Cadmium in PDB 8h8m: Crystal Structure of Apo-E53F/E57F/E60F/E64F-Rhlfr

The structure of Crystal Structure of Apo-E53F/E57F/E60F/E64F-Rhlfr, PDB code: 8h8m was solved by Y.Hishikawa, H.Noya, 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)	20.26 / 1.50
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.108, 181.108, 181.108, 90, 90, 90
R / Rfree (%)	15.9 / 17.6

The structure of Crystal Structure of Apo-E53F/E57F/E60F/E64F-Rhlfr also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Cadmium atom in the Crystal Structure of Apo-E53F/E57F/E60F/E64F-Rhlfr (pdb code 8h8m). 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 Apo-E53F/E57F/E60F/E64F-Rhlfr, PDB code: 8h8m:
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 Apo-E53F/E57F/E60F/E64F-Rhlfr


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 Apo-E53F/E57F/E60F/E64F-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:29.0 occ:0.25 SG A:CYS48 2.7 12.7 1.0 OD1 A:ASP38 2.7 13.3 1.0 O A:HOH442 2.8 51.3 1.0 CG A:ASP38 3.4 10.2 1.0 CB A:ASP38 3.5 8.3 1.0 CB A:CYS48 3.5 9.5 1.0 O A:HOH449 3.5 45.2 1.0 O A:HOH448 3.5 29.2 1.0 CD A:CD209 3.9 42.1 0.2 CA A:ASP38 4.1 7.8 1.0 CG A:GLU45 4.4 14.9 0.5 OD2 A:ASP38 4.5 11.5 1.0 NE2 A:HIS49 4.5 23.5 0.8 CD2 A:HIS49 4.5 19.6 0.8 OE2 A:GLU45 4.7 22.4 0.5 CA A:GLU45 4.8 10.1 0.5 N A:ASP38 4.8 7.7 1.0 CA A:GLU45 4.8 9.8 0.5 CD A:GLU45 4.9 19.4 0.5 CA A:CYS48 4.9 8.2 1.0 CB A:GLU45 5.0 12.0 0.5 O A:GLU45 5.0 8.5 1.0

Cadmium binding site 2 out of 8 in the Crystal Structure of Apo-E53F/E57F/E60F/E64F-Rhlfr


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 Apo-E53F/E57F/E60F/E64F-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:17.0 occ:0.50 OD2 A:ASP80 1.6 7.1 1.0 OD1 A:ASP80 2.3 12.2 1.0 CG A:ASP80 2.4 16.5 1.0 CL A:CL212 2.5 32.6 1.0 CB A:ASP80 4.0 13.4 1.0 O A:HOH365 4.4 17.8 1.0 O A:HOH444 4.5 20.3 1.0

Cadmium binding site 3 out of 8 in the Crystal Structure of Apo-E53F/E57F/E60F/E64F-Rhlfr


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 Apo-E53F/E57F/E60F/E64F-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:30.3 occ:0.20 O A:HOH331 2.3 30.3 1.0 O A:HOH301 2.5 27.4 1.0 OD1 A:ASP127 3.6 17.5 1.0 OG A:SER131 3.7 15.2 0.5 CD A:CD206 4.1 20.3 0.1 OE1 A:GLU130 4.2 19.7 1.0 CG A:ASP127 4.7 17.1 1.0

Cadmium binding site 4 out of 8 in the Crystal Structure of Apo-E53F/E57F/E60F/E64F-Rhlfr


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 Apo-E53F/E57F/E60F/E64F-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd206 b:20.3 occ:0.10 CD A:CD207 1.7 19.8 0.3 OE1 A:GLU130 2.3 19.7 1.0 CD A:GLU130 3.2 19.8 1.0 O A:HOH301 3.6 27.4 1.0 OE2 A:GLU130 3.6 17.8 1.0 CD A:CD205 4.1 30.3 0.2 O A:HOH319 4.3 29.4 1.0 CG A:GLU130 4.6 15.4 1.0 CB A:GLU130 4.9 14.0 1.0

Cadmium binding site 5 out of 8 in the Crystal Structure of Apo-E53F/E57F/E60F/E64F-Rhlfr


