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Cadmium in PDB 5tk2: Crystal Structure of Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis

Protein crystallography data

The structure of Crystal Structure of Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis, PDB code: 5tk2 was solved by Y.Kim, N.Maltseva, S.Shatsman, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.25 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.226, 58.023, 108.796, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 16.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis (pdb code 5tk2). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis, PDB code: 5tk2:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 5tk2

Go back to Cadmium Binding Sites List in 5tk2
Cadmium binding site 1 out of 4 in the Crystal Structure of Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis


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 Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:13.1
occ:0.90
O A:HOH340 2.4 15.3 1.0
NE2 A:HIS116 2.4 15.0 1.0
ND1 A:HIS78 2.4 14.2 1.0
SG A:CYS113 2.5 13.2 1.0
SE A:MSE121 2.9 17.1 0.9
CE1 A:HIS78 3.2 16.1 1.0
CD2 A:HIS116 3.3 14.9 1.0
CB A:CYS113 3.3 12.5 1.0
CE1 A:HIS116 3.4 14.3 1.0
CG A:HIS78 3.5 14.1 1.0
CB A:HIS78 3.8 13.8 1.0
CE A:MSE121 4.0 17.3 1.0
CA A:HIS78 4.0 12.1 1.0
O A:GLU77 4.1 16.6 0.6
O A:GLU77 4.1 16.6 0.4
CG A:MSE121 4.3 18.2 1.0
NE2 A:HIS78 4.4 15.2 1.0
O A:HOH392 4.4 23.3 1.0
ND1 A:HIS116 4.4 13.6 1.0
CG A:HIS116 4.4 13.4 1.0
CB A:TYR115 4.4 12.2 1.0
CB A:MSE121 4.5 16.4 1.0
CD2 A:HIS78 4.5 15.8 1.0
OD2 A:ASP51 4.5 18.1 1.0
CA A:CYS113 4.7 11.3 1.0
N A:THR79 4.7 14.7 1.0
CD2 A:TYR115 4.8 11.0 1.0
CG A:ASP51 4.9 15.3 1.0
N A:TYR115 4.9 12.4 1.0
O A:TYR115 5.0 13.1 1.0
C A:GLU77 5.0 15.0 0.6
C A:GLU77 5.0 15.0 0.4

Cadmium binding site 2 out of 4 in 5tk2

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Cadmium binding site 2 out of 4 in the Crystal Structure of Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis


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 Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:13.6
occ:0.90
NE2 B:HIS116 2.4 13.1 1.0
O B:HOH311 2.4 13.4 1.0
ND1 B:HIS78 2.4 12.7 1.0
SG B:CYS113 2.5 14.2 1.0
SE B:MSE121 3.1 22.5 0.8
CE1 B:HIS78 3.2 14.3 1.0
CB B:CYS113 3.2 13.2 1.0
CE1 B:HIS116 3.3 14.3 1.0
CD2 B:HIS116 3.3 13.8 1.0
CG B:HIS78 3.5 13.2 1.0
CE B:MSE121 3.9 18.0 1.0
CB B:HIS78 3.9 13.3 1.0
CA B:HIS78 4.0 12.3 1.0
O B:GLU77 4.1 15.4 0.4
O B:GLU77 4.1 15.3 0.6
O B:HOH335 4.3 17.2 1.0
NE2 B:HIS78 4.4 13.8 1.0
CG B:MSE121 4.4 18.6 1.0
ND1 B:HIS116 4.4 15.5 1.0
OD2 B:ASP51 4.4 18.0 1.0
CG B:HIS116 4.4 13.7 1.0
CB B:TYR115 4.5 14.7 1.0
CB B:MSE121 4.5 17.8 1.0
CD2 B:HIS78 4.5 13.8 1.0
CA B:CYS113 4.7 13.7 1.0
N B:THR79 4.8 12.8 1.0
N B:TYR115 5.0 13.8 1.0
CG B:ASP51 5.0 18.1 1.0
C B:GLU77 5.0 14.4 0.4
C B:HIS78 5.0 12.0 1.0
C B:GLU77 5.0 14.3 0.6

