Cadmium in PDB 7ryw: Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose

The structure of Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose, PDB code: 7ryw was solved by S.Aditya, R.Priyadharshine, I.Maham, D.J.Miller, V.Stojanoff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.70 / 2.09
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.507, 181.507, 181.507, 90, 90, 90
R / Rfree (%)	17 / 19.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose (pdb code 7ryw). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose, PDB code: 7ryw:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose


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 Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:29.5 occ:0.50 OD2 A:ASP80 2.4 25.0 1.0 OD1 A:ASP80 2.6 26.3 1.0 CD A:CD204 2.6 36.6 0.3 CG A:ASP80 2.8 26.5 1.0 CD A:CD207 4.3 60.8 0.3 CB A:ASP80 4.3 22.9 1.0

Cadmium binding site 2 out of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose


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 Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:68.0 occ:0.30 OE1 A:GLU130 2.7 50.5 1.0 OE2 A:GLU130 3.5 41.7 1.0 CD A:GLU130 3.5 41.6 1.0 CD A:CD203 3.8 93.7 0.2 CG A:GLU130 4.9 37.0 1.0

Cadmium binding site 3 out of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose


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 Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:93.7 occ:0.18 OD1 A:ASP127 3.1 55.4 1.0 OE1 A:GLU130 3.6 50.5 1.0 CD A:CD202 3.8 68.0 0.3 CG A:ASP127 4.4 45.5 1.0 CD A:GLU130 4.8 41.6 1.0 OG A:SER131 4.8 62.3 1.0 CB A:GLU130 4.9 38.0 1.0

Cadmium binding site 4 out of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose


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 Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:36.6 occ:0.31 CD A:CD201 2.6 29.5 0.5 CD A:CD207 3.4 60.8 0.3 OD2 A:ASP80 3.7 25.0 1.0 OD1 A:ASP80 4.1 26.3 1.0 CG A:ASP80 4.3 26.5 1.0

Cadmium binding site 5 out of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose


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 Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:88.2 occ:0.46 OE1 A:GLU56 2.9 69.1 1.0 O A:HOH372 3.2 64.8 1.0 OE1 A:GLU53 3.2 71.9 1.0 CD A:GLU56 3.6 64.8 1.0 OE2 A:GLU56 3.8 65.3 1.0 OE2 A:GLU53 3.9 76.0 1.0 CD A:GLU53 4.0 65.5 1.0 CG A:GLU56 4.9 46.4 1.0

Cadmium binding site 6 out of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose


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 Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:78.4 occ:0.41 OE2 A:GLU60 2.8 56.9 1.0 OE2 A:GLU56 2.9 65.3 1.0 OE1 A:GLU60 2.9 60.0 1.0 CD A:CD209 3.0 92.2 0.4 CD A:GLU60 3.2 58.3 1.0 OE2 A:GLU57 3.2 72.4 1.0 O A:HOH390 3.3 65.4 1.0 CD A:GLU56 3.7 64.8 1.0 CG A:GLU56 3.9 46.4 1.0 CD A:GLU57 4.3 67.0 1.0 CG A:GLU60 4.7 44.2 1.0 OE1 A:GLU56 4.7 69.1 1.0 OE1 A:GLU57 4.8 74.5 1.0

Cadmium binding site 7 out of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose


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 Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:60.8 occ:0.26 OE1 A:GLN79 2.9 47.2 1.0 N A:ASP80 3.0 26.2 1.0 OD2 A:ASP80 3.3 25.0 1.0 CD A:CD204 3.4 36.6 0.3 CG A:ASP80 3.4 26.5 1.0 CB A:GLN79 3.5 29.0 1.0 CA A:GLN79 3.5 26.5 1.0 OD1 A:ASP80 3.7 26.3 1.0 C A:GLN79 3.7 23.9 1.0 CB A:ASP80 3.8 22.9 1.0 CD A:GLN79 3.9 49.9 1.0 CA A:ASP80 4.0 23.4 1.0 CD A:CD201 4.3 29.5 0.5 CG A:GLN79 4.3 36.3 1.0 N A:GLN79 4.9 24.9 1.0 O A:GLN79 5.0 20.5 1.0

Cadmium binding site 8 out of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose


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 Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:104.1 occ:0.56 SG A:CYS126 3.2 40.0 1.0 O A:HOH396 3.2 44.5 1.0 CB A:CYS126 3.5 30.7 1.0 CA A:PRO123 4.4 29.4 1.0 CA A:SER118 4.4 34.7 1.0 CB A:SER118 4.5 41.1 1.0 OG A:SER118 4.7 48.6 1.0 CB A:PRO123 4.8 30.7 1.0 CE1 A:HIS114 4.8 31.3 1.0 O A:ASP122 5.0 30.9 1.0 N A:PRO123 5.0 30.2 1.0 N A:SER118 5.0 36.0 1.0

Cadmium binding site 9 out of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose


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 Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd209 b:92.2 occ:0.39 OE2 A:GLU60 2.8 56.9 1.0 O A:HOH390 2.9 65.4 1.0 OE2 A:GLU57 3.0 72.4 1.0 OE1 A:GLU57 3.0 74.5 1.0 CD A:CD206 3.0 78.4 0.4 CD A:GLU57 3.4 67.0 1.0 CD A:GLU60 4.0 58.3 1.0 OE1 A:GLU60 4.6 60.0 1.0 NH1 A:ARG64 4.6 67.0 1.0 CG A:GLU57 4.9 44.2 1.0 CB A:GLU60 5.0 30.0 1.0

Cadmium binding site 10 out of 13 in the Crystal Structure of Ferritin Grown By the Microbatch Method in the Presence of Agarose


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 Ferritin Grown By the Microbatch Method in the Presence of Agarose within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd210 b:78.5 occ:0.45 SG A:CYS48 2.8 34.1 1.0 CE1 A:HIS49 3.2 39.9 0.5 ND1 A:HIS49 3.3 38.9 0.5 CB A:CYS48 3.6 25.5 1.0 NE2 A:HIS49 3.6 39.5 0.5 CG A:HIS49 3.8 35.6 0.5 CD2 A:HIS49 3.9 39.7 0.5 N A:HIS49 4.0 25.4 1.0 C A:CYS48 4.1 27.3 1.0 NH1 A:ARG52 4.2 58.4 1.0 CA A:HIS49 4.3 29.3 0.5 CA A:HIS49 4.3 29.3 0.5 CD A:ARG52 4.3 45.5 1.0 O A:GLU45 4.4 28.6 1.0 CA A:CYS48 4.5 26.1 1.0 O A:HOH309 4.5 47.3 1.0 O A:CYS48 4.5 22.4 1.0 CG A:GLU45 4.5 48.2 1.0 CB A:HIS49 4.6 31.5 0.5 CB A:HIS49 4.7 31.6 0.5

S.Aditya, R.Priyadharshine, I.Maham, D.J.Miller, V.Stojanoff. Crystal Structure of Ferritin Grown By Microbatch Method in the Presence of Agarose To Be Published.