Cadmium in PDB 9kkr: Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F)

The structure of Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F), PDB code: 9kkr was solved by T.Suzuki, Y.Hishikawa, B.Maity, S.Abe, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 1.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.43, 181.43, 181.43, 90, 90, 90
R / Rfree (%)	18.5 / 20.3

The structure of Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F) (pdb code 9kkr). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F), PDB code: 9kkr:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F)


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 Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:15.4 occ:0.44 O A:HOH445 2.3 25.6 0.9 OD1 A:ASP38 2.5 14.8 1.0 SG A:CYS48 2.6 13.6 1.0 CG A:ASP38 3.3 11.7 1.0 CB A:ASP38 3.4 10.2 1.0 CB A:CYS48 3.5 10.8 1.0 NH2 A:ARG52 3.6 26.9 0.5 NH1 A:ARG52 3.6 19.7 0.5 CZ A:ARG52 3.8 22.9 0.5 CA A:ASP38 3.9 9.6 1.0 O A:HOH441 4.3 39.5 1.0 CD2 A:HIS49 4.3 17.0 0.6 NE2 A:HIS49 4.4 16.7 0.6 OD2 A:ASP38 4.4 13.2 1.0 NE A:ARG52 4.6 26.1 0.5 N A:ASP38 4.7 9.4 1.0 CG A:GLU45 4.8 20.0 1.0 CA A:GLU45 4.9 11.6 1.0 CA A:CYS48 4.9 10.2 1.0

Cadmium binding site 2 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F)


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 Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:15.1 occ:0.12 O A:HOH317 2.1 28.1 0.7 OD1 A:ASP127 3.4 28.4 1.0 OG A:SER131 3.7 24.6 1.0 CG A:ASP127 4.6 19.6 1.0 CD A:CD203 4.8 21.6 0.1 OE1 A:GLU130 4.9 22.9 1.0 CB A:SER131 5.0 19.7 1.0

Cadmium binding site 3 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F)


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 Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:21.6 occ:0.08 CD A:CD205 1.7 21.6 0.2 OE1 A:GLU130 2.3 22.9 1.0 CD A:GLU130 3.3 19.8 1.0 CD A:CD207 3.3 36.5 0.1 OE2 A:GLU130 3.6 18.0 1.0 CG A:GLU130 4.6 15.7 1.0 OD1 A:ASP127 4.7 28.4 1.0 CD A:CD202 4.8 15.1 0.1 CB A:GLU130 5.0 14.3 1.0

Cadmium binding site 4 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F)


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 Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:8.1 occ:0.48 OD1 A:ASP80 2.3 7.9 1.0 OD2 A:ASP80 2.4 9.6 1.0 CL A:CL209 2.5 12.9 1.0 CG A:ASP80 2.7 8.0 1.0 CB A:ASP80 4.2 8.3 1.0 O A:HOH400 4.3 12.9 1.0 O A:HOH330 4.8 14.7 1.0

Cadmium binding site 5 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F)


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 Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:21.6 occ:0.22 CD A:CD203 1.7 21.6 0.1 OE1 A:GLU130 2.5 22.9 1.0 CD A:CD207 2.6 36.5 0.1 OE2 A:GLU130 2.9 18.0 1.0 CD A:GLU130 3.1 19.8 1.0 O A:HOH460 4.0 44.4 1.0 N A:ASP127 4.4 12.6 1.0 CA A:ASP127 4.4 14.4 1.0 CG A:GLU130 4.6 15.7 1.0 O A:HOH486 4.6 28.9 1.0 CB A:ASP127 4.6 16.1 1.0 CB A:CYS126 4.6 12.5 1.0 C A:CYS126 4.7 12.3 1.0 O A:CYS126 4.9 12.8 1.0 OD1 A:ASP127 5.0 28.4 1.0

Cadmium binding site 6 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F)


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 Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:59.5 occ:0.29 NE2 A:HIS132 2.6 26.2 1.0 CE1 A:HIS132 3.5 26.7 1.0 CD2 A:HIS132 3.6 23.9 1.0 ND1 A:HIS132 4.6 24.7 1.0 CB A:SER131 4.7 19.7 1.0 O A:HOH397 4.7 17.2 1.0 OD2 A:ASP127 4.7 26.2 1.0 CG A:HIS132 4.7 21.2 1.0

Cadmium binding site 7 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F)


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 Horse Spleen L-Ferritin Mutant (E53F/E56F/E57F/R59F/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:36.5 occ:0.10 CD A:CD205 2.6 21.6 0.2 O A:HOH460 2.7 44.4 1.0 CD A:CD203 3.3 21.6 0.1 OE2 A:GLU130 3.8 18.0 1.0 O A:HOH486 4.1 28.9 1.0 OE1 A:GLU130 4.4 22.9 1.0 CD A:GLU130 4.5 19.8 1.0

Y.Hishikawa, T.Suzuki, B.Maity, H.Noya, M.Yoshizawa, A.Asanuma, Y.Katagiri, S.Abe, S.Nagatoishi, K.Tsumoto, T.Ueno. Design of Aromatic Interaction Networks in A Protein Cage Modulated By Fluorescent Ligand Binding. Adv Sci 17030 2025.
ISSN: ESSN 2198-3844
PubMed: 39973762
DOI: 10.1002/ADVS.202417030