Cadmium in PDB 9kp5: Crystal Structure of Horse Spleen L-Ferritin Mutant (E56F/R59F)

The structure of Crystal Structure of Horse Spleen L-Ferritin Mutant (E56F/R59F), PDB code: 9kp5 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)	18.97 / 1.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.928, 180.928, 180.928, 90, 90, 90
R / Rfree (%)	17.8 / 18.8

The structure of Crystal Structure of Horse Spleen L-Ferritin Mutant (E56F/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 (E56F/R59F) (pdb code 9kp5). 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 (E56F/R59F), PDB code: 9kp5:
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 (E56F/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 (E56F/R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:13.7 occ:0.11 SG A:CYS48 2.7 8.2 1.0 O1 A:EDO212 2.7 22.9 1.0 C1 A:EDO212 2.9 21.2 1.0 OD1 A:ASP38 2.9 11.7 1.0 CG A:ASP38 3.3 8.6 1.0 CB A:ASP38 3.4 6.3 1.0 C2 A:EDO212 3.4 23.3 1.0 CB A:CYS48 3.6 6.6 1.0 CA A:ASP38 4.0 7.3 1.0 O A:HOH308 4.2 29.4 1.0 OD2 A:ASP38 4.3 8.4 1.0 NE2 A:HIS49 4.4 19.6 0.5 NE2 A:HIS49 4.4 19.6 0.5 CD2 A:HIS49 4.4 14.8 0.5 CD2 A:HIS49 4.5 17.9 0.5 O2 A:EDO212 4.5 23.3 1.0 N A:ASP38 4.8 6.7 1.0 CG A:GLU45 4.8 12.8 1.0 CA A:GLU45 4.8 6.4 1.0 O A:GLU45 5.0 7.9 1.0 CA A:CYS48 5.0 6.7 1.0

Cadmium binding site 2 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E56F/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 (E56F/R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:7.0 occ:0.43 OD1 A:ASP80 2.3 7.0 1.0 OD2 A:ASP80 2.3 10.8 1.0 CL A:CL210 2.4 17.7 1.0 CG A:ASP80 2.6 9.0 1.0 CB A:ASP80 4.1 7.1 1.0 O A:HOH389 4.3 12.3 1.0 O A:HOH341 4.7 16.7 1.0

Cadmium binding site 3 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E56F/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 (E56F/R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:32.0 occ:0.14 O A:HOH315 2.5 25.9 1.0 OD1 A:ASP127 3.5 19.8 1.0 OG A:SER131 4.0 22.4 1.0 CD A:CD204 4.3 19.5 0.1 OE1 A:GLU130 4.4 23.0 1.0 CG A:ASP127 4.6 16.5 1.0

Cadmium binding site 4 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E56F/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 (E56F/R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:19.5 occ:0.11 CD A:CD205 1.7 18.4 0.2 OE1 A:GLU130 2.3 23.0 1.0 CD A:GLU130 3.2 21.4 1.0 OE2 A:GLU130 3.5 14.8 1.0 CD A:CD203 4.3 32.0 0.1 CG A:GLU130 4.6 12.6 1.0 CB A:GLU130 5.0 11.2 1.0 OD1 A:ASP127 5.0 19.8 1.0

Cadmium binding site 5 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E56F/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 (E56F/R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:18.4 occ:0.23 CD A:CD204 1.7 19.5 0.1 OE1 A:GLU130 2.6 23.0 1.0 OE2 A:GLU130 2.8 14.8 1.0 CD A:GLU130 2.9 21.4 1.0 CG A:GLU130 4.2 12.6 1.0

Cadmium binding site 6 out of 7 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (E56F/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 (E56F/R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:29.8 occ:0.23 NE2 A:HIS132 2.2 21.6 1.0 CE1 A:HIS132 2.9 21.2 1.0 CD2 A:HIS132 3.4 17.8 1.0 O A:HOH350 3.8 29.0 1.0 ND1 A:HIS132 4.1 17.6 1.0 NH1 A:ARG64 4.1 25.3 1.0 CG A:HIS132 4.4 13.9 1.0

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


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 (E56F/R59F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:16.8 occ:0.26 OE1 A:GLU63 2.3 24.0 1.0 OE1 A:GLU60 2.4 41.2 1.0 OE2 A:GLU60 2.6 25.3 1.0 CD A:GLU60 2.8 30.3 1.0 CD A:GLU63 3.2 26.7 1.0 OE2 A:GLU63 3.4 14.9 1.0 O A:HOH426 4.0 24.7 1.0 CG A:GLU60 4.3 12.0 1.0 CG A:GLU63 4.6 13.4 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