Cadmium in PDB 9kpa: Crystal Structure of Horse Spleen L-Ferritin Mutant (R59F)

The structure of Crystal Structure of Horse Spleen L-Ferritin Mutant (R59F), PDB code: 9kpa 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)	18.46 / 1.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.843, 180.843, 180.843, 90, 90, 90
R / Rfree (%)	18 / 19.4

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

Cadmium binding site 1 out of 6 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (R59F)


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 (R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:8.6 occ:0.47 OD1 A:ASP80 2.3 7.5 1.0 OD2 A:ASP80 2.4 10.0 1.0 CL A:CL209 2.5 16.3 1.0 CG A:ASP80 2.6 9.8 1.0 CB A:ASP80 4.1 7.7 1.0 O A:HOH405 4.4 12.6 1.0 O A:HOH369 4.8 18.0 1.0

Cadmium binding site 2 out of 6 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (R59F)


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 (R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:50.6 occ:0.18 O A:HOH313 2.6 29.3 1.0 OD1 A:ASP127 3.5 19.9 1.0 CD A:CD203 3.9 26.6 0.1 OG A:SER131 4.0 23.9 1.0 OE1 A:GLU130 4.3 20.8 1.0 CG A:ASP127 4.6 16.5 1.0

Cadmium binding site 3 out of 6 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (R59F)


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 (R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:26.6 occ:0.14 CD A:CD204 1.9 22.4 0.2 OE1 A:GLU130 2.3 20.8 1.0 CD A:GLU130 3.3 21.6 1.0 OE2 A:GLU130 3.6 16.9 1.0 CD A:CD202 3.9 50.6 0.2 CG A:GLU130 4.6 14.8 1.0 OD1 A:ASP127 4.9 19.9 1.0 CB A:GLU130 4.9 12.3 1.0 CA A:ASP127 5.0 10.8 1.0

Cadmium binding site 4 out of 6 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (R59F)


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 (R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:22.4 occ:0.25 CD A:CD203 1.9 26.6 0.1 OE1 A:GLU130 2.6 20.8 1.0 OE2 A:GLU130 2.8 16.9 1.0 CD A:GLU130 2.9 21.6 1.0 CG A:GLU130 4.2 14.8 1.0 O A:HOH522 4.5 24.9 1.0

Cadmium binding site 5 out of 6 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (R59F)


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 (R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:27.6 occ:0.21 NE2 A:HIS132 2.2 23.4 1.0 CE1 A:HIS132 2.8 19.2 1.0 CD2 A:HIS132 3.4 18.5 1.0 O A:HOH397 3.7 29.6 1.0 ND1 A:HIS132 4.0 19.3 1.0 NH1 A:ARG64 4.1 23.7 1.0 O A:HOH379 4.2 35.2 1.0 CG A:HIS132 4.3 14.3 1.0

Cadmium binding site 6 out of 6 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (R59F)


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 (R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:78.1 occ:0.20 OE1 A:GLU60 2.3 18.6 0.4 OE1 A:GLU63 2.4 12.4 1.0 OE2 A:GLU60 2.6 12.3 0.4 CD A:GLU60 2.7 15.3 0.4 CD A:GLU63 3.4 16.3 1.0 OE2 A:GLU63 3.7 12.1 1.0 O A:HOH435 4.0 21.9 1.0 CG A:GLU60 4.1 12.0 0.6 CG A:GLU60 4.2 12.2 0.4 OE2 A:GLU60 4.6 25.1 0.6 CG A:GLU63 4.8 10.5 1.0 CD A:GLU60 4.8 23.1 0.6 CB A:GLU60 5.0 10.8 0.6

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