Cadmium in PDB 7ek5: Prawn Ferritin to Coordinate with Heavy Metal Ions

All present enzymatic activity of Prawn Ferritin to Coordinate with Heavy Metal Ions:
1.16.3.1;

The structure of Prawn Ferritin to Coordinate with Heavy Metal Ions, PDB code: 7ek5 was solved by Y.Wang, J.Zang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.02 / 3.00
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	155.613, 155.613, 162.729, 90, 90, 120
R / Rfree (%)	18.1 / 22.4

The structure of Prawn Ferritin to Coordinate with Heavy Metal Ions also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Cadmium atom in the Prawn Ferritin to Coordinate with Heavy Metal Ions (pdb code 7ek5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Prawn Ferritin to Coordinate with Heavy Metal Ions, PDB code: 7ek5:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Prawn Ferritin to Coordinate with Heavy Metal Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Prawn Ferritin to Coordinate with Heavy Metal Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:182.7 occ:1.00 OD2 A:ASP125 3.1 36.9 1.0 N A:HIS10 3.2 34.8 1.0 SG A:CYS13 3.3 41.4 1.0 CB A:ASP125 3.4 31.8 1.0 CG A:ASP125 3.7 38.7 1.0 CB A:CYS13 3.8 38.4 1.0 CA A:TYR9 3.8 31.1 1.0 O A:ASN8 3.8 27.9 1.0 CB A:HIS10 3.9 39.3 1.0 C A:TYR9 4.0 31.1 1.0 CA A:HIS10 4.1 35.0 1.0 CG A:HIS10 4.1 43.5 1.0 CB A:ASN123 4.2 30.4 1.0 CD1 A:TYR9 4.3 25.4 1.0 C A:ASN8 4.5 24.5 1.0 O A:HIS10 4.5 34.7 1.0 N A:TYR9 4.5 34.3 1.0 CD2 A:HIS10 4.6 42.7 1.0 CA A:ASP125 4.6 35.5 1.0 ND1 A:HIS10 4.6 38.1 1.0 O A:ASN123 4.8 34.7 1.0 C A:HIS10 4.8 35.9 1.0 CB A:TYR9 4.9 28.4 1.0 CG A:TYR9 4.9 32.8 1.0 N A:ASP125 4.9 28.1 1.0 OD1 A:ASP125 4.9 49.5 1.0 CE1 A:TYR9 4.9 26.5 1.0 NH2 A:ARG74 5.0 21.9 1.0

Cadmium binding site 2 out of 4 in the Prawn Ferritin to Coordinate with Heavy Metal Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Prawn Ferritin to Coordinate with Heavy Metal Ions within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd202 b:183.9 occ:1.00 N B:HIS10 3.0 44.7 1.0 OD2 B:ASP125 3.3 40.5 1.0 O B:ASN8 3.3 45.1 1.0 CB B:ASP125 3.5 31.1 1.0 CG B:HIS10 3.6 57.0 1.0 CA B:TYR9 3.6 41.2 1.0 CD2 B:HIS10 3.6 45.5 1.0 CG B:ASP125 3.6 35.4 1.0 CB B:HIS10 3.6 55.8 1.0 C B:TYR9 3.8 46.1 1.0 C B:ASN8 3.8 39.2 1.0 CA B:HIS10 3.9 55.1 1.0 N B:TYR9 3.9 46.0 1.0 SG B:CYS13 4.2 42.2 1.0 OD1 B:ASN8 4.2 43.1 1.0 O B:ASN123 4.2 45.3 1.0 CB B:ASN123 4.2 42.5 1.0 ND1 B:HIS10 4.3 64.8 1.0 NE2 B:HIS10 4.4 59.5 1.0 CA B:ASP125 4.5 29.0 1.0 CD1 B:TYR9 4.6 38.0 1.0 OD1 B:ASP125 4.6 39.5 1.0 CG B:ASN8 4.7 36.3 1.0 CE1 B:HIS10 4.7 63.4 1.0 CB B:CYS13 4.8 44.8 1.0 N B:ASP125 4.8 34.9 1.0 NH2 B:ARG74 4.8 38.6 1.0 O B:HIS10 4.8 41.2 1.0 CB B:TYR9 4.9 41.6 1.0 C B:ASN123 4.9 42.0 1.0 C B:HIS10 4.9 50.3 1.0 CA B:ASN8 4.9 37.8 1.0 O B:TYR9 5.0 47.3 1.0

