Cadmium in PDB 3nqi: Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution

The structure of Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution, PDB code: 3nqi was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.29 / 1.87
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.490, 77.227, 97.406, 90.00, 103.85, 90.00
R / Rfree (%)	19.1 / 22

The structure of Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

9 atoms

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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution (pdb code 3nqi). 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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution, PDB code: 3nqi:
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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution


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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd300 b:42.0 occ:0.50 OD2 A:ASP184 2.2 30.3 0.5 O A:ILE186 2.3 28.2 1.0 O A:HOH678 2.4 46.3 1.0 O A:HOH530 2.7 32.8 1.0 O A:HOH384 2.7 22.6 1.0 CG A:ASP184 2.8 23.4 0.5 OD1 A:ASP184 2.8 20.3 0.5 OD2 A:ASP184 3.4 24.3 0.5 C A:ILE186 3.4 25.0 1.0 CG A:ASP184 3.8 32.5 0.5 CB A:ASP184 4.1 28.9 0.5 CB A:ILE186 4.2 27.9 1.0 CB A:ASP184 4.2 28.3 0.5 N A:LYS188 4.2 23.9 1.0 CA A:ILE186 4.3 24.7 1.0 N A:LEU187 4.3 23.1 1.0 CA A:LEU187 4.4 22.1 1.0 N A:ILE186 4.5 26.5 1.0 OD1 A:ASP184 4.5 32.5 0.5 CB A:LYS188 4.6 24.7 1.0 CG2 A:ILE186 4.6 27.9 1.0 C A:LEU187 4.7 21.2 1.0 O A:HOH647 4.7 41.1 1.0 O A:ASP179 4.8 38.8 1.0

Cadmium binding site 2 out of 27 in the Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution


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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:31.9 occ:1.00 O A:HOH354 2.1 24.5 1.0 OD1 A:ASP97 2.2 27.9 1.0 O A:HOH496 2.4 35.6 1.0 O A:HOH347 2.5 22.4 1.0 CL A:CL328 2.5 34.0 1.0 O A:HOH356 2.5 23.4 1.0 CG A:ASP97 3.0 30.0 1.0 OD2 A:ASP97 3.2 37.7 1.0 O A:HOH566 3.5 41.3 1.0 OG1 A:THR65 4.2 34.6 1.0 O A:HOH590 4.2 42.9 1.0 O A:HOH353 4.4 25.5 1.0 O A:PRO98 4.5 27.4 1.0 N A:LEU66 4.5 29.6 1.0 CD A:PRO98 4.5 27.4 1.0 CB A:ASP97 4.5 29.0 1.0 N A:PRO98 4.8 26.7 1.0 CA A:LEU66 4.9 28.9 1.0 N A:THR65 4.9 28.9 1.0 CB A:LEU66 4.9 24.6 1.0

Cadmium binding site 3 out of 27 in the Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution


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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:29.0 occ:0.62 CD A:CD302 0.0 29.0 0.6 CD A:CD302 1.5 41.9 0.4 CL A:CL323 1.9 36.4 1.0 OE1 A:GLU160 2.5 33.7 1.0 OE2 A:GLU160 2.7 42.8 1.0 CD A:GLU160 3.0 36.8 1.0 CB A:THR158 4.3 40.5 1.0 CG A:GLU160 4.5 37.5 1.0 N A:THR159 4.6 37.5 1.0 O A:HOH415 4.7 30.9 1.0 CG2 A:THR158 4.8 35.5 1.0 N A:GLU160 4.8 30.4 1.0 OG1 A:THR158 5.0 32.6 1.0

Cadmium binding site 4 out of 27 in the Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution


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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:41.9 occ:0.38 CD A:CD302 0.0 41.9 0.4 CD A:CD302 1.5 29.0 0.6 OE2 A:GLU160 1.7 42.8 1.0 CD A:GLU160 2.4 36.8 1.0 OE1 A:GLU160 2.5 33.7 1.0 CL A:CL323 3.3 36.4 1.0 CG A:GLU160 3.8 37.5 1.0 O A:HOH415 4.4 30.9 1.0 CB A:GLU160 4.7 31.4 1.0

Cadmium binding site 5 out of 27 in the Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution


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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd307 b:29.8 occ:1.00 OE2 B:GLU223 2.0 29.0 1.0 O A:HOH489 2.2 33.3 1.0 OE1 A:GLU142 2.4 23.6 1.0 OE1 A:GLU267 2.5 34.1 1.0 OE2 A:GLU142 2.6 24.7 1.0 OE2 A:GLU267 2.6 52.8 1.0 CD B:GLU223 2.7 30.9 1.0 OE1 B:GLU223 2.8 49.9 1.0 CD A:GLU142 2.8 21.9 1.0 O B:HOH705 2.9 57.5 1.0 CD A:GLU267 2.9 52.1 1.0 CD1 B:LEU226 3.9 26.5 1.0 CG B:GLU223 4.1 36.0 1.0 NH1 B:ARG222 4.2 23.4 0.5 CG A:GLU142 4.3 21.7 1.0 CG A:GLU267 4.4 54.2 1.0 CB A:ALA266 4.5 40.0 1.0 N A:ALA266 4.6 36.1 1.0 NZ B:LYS227 4.9 56.6 1.0 N A:GLU267 4.9 51.5 1.0

