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Gold 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:

Cadmium (Cd) 6 atoms

Gold Binding Sites:

The binding sites of Gold 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 Gold atom.
In total 9 binding sites of Gold where determined in the Crystal Structure of Au(L).Cl-Apo-E45C/R52C-Rhlfr, PDB code: 5gu1:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Gold binding site 1 out of 9 in 5gu1

Go back to Gold Binding Sites List in 5gu1
Gold binding site 1 out of 9 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au201

b:50.0
occ:0.40
 AU X:AU209 1.9 44.0 0.2
SG X:CYS126 2.4 57.5 1.0
CB X:CYS126 3.2 46.9 1.0
O X:ASP122 3.6 33.8 1.0
CA X:SER118 3.6 49.4 1.0
N X:SER118 3.6 45.7 1.0
AU X:AU202 3.7 47.5 0.6
C X:GLY117 3.8 43.6 1.0
O X:GLY117 3.9 42.3 1.0
C X:ASP122 3.9 36.6 1.0
CA X:PRO123 4.1 35.0 1.0
CB X:SER118 4.1 48.2 1.0
N X:PRO123 4.2 34.9 1.0
N X:ASP122 4.3 36.5 1.0
CA X:CYS126 4.6 40.5 1.0
OG X:SER118 4.8 52.4 1.0
CA X:ASP122 4.8 36.7 1.0
N X:CYS126 4.8 36.4 1.0
CA X:GLY117 4.8 39.0 1.0
C X:SER118 4.8 46.9 1.0
CB X:PRO123 4.9 42.0 1.0
O X:SER118 5.0 46.3 1.0

Gold binding site 2 out of 9 in 5gu1

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Gold binding site 2 out of 9 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au202

b:47.5
occ:0.55
 SG X:CYS126 2.3 57.5 1.0
ND1 X:HIS114 2.6 55.0 1.0
AU X:AU209 3.0 44.0 0.2
O X:HIS114 3.1 38.0 1.0
CB X:CYS126 3.2 46.9 1.0
CB X:HIS114 3.2 40.2 1.0
CG X:HIS114 3.3 53.8 1.0
CA X:HIS114 3.4 36.2 1.0
C X:HIS114 3.6 35.6 1.0
AU X:AU201 3.7 50.0 0.4
CE1 X:HIS114 3.7 59.5 1.0
CA X:CYS126 4.0 40.5 1.0
N X:SER118 4.1 45.7 1.0
CB X:SER118 4.4 48.2 1.0
CD2 X:HIS114 4.5 59.7 1.0
NE2 X:HIS114 4.7 63.0 1.0
CA X:SER118 4.7 49.4 1.0
N X:ALA115 4.8 33.3 1.0
N X:CYS126 4.8 36.4 1.0
C X:GLY117 4.8 43.6 1.0
N X:HIS114 4.9 30.6 1.0
CA X:GLY117 5.0 39.0 1.0

Gold binding site 3 out of 9 in 5gu1

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Gold binding site 3 out of 9 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au203

b:26.4
occ:0.50
 SD X:MET96 1.9 36.0 1.0
ND1 X:HIS147 2.3 29.2 1.0
AU X:AU207 2.3 35.7 0.3
CE X:MET96 2.6 34.7 1.0
CG X:HIS147 3.1 24.1 1.0
CG X:MET96 3.1 35.4 1.0
CB X:HIS147 3.2 22.2 1.0
CE1 X:HIS147 3.4 24.1 1.0
CE2 X:PHE50 3.6 31.6 1.0
CZ X:PHE50 3.8 31.5 1.0
CD2 X:PHE50 4.2 30.5 1.0
CB X:MET96 4.2 26.3 1.0
CD2 X:HIS147 4.3 24.3 1.0
NE2 X:HIS147 4.4 26.3 1.0
CE1 X:PHE50 4.5 31.0 1.0
CD1 X:LEU171 4.7 31.9 1.0
CE2 X:PHE166 4.7 28.2 1.0
CA X:HIS147 4.7 20.4 1.0
CZ X:PHE166 4.7 24.6 1.0
CG X:PHE50 4.8 25.9 1.0
CD1 X:ILE151 4.9 29.6 1.0
CD1 X:PHE50 4.9 30.6 1.0

Gold binding site 4 out of 9 in 5gu1

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Gold binding site 4 out of 9 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au204

b:51.6
occ:0.50
 SG X:CYS52 2.3 36.9 0.6
SG X:CYS52 2.8 30.3 0.4
CB X:CYS52 3.0 30.3 0.6
AU X:AU205 3.2 33.0 0.6
CB X:CYS52 3.4 26.2 0.4
CE2 X:PHE35 3.8 26.4 1.0
CZ X:PHE35 3.9 27.3 1.0
CA X:CYS52 4.3 25.0 0.4
CA X:CYS52 4.4 26.2 0.6
CD2 X:PHE35 4.7 24.6 1.0
CE1 X:PHE35 4.8 25.5 1.0

