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Gold in PDB 5gu3: Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr

Protein crystallography data

The structure of Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr, PDB code: 5gu3 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) 26.20 / 2.03
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 181.502, 181.502, 181.502, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 24.4

Other elements in 5gu3:

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

Cadmium (Cd) 5 atoms

Gold Binding Sites:

The binding sites of Gold atom in the Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr (pdb code 5gu3). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 6 binding sites of Gold where determined in the Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr, PDB code: 5gu3:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6;

Gold binding site 1 out of 6 in 5gu3

Go back to Gold Binding Sites List in 5gu3
Gold binding site 1 out of 6 in the Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au203

b:50.4
occ:0.30
SG X:CYS48 2.1 37.3 1.0
CB X:CYS48 3.0 31.3 1.0
AU X:AU204 3.2 33.9 0.3
N X:HIS49 3.3 25.7 1.0
C X:CYS48 3.3 28.4 1.0
CA X:HIS49 3.6 26.9 1.0
CA X:CYS48 3.7 27.8 1.0
O X:CYS45 3.8 23.0 1.0
O X:CYS48 3.8 25.6 1.0
CB X:HIS49 4.1 31.1 1.0
N X:CYS48 4.8 25.7 1.0
C X:CYS45 4.9 23.8 1.0
CB X:CYS52 4.9 28.1 0.5
SG X:CYS52 5.0 39.2 0.5
C X:HIS49 5.0 26.0 1.0

Gold binding site 2 out of 6 in 5gu3

Go back to Gold Binding Sites List in 5gu3
Gold binding site 2 out of 6 in the Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au204

b:33.9
occ:0.35
SG X:CYS52 2.2 39.2 0.5
SG X:CYS48 2.2 37.3 1.0
O X:CYS48 3.0 25.6 1.0
AU X:AU203 3.2 50.4 0.3
CB X:CYS52 3.2 32.4 0.5
C X:CYS48 3.4 28.4 1.0
CB X:CYS48 3.5 31.3 1.0
CB X:CYS52 3.5 28.1 0.5
CA X:GLY34 3.6 25.3 1.0
O X:GLY34 3.6 26.0 1.0
C X:GLY34 3.6 26.3 1.0
CA X:CYS48 3.7 27.8 1.0
N X:CYS52 4.3 28.1 1.0
CA X:CYS52 4.3 26.9 0.5
CA X:CYS52 4.3 28.1 0.5
N X:PHE35 4.4 27.5 1.0
N X:HIS49 4.4 25.7 1.0
SG X:CYS52 4.5 35.1 0.5
CA X:HIS49 4.8 26.9 1.0
N X:GLY34 5.0 20.7 1.0

Gold binding site 3 out of 6 in 5gu3

Go back to Gold Binding Sites List in 5gu3
Gold binding site 3 out of 6 in the Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au205

b:89.1
occ:0.25
AU X:AU208 2.8 91.0 0.2
AU X:AU206 2.9 89.7 0.1
CD X:CD210 3.0 54.4 0.2
OE2 X:GLU130 3.3 51.6 1.0
AU X:AU207 3.4 96.0 0.2
CB X:CYS126 3.7 45.2 1.0
OE1 X:GLU130 3.9 52.7 1.0
CD X:GLU130 4.0 47.6 1.0
C X:CYS126 4.8 40.2 1.0
N X:ASP127 4.8 35.4 1.0
SG X:CYS126 4.8 54.5 1.0
CA X:CYS126 4.9 38.7 1.0
O X:PRO123 5.0 33.3 1.0

Gold binding site 4 out of 6 in 5gu3

Go back to Gold Binding Sites List in 5gu3
Gold binding site 4 out of 6 in the Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au206

b:89.7
occ:0.10
AU X:AU207 2.5 96.0 0.2
AU X:AU205 2.9 89.1 0.2
AU X:AU208 3.0 91.0 0.2
CD X:CD210 4.8 54.4 0.2
OE2 X:GLU130 4.8 51.6 1.0

Gold binding site 5 out of 6 in 5gu3

Go back to Gold Binding Sites List in 5gu3
Gold binding site 5 out of 6 in the Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au207

b:96.0
occ:0.20
AU X:AU206 2.5 89.7 0.1
AU X:AU208 2.7 91.0 0.2
NE2 X:HIS114 2.8 44.7 1.0
AU X:AU205 3.4 89.1 0.2
CE1 X:HIS114 3.5 47.0 1.0
OE2 X:GLU130 3.6 51.6 1.0
CD2 X:HIS114 3.9 44.1 1.0
SG X:CYS126 4.2 54.5 1.0
CB X:CYS126 4.2 45.2 1.0
ND1 X:HIS114 4.7 50.2 1.0
OG X:SER118 4.8 55.3 1.0
CD X:GLU130 4.9 47.6 1.0
CB X:SER118 4.9 44.7 1.0
CG X:HIS114 5.0 46.6 1.0

Gold binding site 6 out of 6 in 5gu3

Go back to Gold Binding Sites List in 5gu3
Gold binding site 6 out of 6 in the Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of Crystal Structure of Au(E).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au208

b:91.0
occ:0.20
AU X:AU207 2.7 96.0 0.2
AU X:AU205 2.8 89.1 0.2
AU X:AU206 3.0 89.7 0.1
SG X:CYS126 3.3 54.5 1.0
CB X:CYS126 3.4 45.2 1.0
NE2 X:HIS114 4.5 44.7 1.0
OG X:SER118 4.6 55.3 1.0
CA X:PRO123 4.7 35.3 1.0
CB X:SER118 4.7 44.7 1.0
CA X:SER118 4.8 44.4 1.0
OE2 X:GLU130 4.8 51.6 1.0
CA X:CYS126 4.9 38.7 1.0
CE1 X:HIS114 4.9 47.0 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 01:54:18 2020

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