Cadmium in PDB 7bon: Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr

The structure of Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr, PDB code: 7bon was solved by Y.Hishikawa, B.Maity, N.Ito, S.Abe, D.Lu, T.Ueno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.45 / 1.48
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.739, 181.739, 181.739, 90, 90, 90
R / Rfree (%)	16.4 / 18.9

The structure of Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr (pdb code 7bon). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 16 binding sites of Cadmium where determined in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr, PDB code: 7bon:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 16 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:21.3 occ:0.40 CL A:CL220 2.1 51.2 0.8 OD1 A:ASP80 2.2 14.9 1.0 OD2 A:ASP80 2.3 33.0 1.0 CG A:ASP80 2.7 21.5 1.0 CB A:ASP80 4.2 17.7 1.0 O A:HOH327 4.5 23.0 1.0

Cadmium binding site 2 out of 16 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:16.8 occ:0.60 OD1 A:ASP38 2.0 21.6 0.5 OE2 A:GLU45 2.3 23.8 1.0 O A:HOH446 2.3 35.7 1.0 SG A:CYS48 2.5 16.3 0.6 SG A:CYS48 2.6 12.0 0.4 OD2 A:ASP38 2.7 19.9 0.5 OE1 A:GLU45 2.7 30.8 1.0 CG A:ASP38 2.7 16.6 0.5 CD A:GLU45 2.8 23.9 1.0 OD1 A:ASP38 3.3 14.4 0.5 CB A:CYS48 3.4 13.5 0.6 CB A:CYS48 3.7 11.0 0.4 O A:HOH478 4.0 40.5 1.0 CG A:ASP38 4.0 12.8 0.5 O A:HOH359 4.1 30.4 1.0 CD A:CD204 4.1 15.6 0.6 CB A:ASP38 4.2 13.5 0.5 CB A:ASP38 4.3 11.9 0.5 O A:HOH421 4.3 22.5 1.0 CG A:GLU45 4.3 18.0 1.0 CD A:CD213 4.4 20.5 0.2 CD2 A:HIS49 4.5 22.6 0.5 CA A:CYS48 4.9 12.8 0.6 NE2 A:HIS49 4.9 21.2 0.5 CA A:ASP38 4.9 10.9 0.5 CA A:ASP38 4.9 11.7 0.5 CA A:CYS48 5.0 11.8 0.4 O A:GLU45 5.0 11.5 1.0 CA A:GLU45 5.0 12.3 1.0

Cadmium binding site 3 out of 16 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:15.6 occ:0.60 SG A:CYS48 2.3 16.3 0.6 O A:HOH359 2.3 30.4 1.0 SG A:CYS52 2.3 19.6 1.0 SG A:CYS48 2.4 12.0 0.4 O A:HOH478 2.6 40.5 1.0 O A:CYS48 3.1 13.1 1.0 CB A:CYS52 3.2 16.6 1.0 CB A:CYS48 3.5 13.5 0.6 C A:CYS48 3.5 12.0 1.0 CB A:CYS48 3.7 11.0 0.4 CA A:CYS48 3.8 12.8 0.6 CA A:CYS48 3.9 11.8 0.4 O A:HOH446 3.9 35.7 1.0 O A:GLY34 4.0 16.8 1.0 C A:GLY34 4.0 15.3 1.0 CA A:GLY34 4.0 11.6 1.0 CD A:CD203 4.1 16.8 0.6 OD2 A:ASP38 4.1 19.9 0.5 N A:HIS49 4.3 12.4 1.0 CA A:CYS52 4.4 13.4 1.0 N A:CYS52 4.6 11.8 1.0 CG A:ASP38 4.6 16.6 0.5 N A:PHE35 4.7 12.2 1.0 CA A:HIS49 4.7 13.0 0.5 OD1 A:ASP38 4.7 21.6 0.5 CA A:HIS49 4.8 13.3 0.5

Cadmium binding site 4 out of 16 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:16.8 occ:0.75 O A:HOH441 2.0 28.7 1.0 SG A:CYS63 2.3 18.5 1.0 SG A:CYS59 2.4 20.2 1.0 O A:CYS59 2.5 12.8 1.0 C A:CYS59 3.1 13.0 1.0 CB A:CYS63 3.4 14.2 1.0 CB A:CYS59 3.4 13.4 1.0 CA A:CYS59 3.6 12.3 1.0 N A:GLU60 3.9 12.3 1.0 CD A:CD214 3.9 28.6 0.2 O A:HOH495 4.1 36.5 1.0 N A:CYS63 4.1 10.6 1.0 CA A:CYS63 4.3 11.2 1.0 CA A:GLU60 4.3 13.5 0.5 CA A:GLU60 4.4 13.7 0.5 O A:HOH409 4.5 28.4 1.0

