Cadmium in PDB 8zn8: Mjf-3C-Cds Qds

All present enzymatic activity of Mjf-3C-Cds Qds:
1.16.3.1;

The structure of Mjf-3C-Cds Qds, PDB code: 8zn8 was solved by M.P.Duan, T.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.81 / 2.25
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	126.748, 126.748, 177.949, 90, 90, 90
R / Rfree (%)	16.6 / 20.7

The structure of Mjf-3C-Cds Qds also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Cadmium atom in the Mjf-3C-Cds Qds (pdb code 8zn8). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 24 binding sites of Cadmium where determined in the Mjf-3C-Cds Qds, PDB code: 8zn8:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 24 in the Mjf-3C-Cds Qds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Mjf-3C-Cds Qds within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:44.8 occ:0.72 S A:H2S206 2.6 58.1 0.7 SG A:CYS24 2.8 52.7 1.0 SG A:CYS59 2.9 47.1 1.0 CD2 A:HIS62 2.9 46.4 1.0 CD A:CD204 3.4 73.2 0.3 CG A:HIS62 3.6 46.9 1.0 CB A:CYS59 3.6 34.4 1.0 CA A:CYS59 3.7 35.7 1.0 CB A:CYS24 3.8 35.6 1.0 CB A:HIS62 3.8 38.6 1.0 NE2 A:HIS62 4.0 56.8 1.0 CA A:CYS24 4.3 32.2 1.0 NE2 A:GLN138 4.3 48.4 1.0 O A:CYS59 4.4 35.5 1.0 CG1 A:VAL107 4.5 41.7 1.0 C A:CYS59 4.6 39.2 1.0 N A:CYS59 4.7 34.0 1.0 CB A:ALA27 4.9 29.8 1.0 ND1 A:HIS62 4.9 47.1 1.0 O A:CYS24 4.9 30.9 1.0

Cadmium binding site 2 out of 24 in the Mjf-3C-Cds Qds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Mjf-3C-Cds Qds within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:71.6 occ:0.64 S A:H2S207 2.7 64.3 0.7 S A:H2S205 2.8 86.0 1.0 S A:H2S209 2.8 55.1 0.7 SG A:CYS58 3.0 67.7 1.0 CD A:CD203 3.5 61.0 0.4 S A:H2S210 3.6 57.6 0.4 O A:HOH359 3.6 51.3 1.0 CB A:CYS58 3.7 39.8 1.0 OG A:SER141 3.8 50.0 1.0 OE1 A:GLU137 4.2 66.3 1.0 CD A:CD204 4.3 73.2 0.3 S A:H2S208 4.9 75.4 0.9

Cadmium binding site 3 out of 24 in the Mjf-3C-Cds Qds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Mjf-3C-Cds Qds within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:61.0 occ:0.40 S A:H2S208 2.5 75.4 0.9 SG A:CYS58 2.8 67.7 1.0 S A:H2S205 2.9 86.0 1.0 CB A:CYS58 3.5 39.8 1.0 CD A:CD202 3.5 71.6 0.6 CE1 A:HIS62 3.9 50.6 1.0 CA A:CYS58 4.2 39.5 1.0 NE2 A:HIS62 4.4 56.8 1.0 O A:CYS58 4.7 36.5 1.0 ND1 A:HIS62 4.8 47.1 1.0 C A:CYS58 4.8 37.6 1.0 OE1 A:GLU137 4.9 66.3 1.0