Gold binding site 5 out of 9 in 5gu1

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Gold binding site 5 out of 9 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au205

b:33.0
occ:0.55
 SG X:CYS48 2.2 33.0 1.0
SG X:CYS52 2.3 36.9 0.6
O X:CYS48 3.0 23.6 1.0
AU X:AU206 3.2 46.6 0.5
AU X:AU204 3.2 51.6 0.5
CB X:CYS52 3.3 30.3 0.6
C X:CYS48 3.4 25.6 1.0
CB X:CYS48 3.4 30.1 1.0
O X:GLY34 3.5 24.7 1.0
CB X:CYS52 3.5 26.2 0.4
C X:GLY34 3.6 25.5 1.0
CA X:GLY34 3.6 25.0 1.0
CA X:CYS48 3.6 27.4 1.0
N X:PHE35 4.3 23.5 1.0
N X:HIS49 4.3 24.3 1.0
CA X:CYS52 4.4 25.0 0.4
N X:CYS52 4.4 24.3 1.0
CA X:CYS52 4.4 26.2 0.6
SG X:CYS52 4.5 30.3 0.4
CA X:HIS49 4.8 26.3 0.5
CA X:HIS49 4.9 26.1 0.5
CA X:PHE35 5.0 22.1 1.0

Gold binding site 6 out of 9 in 5gu1

Go back to Gold Binding Sites List in 5gu1
Gold binding site 6 out of 9 in the Crystal Structure of Au(L).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(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au206

b:46.6
occ:0.50
 SG X:CYS48 2.2 33.0 1.0
ND1 X:HIS49 2.4 31.1 0.5
CE1 X:HIS49 2.8 30.5 0.5
CB X:CYS48 3.0 30.1 1.0
N X:HIS49 3.2 24.3 1.0
CG X:HIS49 3.2 32.8 0.5
AU X:AU205 3.2 33.0 0.6
C X:CYS48 3.2 25.6 1.0
CA X:HIS49 3.6 26.3 0.5
NE2 X:HIS49 3.6 28.8 0.5
CA X:HIS49 3.6 26.1 0.5
CA X:CYS48 3.7 27.4 1.0
O X:CYS45 3.7 22.7 1.0
O X:CYS48 3.8 23.6 1.0
CD2 X:HIS49 3.8 28.3 0.5
CB X:HIS49 3.9 29.8 0.5
CB X:HIS49 4.2 28.5 0.5
N X:CYS48 4.7 23.0 1.0
C X:CYS45 4.7 24.1 1.0
SG X:CYS45 4.8 39.0 1.0
C X:HIS49 5.0 25.6 1.0

Gold binding site 7 out of 9 in 5gu1

Go back to Gold Binding Sites List in 5gu1
Gold binding site 7 out of 9 in the Crystal Structure of Au(L).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 7 of Crystal Structure of Au(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au207

b:35.7
occ:0.30
 AU X:AU203 2.3 26.4 0.5
ND1 X:HIS147 2.5 29.2 1.0
CZ X:PHE50 2.9 31.5 1.0
CG X:MET144 3.0 28.6 1.0
SD X:MET96 3.3 36.0 1.0
CA X:MET144 3.3 24.0 1.0
CE1 X:HIS147 3.3 24.1 1.0
CE2 X:PHE50 3.4 31.6 1.0
CG X:HIS147 3.4 24.1 1.0
CB X:MET144 3.6 26.7 1.0
CB X:HIS147 3.7 22.2 1.0
CE1 X:PHE50 3.8 31.0 1.0
N X:MET144 3.9 24.1 1.0
O X:LYS143 4.1 20.9 1.0
C X:LYS143 4.2 27.0 1.0
C X:MET144 4.3 25.5 1.0
NE2 X:HIS147 4.3 26.3 1.0
O X:MET144 4.4 22.5 1.0
CD2 X:HIS147 4.4 24.3 1.0
CE X:MET96 4.4 34.7 1.0
SD X:MET144 4.5 36.0 1.0
CD2 X:PHE50 4.5 30.5 1.0
CE X:MET144 4.6 32.4 1.0
CG X:MET96 4.7 35.4 1.0
CG X:LYS143 4.8 43.4 1.0
CD1 X:PHE50 4.8 30.6 1.0

Gold binding site 8 out of 9 in 5gu1

Go back to Gold Binding Sites List in 5gu1
Gold binding site 8 out of 9 in the Crystal Structure of Au(L).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 8 of Crystal Structure of Au(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au208

b:42.4
occ:0.30
 NE2 X:HIS147 2.1 26.3 1.0
CE1 X:HIS147 2.5 24.1 1.0
CD2 X:HIS147 3.4 24.3 1.0
ND1 X:HIS147 3.8 29.2 1.0
CD1 X:LEU171 3.9 31.9 1.0
CG2 X:THR170 4.0 27.6 1.0
CG X:HIS147 4.2 24.1 1.0
CG X:LYS143 4.4 43.4 1.0
CD X:LYS143 4.4 54.6 1.0
O X:THR170 4.5 24.0 1.0
CE1 X:PHE50 4.7 31.0 1.0
CD1 X:PHE50 4.9 30.6 1.0

Gold binding site 9 out of 9 in 5gu1

Go back to Gold Binding Sites List in 5gu1
Gold binding site 9 out of 9 in the Crystal Structure of Au(L).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 9 of Crystal Structure of Au(L).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au209

b:44.0
occ:0.20
 AU X:AU201 1.9 50.0 0.4
SG X:CYS126 2.9 57.5 1.0
AU X:AU202 3.0 47.5 0.6
CB X:CYS126 3.0 46.9 1.0
CB X:SER118 4.3 48.2 1.0
CA X:SER118 4.5 49.4 1.0
CA X:CYS126 4.5 40.5 1.0
N X:SER118 4.7 45.7 1.0
ND1 X:HIS114 4.7 55.0 1.0
OG X:SER118 4.9 52.4 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: Wed Jul 10 14:29:15 2024

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