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Cadmium in PDB 5gu1: Crystal Structure of Au(L).Cl-Apo-E45C/R52C-Rhlfr

Protein crystallography data

The structure of Crystal Structure of Au(L).Cl-Apo-E45C/R52C-Rhlfr, PDB code: 5gu1 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) 34.87 / 2.05
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.170, 181.170, 181.170, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.3

Other elements in 5gu1:

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

Gold (Au) 9 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Au(L).Cl-Apo-E45C/R52C-Rhlfr (pdb code 5gu1). 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(L).Cl-Apo-E45C/R52C-Rhlfr, PDB code: 5gu1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 5gu1

Go back to Cadmium Binding Sites List in 5gu1
Cadmium binding site 1 out of 6 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd210

b:38.9
occ:0.50
OD2 X:ASP80 1.8 30.2 1.0
OD1 X:ASP80 2.6 17.6 1.0
CG X:ASP80 2.7 24.4 1.0
CB X:ASP80 4.2 29.7 1.0
O X:HOH352 4.5 38.6 1.0

Cadmium binding site 2 out of 6 in 5gu1

Go back to Cadmium Binding Sites List in 5gu1
Cadmium binding site 2 out of 6 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd211

b:35.8
occ:0.25
OE1 X:GLU130 2.3 48.7 1.0
OE2 X:GLU130 2.5 58.5 1.0
CD X:GLU130 2.8 44.1 1.0
CG X:GLU130 4.3 43.1 1.0

Cadmium binding site 3 out of 6 in 5gu1

Go back to Cadmium Binding Sites List in 5gu1
Cadmium binding site 3 out of 6 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd212

b:48.8
occ:0.40
OE2 X:GLU60 2.3 43.6 1.0
OE1 X:GLU56 2.6 48.4 1.0
OE1 X:GLU60 2.7 40.9 1.0
CD X:GLU60 2.9 39.3 1.0
OE2 X:GLU57 3.0 52.9 1.0
CD X:GLU56 3.3 38.9 1.0
CG X:GLU56 3.8 30.4 1.0
OE2 X:GLU56 4.0 50.4 1.0
CD X:GLU57 4.2 51.4 1.0
CG X:GLU60 4.4 34.1 1.0
OE1 X:GLU57 4.8 64.5 1.0

Cadmium binding site 4 out of 6 in 5gu1

Go back to Cadmium Binding Sites List in 5gu1
Cadmium binding site 4 out of 6 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd213

b:58.5
occ:0.45
NE2 X:HIS132 2.5 83.2 1.0
CD X:CD215 2.5 48.2 0.3
CD2 X:HIS132 3.3 72.9 1.0
CE1 X:HIS132 3.5 80.3 1.0
CG X:HIS132 4.4 69.8 1.0
ND1 X:HIS132 4.5 72.2 1.0
CB X:SER131 4.9 57.6 1.0
NH1 X:ARG64 5.0 68.8 1.0

Cadmium binding site 5 out of 6 in 5gu1

Go back to Cadmium Binding Sites List in 5gu1
Cadmium binding site 5 out of 6 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd214

b:70.6
occ:0.25
OE1 X:GLU57 2.5 64.5 1.0
OE2 X:GLU136 2.9 81.1 1.0
CD X:GLU57 3.7 51.4 1.0
CD X:GLU136 3.9 70.3 1.0
OE1 X:GLU60 4.3 40.9 1.0
OE1 X:GLU136 4.3 83.4 1.0
OE2 X:GLU57 4.3 52.9 1.0
CG X:GLU57 4.8 43.8 1.0

Cadmium binding site 6 out of 6 in 5gu1

Go back to Cadmium Binding Sites List in 5gu1
Cadmium binding site 6 out of 6 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Cd215

b:48.2
occ:0.30
CD X:CD213 2.5 58.5 0.5
OG X:SER131 3.6 51.0 1.0
OD2 X:ASP127 3.6 56.1 1.0
CB X:SER131 3.7 57.6 1.0
NE2 X:HIS132 3.8 83.2 1.0
CD2 X:HIS132 4.1 72.9 1.0
CG X:ASP127 4.4 46.6 1.0
OD1 X:ASP127 4.6 42.1 1.0
O X:ASP127 5.0 37.3 1.0

Reference:

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
Page generated: Sat Dec 12 08:26:42 2020

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