Cadmium binding site 4 out of 24 in the Mjf-3C-Cds Qds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Mjf-3C-Cds Qds within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:73.2 occ:0.35 S A:H2S206 2.8 58.1 0.7 SG A:CYS59 3.0 47.1 1.0 SG A:CYS58 3.1 67.7 1.0 S A:H2S210 3.2 57.6 0.4 NE2 A:HIS62 3.3 56.8 1.0 CD2 A:HIS62 3.4 46.4 1.0 S A:H2S207 3.4 64.3 0.7 CD A:CD201 3.4 44.8 0.7 OE2 A:GLU104 3.9 52.6 1.0 N A:CYS59 3.9 34.0 1.0 CA A:CYS59 4.1 35.7 1.0 CB A:CYS58 4.1 39.8 1.0 CB A:CYS59 4.2 34.4 1.0 OE1 A:GLU137 4.2 66.3 1.0 NE2 A:GLN138 4.2 48.4 1.0 OE1 A:GLU104 4.2 61.9 1.0 C A:CYS58 4.3 37.6 1.0 CD A:CD202 4.3 71.6 0.6 O A:SER55 4.4 36.1 1.0 CD A:GLU104 4.5 51.9 1.0 CE1 A:HIS62 4.5 50.6 1.0 CG A:HIS62 4.6 46.9 1.0 O A:CYS58 4.7 36.5 1.0 OE2 A:GLU137 4.8 61.9 1.0 CA A:CYS58 4.9 39.5 1.0 CD A:GLU137 4.9 62.3 1.0

Cadmium binding site 5 out of 24 in the Mjf-3C-Cds Qds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Mjf-3C-Cds Qds within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd201 b:47.1 occ:0.80 S B:H2S205 2.6 60.6 0.7 O B:HOH331 2.7 61.0 1.0 SG B:CYS59 2.9 47.5 1.0 SG B:CYS24 2.9 52.0 1.0 ND1 B:HIS62 3.0 47.8 1.0 CB B:CYS59 3.5 31.6 1.0 CA B:CYS59 3.6 34.5 1.0 CB B:CYS24 3.8 36.8 1.0 CG B:HIS62 3.8 45.9 1.0 CB B:HIS62 3.9 41.1 1.0 CE1 B:HIS62 3.9 58.6 1.0 CA B:CYS24 4.3 29.4 1.0 O B:CYS59 4.4 35.8 1.0 CG1 B:VAL107 4.5 34.8 1.0 C B:CYS59 4.5 36.2 1.0 N B:CYS59 4.7 34.7 1.0 CD B:CD204 4.8 64.0 0.2 CB B:ALA27 4.9 29.4 1.0 O B:CYS24 4.9 32.1 1.0 OE1 B:GLU104 5.0 53.1 1.0 OE1 B:GLN138 5.0 45.9 1.0 CG2 B:VAL107 5.0 35.1 1.0

Cadmium binding site 6 out of 24 in the Mjf-3C-Cds Qds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Mjf-3C-Cds Qds within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd202 b:79.8 occ:0.65 S B:H2S208 2.2 60.8 0.8 SG B:CYS58 3.0 60.1 1.0 S B:H2S206 3.0 82.7 1.0 CD B:CD203 3.4 74.6 0.5 OE2 B:GLU137 3.6 69.3 1.0 CB B:CYS58 3.6 32.9 1.0 OG B:SER141 3.8 52.4 1.0 S B:H2S207 4.0 71.6 0.9 CD B:CD204 4.1 64.0 0.2 CD B:GLU137 4.7 70.0 1.0

Cadmium binding site 7 out of 24 in the Mjf-3C-Cds Qds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Mjf-3C-Cds Qds within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd203 b:74.6 occ:0.52 OE2 B:GLU137 2.6 69.3 1.0 SG B:CYS58 3.0 60.1 1.0 S B:H2S209 3.0 75.0 0.9 S B:H2S206 3.1 82.7 1.0 CB B:CYS58 3.4 32.9 1.0 CD B:CD202 3.4 79.8 0.7 CD B:GLU137 3.6 70.0 1.0 OE1 B:GLU137 4.0 70.4 1.0 CA B:CYS58 4.1 36.0 1.0 NE2 B:HIS62 4.3 58.6 1.0 O B:CYS58 4.8 32.9 1.0 C B:CYS58 4.8 34.8 1.0 CE1 B:HIS62 4.9 58.6 1.0 CG B:GLU137 4.9 61.5 1.0

