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

Protein crystallography data

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

Other elements in 3nqi:

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

Cadmium Binding Sites:

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 3nqi

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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 3nqi

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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 3nqi

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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 3nqi

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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 3nqi

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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 3nqi

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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 3nqi

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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 3nqi

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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 3nqi

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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 3nqi

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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

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Thu Jul 10 12:48:12 2025

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