9 1.0 NZ A:LYS46 3.3 23.9 0.5 CD A:GLU42 3.7 29.5 1.0 O A:HOH274 3.8 14.2 0.4 NZ A:LYS46 4.0 21.1 0.5 CE A:LYS46 4.0 19.7 0.5 O A:HOH265 4.2 32.8 1.0 O A:ILE36 4.4 18.2 1.0 CG A:GLU42 4.5 24.0 1.0 CB A:ASP35 4.5 19.6 1.0 OE2 A:GLU42 4.6 30.9 1.0 CE A:LYS46 4.8 23.4 0.5

Cadmium binding site 4 out of 9 in the Structure of CNAG_02591 From Cryptococcus Neoformans


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of CNAG_02591 From Cryptococcus Neoformans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd102 b:22.8 occ:0.40 CD A:CD102 0.0 22.8 0.4 O A:HOH274 1.8 14.2 0.4 OE1 A:GLU42 2.3 33.4 1.0 O A:ILE36 2.5 18.2 1.0 CD A:CD102 2.8 23.3 0.5 OE2 A:GLU42 3.0 30.9 1.0 CD A:GLU42 3.0 29.5 1.0 OD1 A:ASP35 3.6 27.3 1.0 C A:ILE36 3.6 14.7 1.0 O A:HOH265 3.7 32.8 1.0 CA A:VAL37 4.2 12.3 1.0 N A:VAL37 4.3 11.5 1.0 CG A:GLU42 4.4 24.0 1.0 CG A:ASP35 4.5 24.9 1.0 N A:ILE36 4.6 13.6 1.0 CA A:ILE36 4.7 13.2 1.0 N A:THR38 4.8 12.5 1.0 OD2 A:ASP35 4.8 31.9 1.0 C A:VAL37 5.0 14.0 1.0

Cadmium binding site 5 out of 9 in the Structure of CNAG_02591 From Cryptococcus Neoformans


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of CNAG_02591 From Cryptococcus Neoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd101 b:16.4 occ:0.50 OD1 B:ASN50 2.4 27.2 1.0 CG B:ASN50 3.4 21.5 1.0 ND2 B:ASN50 3.6 27.3 1.0 O B:PRO51 3.9 21.9 1.0 CB B:ASN50 4.8 19.7 1.0 O B:ASN50 4.9 19.5 1.0 C B:PRO51 5.0 18.5 1.0

Cadmium binding site 6 out of 9 in the Structure of CNAG_02591 From Cryptococcus Neoformans


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of CNAG_02591 From Cryptococcus Neoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd102 b:12.0 occ:0.80 O B:HOH213 2.0 17.6 0.8 O B:HOH211 2.2 18.4 0.8 NE2 B:HIS66 2.3 12.3 1.0 O B:HOH216 2.4 17.0 0.8 OG1 B:THR22 2.4 10.7 1.0 O B:HOH242 2.4 13.2 0.8 CE1 B:HIS66 3.2 11.0 1.0 CD2 B:HIS66 3.3 11.4 1.0 CB B:THR22 3.4 9.3 1.0 CG2 B:THR22 3.6 9.9 1.0 O3 B:SO4106 4.3 27.4 0.8 O4 B:SO4106 4.3 21.1 0.8 ND1 B:HIS66 4.3 11.4 1.0 O A:HOH250 4.3 34.5 1.0 CG B:HIS66 4.4 9.9 1.0 O B:HOH204 4.5 14.9 1.0 O B:PRO23 4.5 11.2 1.0 O B:HOH239 4.5 16.5 1.0 CA B:THR22 4.7 8.2 1.0 S B:SO4106 4.9 22.7 0.8 C B:THR22 5.0 9.4 1.0

Cadmium binding site 7 out of 9 in the Structure of CNAG_02591 From Cryptococcus Neoformans


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of CNAG_02591 From Cryptococcus Neoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd103 b:18.5 occ:0.70 O B:HOH272 2.1 30.3 0.7 OE2 B:GLU42 2.2 26.8 1.0 O B:HOH271 2.3 31.1 0.7 OD1 B:ASP35 2.3 23.1 1.0 OD2 B:ASP35 2.7 26.0 1.0 OE1 B:GLU42 2.7 24.9 1.0 CD B:GLU42 2.8 22.8 1.0 CG B:ASP35 2.9 18.3 1.0 O B:HOH254 3.0 11.0 0.7 O B:HOH257 4.0 26.9 1.0 O B:ILE36 4.2 16.7 1.0 CG B:GLU42 4.3 23.2 1.0 CB B:ASP35 4.4 14.0 1.0 NZ B:LYS46 4.6 32.6 1.0 CE B:LYS46 4.9 24.7 1.0 N B:ILE36 4.9 12.3 1.0 C B:ILE36 5.0 13.1 1.0

Cadmium binding site 8 out of 9 in the Structure of CNAG_02591 From Cryptococcus Neoformans


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of CNAG_02591 From Cryptococcus Neoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd104 b:14.7 occ:0.50 O B:HOH241 2.1 18.4 0.5 O A:HOH219 2.1 14.0 0.5 OD2 B:ASP63 2.1 17.9 1.0 OD1 B:ASP63 2.3 15.5 1.0 CG B:ASP63 2.6 15.0 1.0 OG1 B:THR57 3.9 11.5 1.0 OD2 A:ASP63 4.0 21.3 1.0 O B:HOH252 4.0 17.6 1.0 CB B:ASP63 4.1 13.7 1.0 O B:HOH205 4.1 29.9 1.0 O A:HOH222 4.2 24.0 1.0 CG A:ASP63 4.6 15.9 1.0 CA B:ASP63 5.0 11.7 1.0

Cadmium binding site 9 out of 9 in the Structure of CNAG_02591 From Cryptococcus Neoformans


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of CNAG_02591 From Cryptococcus Neoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd105 b:10.8 occ:1.00 OD1 B:ASP75 2.2 20.5 1.0 OG1 B:THR19 2.3 8.7 1.0 O B:HOH230 2.4 12.9 1.0 CG B:ASP75 2.9 15.9 1.0 OD2 B:ASP75 3.0 20.9 1.0 CB B:THR19 3.3 7.8 1.0 N B:THR19 4.2 8.8 1.0 O B:HOH203 4.2 10.0 1.0 CG2 B:THR19 4.3 9.4 1.0 CA B:THR19 4.3 8.6 1.0 CB B:ASP75 4.4 11.5 1.0 O B:HOH219 4.6 16.5 1.0 CA B:ASP75 5.0 12.3 1.0

E.E.Mcclelland, U.A.Ramagopal, S.C.Almo, A.Casadevall. Deletion of A Novel Gene Induces A Hyper Virulent Phenotype in Cryptococcus Neoformans To Be Published.