Cadmium binding site 5 out of 16 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:17.8 occ:0.33 NE2 A:HIS114 2.2 14.9 1.0 O A:HOH301 2.4 20.3 1.0 CE1 A:HIS114 2.6 16.9 1.0 OE2 A:GLU130 3.2 8.3 0.8 CD A:CD210 3.2 24.5 0.2 CB A:CYS126 3.4 21.2 1.0 CD2 A:HIS114 3.4 18.2 1.0 O A:HOH473 3.6 42.4 1.0 OG A:SER118 3.7 15.1 0.5 SG A:CYS126 3.7 23.4 1.0 ND1 A:HIS114 3.8 20.3 1.0 CG A:HIS114 4.3 14.2 1.0 CD A:GLU130 4.3 20.1 0.8 CA A:CYS126 4.6 17.1 1.0 CB A:SER118 4.9 19.6 0.5 OG A:SER118 4.9 22.4 0.5 CD A:CD207 4.9 20.2 0.3

Cadmium binding site 6 out of 16 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:20.2 occ:0.30 CD A:CD210 1.8 24.5 0.2 OE2 A:GLU130 2.1 10.9 0.2 OE1 A:GLU130 2.5 27.1 0.8 CD A:GLU130 2.7 14.1 0.2 OE1 A:GLU130 2.8 11.3 0.2 CD A:GLU130 3.1 20.1 0.8 OE2 A:GLU130 3.2 8.3 0.8 CG A:GLU130 4.1 14.5 0.2 O A:HOH301 4.3 20.3 1.0 CG A:GLU130 4.5 16.2 0.8 O A:HOH305 4.7 24.4 0.8 CD A:CD206 4.9 17.8 0.3 CB A:GLU130 5.0 16.2 0.8

Cadmium binding site 7 out of 16 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:20.8 occ:0.20 O A:HOH307 1.7 25.8 0.8 O A:HOH305 2.3 24.4 0.8 OD1 A:ASP127 3.8 26.9 1.0 OE1 A:GLU130 3.9 11.3 0.2 OG A:SER131 4.1 28.1 1.0 OE1 A:GLU130 4.5 27.1 0.8 CD A:GLU130 4.5 14.1 0.2 OE2 A:GLU130 4.9 10.9 0.2 CB A:GLU130 4.9 16.7 0.2 CG A:ASP127 4.9 26.3 1.0

Cadmium binding site 8 out of 16 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr


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 Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd209 b:23.1 occ:0.30 CD A:CD215 2.0 27.4 0.2 NE2 A:HIS132 2.1 34.5 1.0 CE1 A:HIS132 2.8 39.4 1.0 CD2 A:HIS132 3.3 29.8 1.0 ND1 A:HIS132 4.0 35.4 1.0 CG A:HIS132 4.2 31.2 1.0

Cadmium binding site 9 out of 16 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd210 b:24.5 occ:0.25 CD A:CD207 1.8 20.2 0.3 OE2 A:GLU130 2.4 8.3 0.8 OE1 A:GLU130 2.8 27.1 0.8 O A:HOH301 2.9 20.3 1.0 CD A:GLU130 2.9 20.1 0.8 OE2 A:GLU130 3.0 10.9 0.2 OE1 A:GLU130 3.1 11.3 0.2 CD A:GLU130 3.1 14.1 0.2 CD A:CD206 3.2 17.8 0.3 CG A:GLU130 4.2 14.5 0.2 O A:HOH473 4.2 42.4 1.0 CE1 A:HIS114 4.4 16.9 1.0 CG A:GLU130 4.4 16.2 0.8 NE2 A:HIS114 4.7 14.9 1.0

Cadmium binding site 10 out of 16 in the Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Recombinant Horse Spleen Apo-R52C/E56C/R59C/E63C- Fr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd211 b:37.8 occ:0.25 OE1 A:GLU53 1.8 35.6 0.5 NE2 A:HIS49 2.2 21.5 0.5 CD A:GLU53 2.9 25.0 0.5 CD2 A:HIS49 3.1 21.2 0.5 CE1 A:HIS49 3.2 23.0 0.5 OE2 A:GLU53 3.5 27.8 0.5 CG A:GLU53 4.0 22.3 0.5 CG A:HIS49 4.3 18.8 0.5 ND1 A:HIS49 4.3 24.6 0.5

Y.Hishikawa, B.Maity, N.Ito, S.Abe, D.Lu, T.Ueno. Design of Multinuclear Gold Binding Site at the Two-Fold Symmetric Interface of the Ferritin Cage Chem Lett. V. 49 840 2021.
ISSN: ESSN 1348-0715
DOI: 10.1246/CL.200217