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Cadmium in PDB 7y74: Apostichopus Japonicus Ferritin Mutant-D129A/E132A

Enzymatic activity of Apostichopus Japonicus Ferritin Mutant-D129A/E132A

All present enzymatic activity of Apostichopus Japonicus Ferritin Mutant-D129A/E132A:
1.16.3.1;

Protein crystallography data

The structure of Apostichopus Japonicus Ferritin Mutant-D129A/E132A, PDB code: 7y74 was solved by Y.Wu, T.H.Ming, X.R.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.91 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.83, 130.95, 122.62, 90, 119.4, 90
R / Rfree (%) 17.6 / 22

Other elements in 7y74:

The structure of Apostichopus Japonicus Ferritin Mutant-D129A/E132A also contains other interesting chemical elements:

Iron (Fe) 36 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Cadmium atom in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A (pdb code 7y74). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 12 binding sites of Cadmium where determined in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A, PDB code: 7y74:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 12 in 7y74

Go back to Cadmium Binding Sites List in 7y74
Cadmium binding site 1 out of 12 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:36.9
occ:0.70
 CE1 A:HIS116 2.3 30.4 1.0
OD1 A:ASP120 2.4 42.1 1.0
SG A:CYS128 2.4 43.0 1.0
OD2 A:ASP120 2.7 48.6 1.0
NE2 A:HIS116 2.8 29.7 1.0
CG A:ASP120 2.9 41.3 1.0
O H:HOH425 3.4 42.9 1.0
ND1 A:HIS116 3.4 32.1 1.0
CB A:CYS128 3.5 34.9 1.0
O A:HOH435 3.6 27.2 1.0
O H:HOH340 4.0 45.0 1.0
CD2 A:HIS116 4.1 30.7 1.0
CG A:HIS116 4.3 29.5 1.0
CB A:ASP120 4.4 35.4 1.0
CA A:CYS128 4.5 32.2 1.0

Cadmium binding site 2 out of 12 in 7y74

Go back to Cadmium Binding Sites List in 7y74
Cadmium binding site 2 out of 12 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd204

b:31.1
occ:0.70
 CE1 B:HIS116 2.3 28.0 1.0
SG B:CYS128 2.3 39.5 1.0
OD2 B:ASP120 2.4 37.8 1.0
OD1 B:ASP120 2.5 36.7 1.0
CG B:ASP120 2.8 35.9 1.0
NE2 B:HIS116 2.8 28.8 1.0
CB B:CYS128 3.4 31.2 1.0
ND1 B:HIS116 3.4 31.6 1.0
CD2 B:HIS116 4.1 28.4 1.0
O I:HOH435 4.2 19.0 1.0
CB B:ASP120 4.3 31.5 1.0
CG B:HIS116 4.4 27.9 1.0
CA B:CYS128 4.6 27.6 1.0
O I:HOH410 4.9 39.6 1.0

Cadmium binding site 3 out of 12 in 7y74

Go back to Cadmium Binding Sites List in 7y74
Cadmium binding site 3 out of 12 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd204

b:29.0
occ:0.60
 SG C:CYS128 2.3 43.5 1.0
CE1 C:HIS116 2.4 31.6 1.0
OD1 C:ASP120 2.4 38.4 1.0
OD2 C:ASP120 2.5 40.1 1.0
CG C:ASP120 2.8 37.3 1.0
NE2 C:HIS116 2.9 30.2 1.0
CB C:CYS128 3.4 30.6 1.0
ND1 C:HIS116 3.5 34.8 1.0
CD2 C:HIS116 4.1 32.1 1.0
CB C:ASP120 4.3 31.1 1.0
CG C:HIS116 4.4 31.3 1.0
CA C:CYS128 4.5 28.9 1.0
O C:HIS116 5.0 28.4 1.0

Cadmium binding site 4 out of 12 in 7y74

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Cadmium binding site 4 out of 12 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd204

b:32.3
occ:0.70
 CE1 D:HIS116 2.4 31.8 1.0
SG D:CYS128 2.4 40.6 1.0
OD2 D:ASP120 2.5 49.6 1.0
OD1 D:ASP120 2.5 43.5 1.0
NE2 D:HIS116 2.7 30.9 1.0
CG D:ASP120 2.8 44.5 1.0
CB D:CYS128 3.4 31.9 1.0
ND1 D:HIS116 3.5 32.3 1.0
CD2 D:HIS116 4.0 29.5 1.0
CB D:ASP120 4.3 37.5 1.0
CG D:HIS116 4.4 29.0 1.0
CA D:CYS128 4.6 30.2 1.0

Cadmium binding site 5 out of 12 in 7y74

Go back to Cadmium Binding Sites List in 7y74
Cadmium binding site 5 out of 12 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd204

b:28.7
occ:0.60
 SG E:CYS128 2.2 44.7 1.0
CE1 E:HIS116 2.4 32.7 1.0
OD2 E:ASP120 2.5 42.2 1.0
OD1 E:ASP120 2.6 45.9 1.0
NE2 E:HIS116 2.7 30.2 1.0
CG E:ASP120 2.9 38.2 1.0
CB E:CYS128 3.3 34.3 1.0
ND1 E:HIS116 3.6 32.3 1.0
CD2 E:HIS116 4.0 29.3 1.0
CB E:ASP120 4.4 35.3 1.0
CG E:HIS116 4.4 26.7 1.0
CA E:CYS128 4.5 29.6 1.0