Cadmium binding site 8 out of 24 in the Mjf-3C-Cds Qds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Mjf-3C-Cds Qds within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd204 b:64.0 occ:0.25 S B:H2S208 2.4 60.8 0.8 O B:HOH331 2.6 61.0 1.0 OE2 B:GLU104 3.1 61.4 1.0 SG B:CYS59 3.1 47.5 1.0 SG B:CYS58 3.4 60.1 1.0 O B:SER55 3.4 33.3 1.0 S B:H2S207 3.8 71.6 0.9 CE2 B:TYR31 3.9 36.6 1.0 CB B:CYS58 3.9 32.9 1.0 S B:H2S205 4.0 60.6 0.7 CA B:SER55 4.1 35.8 1.0 N B:CYS59 4.1 34.7 1.0 CD B:CD202 4.1 79.8 0.7 C B:SER55 4.1 34.5 1.0 CB B:SER55 4.2 34.4 1.0 CD B:GLU104 4.2 52.2 1.0 CB B:CYS59 4.4 31.6 1.0 CD2 B:TYR31 4.5 33.3 1.0 OG B:SER55 4.5 37.4 1.0 OE1 B:GLU104 4.5 53.1 1.0 CA B:CYS59 4.6 34.5 1.0 C B:CYS58 4.6 34.8 1.0 CZ B:TYR31 4.7 42.4 1.0 CD B:CD201 4.8 47.1 0.8 OH B:TYR31 4.8 46.8 1.0 CA B:CYS58 4.9 36.0 1.0 CE1 B:HIS62 4.9 58.6 1.0

Cadmium binding site 9 out of 24 in the Mjf-3C-Cds Qds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Mjf-3C-Cds Qds within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd201 b:45.7 occ:0.77 S C:H2S207 2.5 57.8 0.7 SG C:CYS59 2.9 43.2 1.0 SG C:CYS24 2.9 50.2 1.0 CD2 C:HIS62 3.1 41.6 1.0 CB C:CYS59 3.6 35.2 1.0 CA C:CYS59 3.7 37.2 1.0 CB C:CYS24 3.7 32.0 1.0 CG C:HIS62 3.8 48.3 1.0 CB C:HIS62 3.8 38.3 1.0 CD C:CD204 4.0 63.8 0.3 CA C:CYS24 4.2 32.8 1.0 NE2 C:HIS62 4.3 55.1 1.0 O C:CYS59 4.4 36.6 1.0 C C:CYS59 4.6 39.2 1.0 CG1 C:VAL107 4.6 36.8 1.0 N C:CYS59 4.7 38.4 1.0 CB C:ALA27 4.8 32.9 1.0 O C:CYS24 4.8 32.1 1.0 OE1 C:GLN138 4.9 38.0 1.0 OE2 C:GLU104 5.0 53.2 1.0

Cadmium binding site 10 out of 24 in the Mjf-3C-Cds Qds


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Mjf-3C-Cds Qds within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd202 b:76.6 occ:0.68 S C:H2S208 2.8 63.9 0.8 S C:H2S209 2.9 61.4 0.7 SG C:CYS58 3.0 64.7 1.0 S C:H2S205 3.3 92.4 1.0 OE1 C:GLU137 3.5 76.3 1.0 CB C:CYS58 3.5 34.8 1.0 CD C:CD203 3.5 70.8 0.5 O C:HOH359 3.7 52.8 1.0 OG C:SER141 3.7 42.6 0.6 S C:H2S206 4.0 62.6 0.9 CD C:CD204 4.1 63.8 0.3 O C:HOH306 4.2 46.8 1.0 CD C:GLU137 4.7 78.0 1.0 CB C:SER141 5.0 39.1 0.4 CA C:CYS58 5.0 42.7 1.0

M.P.Duan, T.Zhang. Construction of An Artificial Photosynthesis System By Incorporation of Cds Quantum Dots Into the Intrasubunit Interface of A Four-Helix-Bundle-Structure Enzyme To Be Published.