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 Apo-E53F/E57F/E60F/E64F-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd207 b:19.8 occ:0.30 CD A:CD206 1.7 20.3 0.1 OE1 A:GLU130 2.5 19.7 1.0 OE2 A:GLU130 2.8 17.8 1.0 CD A:GLU130 3.0 19.8 1.0 O A:HOH461 3.9 38.5 1.0 O A:HOH301 4.1 27.4 1.0 O A:HOH319 4.2 29.4 1.0 N A:ASP127 4.5 10.2 1.0 CA A:ASP127 4.5 10.8 1.0 CG A:GLU130 4.5 15.4 1.0 CB A:CYS126 4.7 10.3 1.0 O A:HOH499 4.7 29.2 1.0 CB A:ASP127 4.8 14.2 1.0 C A:CYS126 4.8 9.7 1.0 O A:CYS126 5.0 10.5 1.0

Cadmium binding site 6 out of 8 in the Crystal Structure of Apo-E53F/E57F/E60F/E64F-Rhlfr


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 Apo-E53F/E57F/E60F/E64F-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd208 b:24.6 occ:0.25 NE2 A:HIS132 2.5 23.8 1.0 CD2 A:HIS132 3.4 22.4 1.0 CE1 A:HIS132 3.5 24.0 1.0 OG A:SER131 4.2 19.2 0.5 O A:HOH310 4.5 15.3 1.0 O A:HOH323 4.5 30.7 1.0 CG A:HIS132 4.6 18.6 1.0 ND1 A:HIS132 4.6 22.8 1.0 OD2 A:ASP127 4.7 24.9 1.0 CD1 A:PHE128 4.9 12.5 1.0

Cadmium binding site 7 out of 8 in the Crystal Structure of Apo-E53F/E57F/E60F/E64F-Rhlfr


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 Apo-E53F/E57F/E60F/E64F-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd209 b:42.1 occ:0.20 OE2 A:GLU45 2.2 22.4 0.5 NE2 A:HIS49 2.3 23.5 0.8 CE1 A:HIS49 3.0 22.9 0.8 CD A:GLU45 3.3 19.4 0.5 CD2 A:HIS49 3.4 19.6 0.8 O A:HOH442 3.6 51.3 1.0 CG A:GLU45 3.7 14.9 0.5 CD A:CD203 3.9 29.0 0.2 OE1 A:GLU45 4.1 22.3 0.5 CD A:GLU45 4.2 16.3 0.5 CG A:GLU45 4.2 13.6 0.5 ND1 A:HIS49 4.2 23.0 0.8 OE1 A:GLU45 4.4 22.4 0.5 CG A:HIS49 4.5 17.4 0.8 O A:HOH303 4.6 39.0 1.0 OE2 A:GLU45 4.8 21.9 0.5 O A:HOH449 4.8 45.2 1.0

Cadmium binding site 8 out of 8 in the Crystal Structure of Apo-E53F/E57F/E60F/E64F-Rhlfr


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 Apo-E53F/E57F/E60F/E64F-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd210 b:40.4 occ:0.20 OE2 A:GLU11 2.5 14.1 1.0 O A:HOH428 2.8 22.4 1.0 OE1 A:GLU11 2.9 20.9 1.0 CD A:GLU11 3.0 17.6 1.0 O A:HOH502 3.5 36.5 1.0 OG1 A:THR10 4.1 16.7 1.0 NE2 A:GLN120 4.3 17.4 0.5 CB A:SER9 4.4 9.8 1.0 CG A:GLU11 4.5 13.7 1.0 OE1 A:GLN120 4.6 10.0 0.5 NE2 A:GLN120 4.7 12.6 0.5 N A:THR10 4.7 10.7 1.0 CD A:GLN120 5.0 10.1 0.5

Y.Hishikawa, H.Noya, S.Nagatoishi, T.Yoshidome, B.Maity, K.Tsumoto, S.Abe, T.Ueno. Elucidating Conformational Dynamics and Thermostability of Designed Aromatic Clusters By Using Protein Cages. Chemistry V. 29 00488 2023.
ISSN: ISSN 0947-6539
PubMed: 37070368
DOI: 10.1002/CHEM.202300488