Cadmium binding site 6 out of 27 in the Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution


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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd303 b:29.6 occ:1.00 O B:HOH412 1.9 29.1 1.0 OE2 A:GLU223 2.1 27.9 1.0 OE1 B:GLU142 2.4 24.4 1.0 OE1 B:GLU267 2.4 35.6 1.0 OE1 A:GLU223 2.6 49.0 1.0 OE2 B:GLU267 2.7 53.0 1.0 CD A:GLU223 2.7 27.9 1.0 OE2 B:GLU142 2.7 27.1 1.0 CD B:GLU142 2.9 24.6 1.0 CD B:GLU267 2.9 52.9 1.0 CG A:GLU223 4.1 34.6 1.0 CD1 A:LEU226 4.1 26.3 1.0 NH1 A:ARG222 4.2 21.8 0.5 CG B:GLU142 4.4 23.6 1.0 CG B:GLU267 4.5 54.4 1.0 CB B:ALA266 4.5 42.1 1.0 NH2 A:ARG222 4.5 33.1 0.5 N B:ALA266 4.6 36.9 1.0 N B:GLU267 4.9 51.7 1.0 CZ A:ARG222 4.9 25.3 0.5 CB B:THR265 4.9 27.2 1.0

Cadmium binding site 7 out of 27 in the Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution


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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd304 b:38.2 occ:0.50 O B:ILE186 2.3 27.5 1.0 O B:HOH674 2.3 45.9 1.0 OD2 B:ASP184 2.3 29.4 0.5 OD1 B:ASP184 2.7 23.3 0.5 O B:HOH397 2.8 24.2 1.0 CG B:ASP184 2.8 24.0 0.5 C B:ILE186 3.4 25.5 1.0 OD2 B:ASP184 3.4 27.9 0.5 CG B:ASP184 3.8 28.2 0.5 CB B:ASP184 4.1 28.8 0.5 CB B:ASP184 4.2 29.4 0.5 CA B:ILE186 4.2 26.1 0.5 CA B:ILE186 4.2 27.1 0.5 CB B:ILE186 4.3 28.6 0.5 N B:LEU187 4.3 24.1 1.0 CB B:ILE186 4.3 26.7 0.5 N B:LYS188 4.3 23.3 1.0 CA B:LEU187 4.4 23.7 1.0 N B:ILE186 4.4 26.2 1.0 OD1 B:ASP184 4.6 28.8 0.5 CG2 B:ILE186 4.7 23.6 0.5 CB B:LYS188 4.8 25.9 1.0 C B:LEU187 4.8 21.7 1.0 CG2 B:ILE186 4.9 26.0 0.5

Cadmium binding site 8 out of 27 in the Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution


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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd305 b:29.9 occ:1.00 O B:HOH357 2.2 23.5 1.0 OD1 B:ASP97 2.2 26.5 1.0 O B:HOH448 2.3 31.0 1.0 O B:HOH362 2.5 25.0 1.0 CL B:CL325 2.5 30.6 1.0 O B:HOH350 2.5 23.2 1.0 CG B:ASP97 3.1 28.5 1.0 OD2 B:ASP97 3.3 34.2 1.0 O B:HOH618 3.5 40.8 1.0 O B:HOH488 4.3 33.9 1.0 OG1 B:THR65 4.3 31.6 1.0 O B:PRO98 4.5 26.1 1.0 N B:LEU66 4.5 28.1 1.0 CB B:ASP97 4.6 28.4 1.0 CD B:PRO98 4.6 27.1 1.0 CA B:LEU66 4.9 27.4 1.0 N B:PRO98 4.9 26.4 1.0 N B:THR65 4.9 26.6 1.0

Cadmium binding site 9 out of 27 in the Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution


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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd306 b:42.4 occ:0.60 CD B:CD306 0.0 42.4 0.6 OXT B:ACT342 1.7 33.0 1.0 CD B:CD306 2.2 44.1 0.4 OE2 B:GLU160 2.3 57.3 1.0 OE1 B:GLU160 2.4 48.4 1.0 CD B:GLU160 2.7 49.2 1.0 C B:ACT342 2.9 45.0 1.0 O B:ACT342 3.3 51.4 1.0 CH3 B:ACT342 4.1 47.3 1.0 CG B:GLU160 4.1 50.7 1.0 CB B:THR158 4.5 53.1 1.0 N B:GLU160 4.9 43.3 1.0 CB B:GLU160 4.9 44.0 1.0 CG2 B:THR158 5.0 48.4 1.0

Cadmium binding site 10 out of 27 in the Crystal Structure of A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution


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 A Putative Lipoprotein (BF3042) From Bacteroides Fragilis Nctc 9343 at 1.87 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd306 b:44.1 occ:0.40 CD B:CD306 0.0 44.1 0.4 OE2 B:GLU160 1.9 57.3 1.0 CD B:CD306 2.2 42.4 0.6 CD B:GLU160 2.8 49.2 1.0 OE1 B:GLU160 3.4 48.4 1.0 CG B:GLU160 3.9 50.7 1.0 OXT B:ACT342 3.9 33.0 1.0 CB B:GLU160 5.0 44.0 1.0

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.