Cadmium binding site 3 out of 4 in the Prawn Ferritin to Coordinate with Heavy Metal Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Prawn Ferritin to Coordinate with Heavy Metal Ions within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd202 b:170.6 occ:1.00 N C:HIS10 3.1 39.0 1.0 OD2 C:ASP125 3.2 35.5 1.0 ND1 C:HIS10 3.2 58.2 1.0 CB C:ASP125 3.3 37.8 1.0 O C:ASN8 3.4 43.7 1.0 CG C:ASP125 3.6 40.0 1.0 CA C:TYR9 3.8 31.4 1.0 CB C:HIS10 3.8 42.4 1.0 SG C:CYS13 3.9 37.9 1.0 CG C:HIS10 3.9 60.6 1.0 C C:TYR9 3.9 42.6 1.0 C C:ASN8 4.0 37.7 1.0 CA C:HIS10 4.1 32.5 1.0 CB C:ASN123 4.1 37.2 1.0 CE1 C:HIS10 4.3 52.8 1.0 N C:TYR9 4.3 39.2 1.0 CA C:ASP125 4.3 34.9 1.0 O C:ASN123 4.3 46.9 1.0 CB C:CYS13 4.5 36.9 1.0 N C:ASP125 4.6 31.8 1.0 CD1 C:TYR9 4.6 38.2 1.0 OD1 C:ASP125 4.7 43.1 1.0 O C:HIS10 4.8 38.3 1.0 NH2 C:ARG74 4.8 37.6 1.0 OD1 C:ASN8 4.8 48.8 1.0 C C:ASN123 4.9 40.2 1.0 C C:HIS10 4.9 38.9 1.0 CG C:ASN123 4.9 46.4 1.0

Cadmium binding site 4 out of 4 in the Prawn Ferritin to Coordinate with Heavy Metal Ions


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Prawn Ferritin to Coordinate with Heavy Metal Ions within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd202 b:179.7 occ:1.00 N D:HIS10 3.1 27.1 1.0 O D:ASN8 3.1 38.6 1.0 OD2 D:ASP125 3.4 38.4 1.0 CG D:HIS10 3.5 37.6 1.0 CB D:HIS10 3.5 35.7 1.0 CB D:ASP125 3.6 30.8 1.0 CD2 D:HIS10 3.7 28.6 1.0 CA D:TYR9 3.7 32.1 1.0 C D:ASN8 3.8 32.9 1.0 CG D:ASP125 3.8 36.3 1.0 C D:TYR9 3.9 33.5 1.0 CA D:HIS10 3.9 35.0 1.0 ND1 D:HIS10 4.0 40.7 1.0 CB D:ASN123 4.0 36.4 1.0 SG D:CYS13 4.0 36.0 1.0 N D:TYR9 4.1 35.0 1.0 O D:ASN123 4.2 44.5 1.0 NE2 D:HIS10 4.3 37.4 1.0 CE1 D:HIS10 4.5 40.6 1.0 CA D:ASP125 4.5 34.3 1.0 OD1 D:ASN8 4.6 38.9 1.0 CB D:CYS13 4.6 35.3 1.0 CD1 D:TYR9 4.7 25.9 1.0 CG D:ASN8 4.7 38.5 1.0 N D:ASP125 4.8 34.8 1.0 C D:ASN123 4.8 33.7 1.0 ND2 D:ASN8 4.9 37.8 1.0 CG D:ASN123 4.9 40.2 1.0 NH2 D:ARG74 4.9 25.5 1.0 OD1 D:ASP125 4.9 43.7 1.0 C D:HIS10 5.0 35.1 1.0 CA D:ASN8 5.0 26.8 1.0

Y.Wang, J.Zang, C.Wang, X.Zhang, G.Zhao. Structural Insights For the Stronger Ability of Shrimp Ferritin to Coordinate with Heavy Metal Ions As Compared to Human H-Chain Ferritin. Int J Mol Sci V. 22 2021.
ISSN: ESSN 1422-0067
PubMed: 34360624
DOI: 10.3390/IJMS22157859