Cadmium binding site 3 out of 4 in 5tk2

Go back to Cadmium Binding Sites List in 5tk2
Cadmium binding site 3 out of 4 in the Crystal Structure of Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis


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 Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd201

b:13.2
occ:0.90
O C:HOH342 2.3 16.1 1.0
ND1 C:HIS78 2.3 12.2 1.0
NE2 C:HIS116 2.3 12.7 1.0
SG C:CYS113 2.5 12.3 1.0
SE C:MSE121 3.0 18.6 0.8
CD2 C:HIS116 3.1 13.6 1.0
CE1 C:HIS78 3.2 12.8 1.0
CB C:CYS113 3.2 14.2 1.0
CG C:HIS78 3.4 13.2 1.0
CE1 C:HIS116 3.4 15.0 1.0
CB C:HIS78 3.7 12.7 1.0
CE C:MSE121 3.8 16.6 1.0
CA C:HIS78 4.0 14.4 1.0
O C:GLU77 4.2 13.7 1.0
CG C:MSE121 4.2 17.7 1.0
CB C:TYR115 4.3 13.1 1.0
CG C:HIS116 4.3 14.4 1.0
NE2 C:HIS78 4.3 14.7 1.0
CB C:MSE121 4.4 17.2 1.0
O C:HOH327 4.4 18.0 1.0
CD2 C:HIS78 4.5 13.8 1.0
ND1 C:HIS116 4.5 14.2 1.0
CA C:CYS113 4.7 12.4 1.0
OD2 C:ASP51 4.7 18.8 1.0
N C:THR79 4.7 14.2 1.0
CD2 C:TYR115 4.8 13.7 1.0
N C:TYR115 4.9 13.9 1.0
C C:HIS78 4.9 14.6 1.0
CG C:ASP51 5.0 16.9 1.0
N C:HIS78 5.0 15.1 1.0
C C:GLU77 5.0 13.9 1.0
CA C:TYR115 5.0 12.1 1.0

Cadmium binding site 4 out of 4 in 5tk2

Go back to Cadmium Binding Sites List in 5tk2
Cadmium binding site 4 out of 4 in the Crystal Structure of Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis


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 Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd201

b:13.5
occ:0.90
ND1 D:HIS78 2.3 16.6 1.0
NE2 D:HIS116 2.3 13.3 1.0
SG D:CYS113 2.5 12.0 1.0
O D:HOH326 2.5 15.6 1.0
SE D:MSE121 2.8 17.0 1.0
CD2 D:HIS116 3.1 14.0 1.0
CE1 D:HIS78 3.2 15.4 1.0
CB D:CYS113 3.3 14.3 1.0
CG D:HIS78 3.4 14.3 1.0
CE1 D:HIS116 3.5 15.0 1.0
CB D:HIS78 3.8 11.9 1.0
CE D:MSE121 3.9 15.3 1.0
CA D:HIS78 4.0 11.3 1.0
CG D:MSE121 4.0 13.2 1.0
O D:GLU77 4.2 13.7 1.0
CG D:HIS116 4.3 13.4 1.0
NE2 D:HIS78 4.4 15.6 1.0
CB D:TYR115 4.5 14.3 1.0
ND1 D:HIS116 4.5 16.6 1.0
CD2 D:HIS78 4.5 15.2 1.0
OD2 D:ASP51 4.6 20.2 1.0
O D:HOH327 4.7 18.2 1.0
N D:THR79 4.7 12.1 1.0
CA D:CYS113 4.7 14.5 1.0
C D:HIS78 4.9 12.4 1.0
N D:HIS78 5.0 13.8 1.0
N D:TYR115 5.0 12.8 1.0
C D:GLU77 5.0 13.1 1.0

Reference:

Y.Kim, N.Maltseva, S.Shatsman, W.F.Anderson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Uncharacterized Cupredoxin-Like Domain Protein From Bacillus Anthracis To Be Published.
Page generated: Sat Dec 12 08:27:40 2020

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