Cadmium in PDB 9kf7: Crystal Structure of Ferritin Mutant (R52H/E56H/R59H/E63H)

The structure of Crystal Structure of Ferritin Mutant (R52H/E56H/R59H/E63H), PDB code: 9kf7 was solved by J.Tian, B.Maity, T.Furuta, T.Pan, S.Abe, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.66 / 1.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.7, 181.7, 181.7, 90, 90, 90
R / Rfree (%)	16.8 / 18.7

The structure of Crystal Structure of Ferritin Mutant (R52H/E56H/R59H/E63H) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the Crystal Structure of Ferritin Mutant (R52H/E56H/R59H/E63H) (pdb code 9kf7). 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 Ferritin Mutant (R52H/E56H/R59H/E63H), PDB code: 9kf7:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Crystal Structure of Ferritin Mutant (R52H/E56H/R59H/E63H)


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 Mutant (R52H/E56H/R59H/E63H) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd603 b:7.3 occ:0.50 CL A:CL612 2.5 12.7 1.0 CG A:LYS83 4.4 6.7 1.0 CB A:GLN82 4.5 9.9 1.0 N A:LYS83 4.6 6.6 1.0 CA A:GLN82 4.7 7.7 1.0 CD A:LYS83 4.8 7.2 1.0 O A:HOH862 5.0 13.6 1.0

Cadmium binding site 2 out of 6 in the Crystal Structure of Ferritin Mutant (R52H/E56H/R59H/E63H)


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 Mutant (R52H/E56H/R59H/E63H) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd604 b:29.0 occ:0.10 O A:HOH719 2.2 31.6 1.0 OD1 A:ASP127 2.7 13.4 0.5 OD1 A:ASP127 3.5 10.0 0.5 CG A:ASP127 3.8 11.7 0.5 OG A:SER131 4.1 19.6 1.0 CD A:CD606 4.2 49.1 0.2 OD2 A:ASP127 4.3 13.3 0.5 OE1 A:GLU130 4.3 16.5 1.0 CG A:ASP127 4.7 8.7 0.5 CB A:ASP127 5.0 10.0 0.5

Cadmium binding site 3 out of 6 in the Crystal Structure of Ferritin Mutant (R52H/E56H/R59H/E63H)


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 Mutant (R52H/E56H/R59H/E63H) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd605 b:9.6 occ:0.50 ND1 A:HIS52 2.3 12.8 1.0 O A:HOH884 2.4 24.0 1.0 O A:HOH888 2.5 16.6 1.0 CE1 A:HIS52 3.2 13.6 1.0 CG A:HIS52 3.3 11.8 1.0 CB A:HIS52 3.7 9.7 1.0 NE2 A:HIS52 4.4 10.9 1.0 CD2 A:HIS52 4.5 12.0 1.0 SG A:CYS48 4.6 13.1 1.0 CZ A:PHE35 4.8 6.7 1.0

Cadmium binding site 4 out of 6 in the Crystal Structure of Ferritin Mutant (R52H/E56H/R59H/E63H)


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 Mutant (R52H/E56H/R59H/E63H) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd606 b:49.1 occ:0.25 OE1 A:GLU130 2.5 16.5 1.0 CD A:GLU130 3.4 14.2 1.0 OE2 A:GLU130 3.6 14.4 1.0 OD1 A:ASP127 3.9 13.4 0.5 CD A:CD604 4.2 29.0 0.1 O A:HOH714 4.3 30.4 1.0 CG A:GLU130 4.7 12.2 1.0 CB A:ASP127 4.8 10.0 0.5 CG A:ASP127 4.8 11.7 0.5 CB A:GLU130 5.0 10.8 1.0 CA A:ASP127 5.0 8.9 0.5

Cadmium binding site 5 out of 6 in the Crystal Structure of Ferritin Mutant (R52H/E56H/R59H/E63H)


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 Mutant (R52H/E56H/R59H/E63H) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd607 b:18.5 occ:0.20 O A:HOH891 2.1 34.2 1.0 O A:HOH705 2.2 34.6 1.0 CD2 A:HIS63 2.2 10.7 1.0 NE2 A:HIS63 2.3 11.3 1.0 CE1 A:HIS63 2.6 10.3 1.0 CG A:HIS63 2.7 9.8 1.0 O A:HOH883 2.7 23.0 1.0 ND1 A:HIS63 2.9 11.8 1.0 O A:HOH877 3.5 28.0 1.0 O A:HOH806 3.7 36.7 1.0 CB A:HIS63 3.7 8.4 1.0 OE1 A:GLU60 4.5 36.0 1.0 OE2 A:GLU60 4.7 35.8 1.0 O A:HOH779 4.9 20.5 1.0 O A:HOH827 4.9 24.3 1.0

Cadmium binding site 6 out of 6 in the Crystal Structure of Ferritin Mutant (R52H/E56H/R59H/E63H)


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 Mutant (R52H/E56H/R59H/E63H) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd608 b:19.9 occ:0.20 NE2 A:HIS132 2.2 21.8 1.0 CE1 A:HIS132 2.8 21.3 1.0 CD2 A:HIS132 3.4 18.8 1.0 O A:HOH840 3.6 35.3 1.0 O A:HOH834 3.9 30.1 1.0 ND1 A:HIS132 4.1 19.0 1.0 CG A:HIS132 4.3 16.6 1.0 NH2 A:ARG64 4.3 28.1 1.0 O A:HOH839 4.6 33.5 1.0

J.Tian, B.Maity, T.Furuta, T.Pan, T.Ueno. An Artificial Metal-Free Peroxidase Designed Using A Ferritin Cage For Bioinspired Catalysis Angew.Chem.Int.Ed.Engl. V. 64 2025.
ISSN: ESSN 1521-3773
DOI: 10.1002/ANIE.202504608