Cadmium in PDB 9kn7: Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)

The structure of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F), PDB code: 9kn7 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)	18.94 / 1.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	180.715, 180.715, 180.715, 90, 90, 90
R / Rfree (%)	16.5 / 17.8

The structure of Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/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 (Fr- E53F/E56F/E57F/R59L/E60F/E63F) (pdb code 9kn7). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F), PDB code: 9kn7:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/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 (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:14.7 occ:0.41 O A:HOH453 2.3 35.6 1.0 OD1 A:ASP38 2.5 13.2 1.0 SG A:CYS48 2.6 14.2 1.0 CG A:ASP38 3.3 9.9 1.0 CB A:ASP38 3.5 8.8 1.0 CB A:CYS48 3.5 10.9 1.0 CA A:ASP38 4.0 8.1 1.0 CD A:CD208 4.3 53.5 0.2 OD2 A:ASP38 4.4 10.8 1.0 CD2 A:HIS49 4.4 26.7 1.0 NE2 A:HIS49 4.5 30.0 1.0 N A:ASP38 4.8 7.5 1.0 NH1 A:ARG52 4.8 32.0 0.5 CG A:GLU45 4.8 18.7 1.0 CA A:GLU45 4.9 9.7 1.0 CA A:CYS48 4.9 9.2 1.0 NE A:ARG52 5.0 24.8 0.5

Cadmium binding site 2 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/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 (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:9.8 occ:0.45 OD2 A:ASP80 2.3 14.8 1.0 OD1 A:ASP80 2.3 9.0 1.0 CL A:CL211 2.5 23.2 1.0 CG A:ASP80 2.7 11.5 1.0 CB A:ASP80 4.2 10.1 1.0 O A:HOH348 4.3 14.6 1.0 O A:HOH334 4.6 17.6 1.0

Cadmium binding site 3 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/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 (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:25.0 occ:0.13 O A:HOH314 2.3 29.1 1.0 O A:HOH482 3.0 39.2 0.1 OD1 A:ASP127 3.6 20.2 1.0 OG A:SER131 3.7 23.4 1.0 CD A:CD204 4.2 17.1 0.1 OE1 A:GLU130 4.3 21.5 1.0 CG A:ASP127 4.7 16.7 1.0

Cadmium binding site 4 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/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 (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:17.1 occ:0.08 CD A:CD205 1.6 18.2 0.3 OE1 A:GLU130 2.2 21.5 1.0 CD A:GLU130 3.2 20.3 1.0 OE2 A:GLU130 3.6 15.6 1.0 CD A:CD203 4.2 25.0 0.1 CG A:GLU130 4.6 15.7 1.0 CB A:GLU130 4.9 13.5 1.0

Cadmium binding site 5 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/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 (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:18.2 occ:0.26 CD A:CD204 1.6 17.1 0.1 OE1 A:GLU130 2.4 21.5 1.0 OE2 A:GLU130 2.9 15.6 1.0 CD A:GLU130 3.0 20.3 1.0 N A:ASP127 4.4 11.1 1.0 CG A:GLU130 4.5 15.7 1.0 CA A:ASP127 4.5 12.2 1.0 O A:HOH506 4.7 33.4 1.0 CB A:CYS126 4.7 10.6 1.0 C A:CYS126 4.7 10.5 1.0 CB A:ASP127 4.8 15.0 1.0 O A:CYS126 5.0 11.5 1.0

Cadmium binding site 6 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/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 (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:26.6 occ:0.23 NE2 A:HIS132 2.6 27.9 1.0 CD2 A:HIS132 3.5 22.4 1.0 CE1 A:HIS132 3.6 27.5 1.0 O A:HOH310 4.5 15.9 1.0 O A:HOH304 4.6 31.0 1.0 CG A:HIS132 4.7 21.1 1.0 OD2 A:ASP127 4.7 24.1 1.0 ND1 A:HIS132 4.8 24.1 1.0 CD1 A:PHE128 4.9 11.9 1.0

Cadmium binding site 7 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/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 (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:30.3 occ:0.17 OE1 A:GLU11 2.4 14.1 1.0 O A:HOH429 2.7 20.5 1.0 OE2 A:GLU11 2.9 19.8 1.0 CD A:GLU11 3.0 16.2 1.0 OG1 A:THR10 4.0 16.4 1.0 CB A:SER9 4.3 8.8 1.0 NE2 A:GLN120 4.3 11.8 0.4 OE1 A:GLN120 4.5 16.9 0.6 CG A:GLU11 4.5 13.3 1.0 N A:THR10 4.6 10.3 1.0 O A:HOH432 4.6 44.5 1.0 NE2 A:GLN120 4.7 18.2 0.6 N A:GLU11 4.9 9.8 1.0 CD A:GLN120 4.9 15.2 0.6 CA A:SER9 5.0 8.5 1.0

Cadmium binding site 8 out of 8 in the Crystal Structure of Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F)


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 Horse Spleen L-Ferritin Mutant (Fr- E53F/E56F/E57F/R59L/E60F/E63F) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:53.5 occ:0.22 NE2 A:HIS49 2.5 30.0 1.0 CE1 A:HIS49 3.0 28.0 1.0 CD A:GLU45 3.6 28.3 1.0 CG A:GLU45 3.6 18.7 1.0 CD2 A:HIS49 3.7 26.7 1.0 OE2 A:GLU45 3.8 38.8 1.0 OE1 A:GLU45 4.0 30.8 1.0 ND1 A:HIS49 4.2 31.9 1.0 CD A:CD201 4.3 14.7 0.4 NH1 A:ARG52 4.5 32.0 0.5 CG A:HIS49 4.6 21.2 1.0 O A:HOH453 5.0 35.6 1.0 CB A:GLU45 5.0 12.8 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