Cadmium binding site 6 out of 12 in 7y74

Go back to Cadmium Binding Sites List in 7y74
Cadmium binding site 6 out of 12 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cd204

b:32.1
occ:0.60
 CE1 F:HIS116 2.3 35.6 1.0
SG F:CYS128 2.4 49.7 1.0
OD1 F:ASP120 2.5 40.9 1.0
OD2 F:ASP120 2.5 42.8 1.0
NE2 F:HIS116 2.6 33.6 1.0
CG F:ASP120 2.8 41.5 1.0
CB F:CYS128 3.4 41.2 1.0
ND1 F:HIS116 3.5 34.3 1.0
CD2 F:HIS116 3.9 30.4 1.0
CG F:HIS116 4.3 30.7 1.0
CB F:ASP120 4.3 37.7 1.0
CA F:CYS128 4.6 32.9 1.0

Cadmium binding site 7 out of 12 in 7y74

Go back to Cadmium Binding Sites List in 7y74
Cadmium binding site 7 out of 12 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cd204

b:34.4
occ:0.70
 CE1 G:HIS116 2.3 33.8 1.0
OD1 G:ASP120 2.4 42.0 1.0
SG G:CYS128 2.4 40.8 1.0
OD2 G:ASP120 2.7 44.2 1.0
NE2 G:HIS116 2.8 33.8 1.0
O G:HOH311 2.8 45.2 1.0
CG G:ASP120 2.9 40.0 1.0
ND1 G:HIS116 3.4 35.2 1.0
CB G:CYS128 3.5 32.1 1.0
CD2 G:HIS116 4.1 31.3 1.0
CG G:HIS116 4.3 33.8 1.0
CB G:ASP120 4.4 37.4 1.0
CA G:CYS128 4.6 25.5 1.0

Cadmium binding site 8 out of 12 in 7y74

Go back to Cadmium Binding Sites List in 7y74
Cadmium binding site 8 out of 12 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cd204

b:37.5
occ:0.70
 SG H:CYS128 2.4 47.4 1.0
CE1 H:HIS116 2.4 34.9 1.0
OD1 H:ASP120 2.5 39.5 1.0
OD2 H:ASP120 2.6 39.5 1.0
NE2 H:HIS116 2.8 32.5 1.0
CG H:ASP120 2.9 41.3 1.0
O H:HOH340 2.9 45.0 1.0
O J:HOH389 3.2 52.5 1.0
CB H:CYS128 3.4 36.1 1.0
O H:HOH425 3.4 42.9 1.0
ND1 H:HIS116 3.5 34.1 1.0
CD2 H:HIS116 4.0 31.4 1.0
CG H:HIS116 4.4 33.4 1.0
CB H:ASP120 4.4 32.7 1.0
CA H:CYS128 4.5 30.9 1.0
O H:HIS116 5.0 28.5 1.0

Cadmium binding site 9 out of 12 in 7y74

Go back to Cadmium Binding Sites List in 7y74
Cadmium binding site 9 out of 12 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cd204

b:26.4
occ:0.60
 OD2 I:ASP120 2.2 46.9 1.0
CE1 I:HIS116 2.4 29.3 1.0
SG I:CYS128 2.4 38.5 1.0
OD1 I:ASP120 2.5 45.9 1.0
NE2 I:HIS116 2.6 26.6 1.0
CG I:ASP120 2.7 40.8 1.0
CB I:CYS128 3.4 30.2 1.0
ND1 I:HIS116 3.5 33.1 1.0
O I:HOH435 3.6 19.0 1.0
CD2 I:HIS116 3.9 28.3 1.0
CB I:ASP120 4.2 35.8 1.0
CG I:HIS116 4.4 27.5 1.0
CA I:CYS128 4.6 25.2 1.0
O I:HOH410 4.9 39.6 1.0

Cadmium binding site 10 out of 12 in 7y74

Go back to Cadmium Binding Sites List in 7y74
Cadmium binding site 10 out of 12 in the Apostichopus Japonicus Ferritin Mutant-D129A/E132A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Apostichopus Japonicus Ferritin Mutant-D129A/E132A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cd204

b:34.9
occ:0.70
 SG J:CYS128 2.4 43.9 1.0
CE1 J:HIS116 2.4 33.9 1.0
NE2 J:HIS116 2.5 34.1 1.0
OD1 J:ASP120 2.6 42.5 1.0
OD2 J:ASP120 2.6 50.8 1.0
CG J:ASP120 2.9 43.6 1.0
CB J:CYS128 3.4 32.1 1.0
O H:HOH425 3.5 42.9 1.0
O J:HOH389 3.6 52.5 1.0
ND1 J:HIS116 3.6 35.1 1.0
O A:HOH435 3.7 27.2 1.0
CD2 J:HIS116 3.8 32.8 1.0
CG J:HIS116 4.3 32.3 1.0
CB J:ASP120 4.4 39.0 1.0
CA J:CYS128 4.5 29.5 1.0

Reference:

Y.Wu, Y.Wu, T.H.Ming, X.R.Su. N/A N/A.
Page generated: Wed Jul 26 13:50:10 2023

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