Cadmium in PDB 5gu2: Crystal Structure of Au(M).Cl-Apo-E45C/R52C-Rhlfr

The structure of Crystal Structure of Au(M).Cl-Apo-E45C/R52C-Rhlfr, PDB code: 5gu2 was solved by 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)	25.36 / 2.12
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	181.079, 181.079, 181.079, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.9

The structure of Crystal Structure of Au(M).Cl-Apo-E45C/R52C-Rhlfr also contains other interesting chemical elements:

Gold

(Au)

10 atoms

The binding sites of Cadmium atom in the Crystal Structure of Au(M).Cl-Apo-E45C/R52C-Rhlfr (pdb code 5gu2). 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 Au(M).Cl-Apo-E45C/R52C-Rhlfr, PDB code: 5gu2:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Crystal Structure of Au(M).Cl-Apo-E45C/R52C-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 Au(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd211 b:43.5 occ:0.50 OD2 X:ASP80 1.9 37.9 1.0 OD1 X:ASP80 2.7 22.3 1.0 CG X:ASP80 2.7 29.5 1.0 CB X:ASP80 4.2 35.6 1.0

Cadmium binding site 2 out of 6 in the Crystal Structure of Au(M).Cl-Apo-E45C/R52C-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 Au(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd212 b:50.2 occ:0.25 OE1 X:GLU130 2.2 62.1 1.0 CD X:GLU130 3.0 55.9 1.0 OE2 X:GLU130 3.2 74.1 1.0 AU X:AU210 3.8 82.2 0.2 CG X:GLU130 4.5 60.0 1.0 CB X:GLU130 5.0 59.8 1.0

Cadmium binding site 3 out of 6 in the Crystal Structure of Au(M).Cl-Apo-E45C/R52C-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 Au(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd213 b:46.0 occ:0.25 NE2 X:HIS132 2.4 88.5 1.0 CD X:CD216 2.5 49.5 0.3 CE1 X:HIS132 2.9 89.9 1.0 CD2 X:HIS132 3.6 76.5 1.0 ND1 X:HIS132 4.1 85.5 1.0 CG X:HIS132 4.5 72.9 1.0

Cadmium binding site 4 out of 6 in the Crystal Structure of Au(M).Cl-Apo-E45C/R52C-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 Au(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd214 b:60.3 occ:0.45 OE2 X:GLU60 2.4 51.2 1.0 OE1 X:GLU60 2.7 47.8 1.0 CD X:GLU60 2.9 44.5 1.0 OE2 X:GLU57 2.9 75.1 1.0 CD X:GLU57 4.1 67.7 1.0 CG X:GLU60 4.4 41.5 1.0 OE1 X:GLU57 4.9 78.9 1.0

Cadmium binding site 5 out of 6 in the Crystal Structure of Au(M).Cl-Apo-E45C/R52C-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 Au(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd215 b:59.2 occ:0.20 OE2 X:GLU136 2.3 92.7 1.0 OE1 X:GLU57 2.8 78.9 1.0 CD X:GLU136 3.3 84.4 1.0 OE1 X:GLU136 3.9 96.4 1.0 CD X:GLU57 4.1 67.7 1.0 CG X:GLU136 4.4 67.4 1.0 NE X:ARG64 4.8 64.9 1.0 OE2 X:GLU57 4.8 75.1 1.0 O X:HIS132 4.9 45.8 1.0 NH2 X:ARG64 5.0 87.0 1.0 OE1 X:GLU60 5.0 47.8 1.0

Cadmium binding site 6 out of 6 in the Crystal Structure of Au(M).Cl-Apo-E45C/R52C-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 Au(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range: probe atom residue distance (Å) B Occ X:Cd216 b:49.5 occ:0.30 CD X:CD213 2.5 46.0 0.2 NE2 X:HIS132 3.2 88.5 1.0 OD2 X:ASP127 3.9 63.4 1.0 CD2 X:HIS132 3.9 76.5 1.0 CB X:SER131 4.1 60.0 1.0 CE1 X:HIS132 4.3 89.9 1.0 CG X:ASP127 4.7 54.6 1.0 OD1 X:ASP127 5.0 65.7 1.0

B.Maity, S.Abe, T.Ueno. Observation of Gold Sub-Nanocluster Nucleation Within A Crystalline Protein Cage Nat Commun V. 8 14820 2017.
ISSN: ESSN 2041-1723
PubMed: 28300064
DOI: 10.1038/NCOMMS14820