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

Protein crystallography data

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

Other elements in 5gu2:

The structure of Crystal Structure of Au(M).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(M).Cl-Apo-E45C/R52C-Rhlfr (pdb code 5gu2). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 10 binding sites of Gold where determined in the Crystal Structure of Au(M).Cl-Apo-E45C/R52C-Rhlfr, PDB code: 5gu2:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Gold binding site 1 out of 10 in 5gu2

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Gold binding site 1 out of 10 in the Crystal Structure of Au(M).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(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au201

b:89.1
occ:0.30
 SG X:CYS126 2.3 86.0 1.0
AU X:AU203 3.1 76.6 0.2
CB X:CYS126 3.6 65.5 1.0
OG X:SER118 3.7 68.6 1.0
CA X:SER118 3.8 57.3 1.0
O X:ASP122 3.9 38.3 1.0
O X:GLY117 3.9 44.2 1.0
AU X:AU210 4.0 82.2 0.2
N X:SER118 4.0 51.4 1.0
AU X:AU202 4.1 66.5 0.4
CA X:PRO123 4.2 39.9 1.0
C X:GLY117 4.2 49.2 1.0
C X:ASP122 4.2 41.3 1.0
N X:PRO123 4.3 40.2 1.0
N X:ASP122 4.4 43.9 1.0
CB X:SER118 4.4 55.8 1.0
CB X:PRO123 4.8 48.7 1.0
CA X:ASP122 5.0 43.5 1.0
CA X:CYS126 5.0 57.0 1.0
C X:SER118 5.0 53.7 1.0

Gold binding site 2 out of 10 in 5gu2

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Gold binding site 2 out of 10 in the Crystal Structure of Au(M).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(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au202

b:66.5
occ:0.40
 ND1 X:HIS114 2.2 71.3 1.0
SG X:CYS126 2.4 86.0 1.0
CE1 X:HIS114 2.8 79.7 1.0
CG X:HIS114 2.9 56.1 1.0
O X:HIS114 3.1 49.1 1.0
AU X:AU203 3.3 76.6 0.2
CB X:CYS126 3.3 65.5 1.0
CB X:HIS114 3.4 51.1 1.0
CA X:HIS114 3.5 42.8 1.0
C X:HIS114 3.6 45.9 1.0
NE2 X:HIS114 3.7 68.0 1.0
CD2 X:HIS114 3.8 64.9 1.0
CA X:CYS126 3.8 57.0 1.0
AU X:AU201 4.1 89.1 0.3
OG X:SER118 4.1 68.6 1.0
N X:SER118 4.3 51.4 1.0
N X:CYS126 4.6 49.2 1.0
CB X:SER118 4.7 55.8 1.0
N X:ALA115 4.8 40.7 1.0
C X:GLY117 4.8 49.2 1.0
OE2 X:GLU130 4.9 74.1 1.0
CA X:SER118 4.9 57.3 1.0
N X:HIS114 4.9 36.7 1.0

Gold binding site 3 out of 10 in 5gu2

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Gold binding site 3 out of 10 in the Crystal Structure of Au(M).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(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au203

b:76.6
occ:0.20
 AU X:AU210 2.6 82.2 0.2
AU X:AU201 3.1 89.1 0.3
SG X:CYS126 3.1 86.0 1.0
AU X:AU202 3.3 66.5 0.4
OG X:SER118 3.5 68.6 1.0
CE1 X:HIS114 3.6 79.7 1.0
CB X:CYS126 3.7 65.5 1.0
ND1 X:HIS114 4.1 71.3 1.0
OE2 X:GLU130 4.3 74.1 1.0
NE2 X:HIS114 4.6 68.0 1.0
CB X:SER118 4.8 55.8 1.0

Gold binding site 4 out of 10 in 5gu2

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Gold binding site 4 out of 10 in the Crystal Structure of Au(M).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(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au204

b:44.6
occ:0.25
 CE X:MET96 1.8 36.0 1.0
SD X:MET96 2.1 37.8 1.0
AU X:AU208 2.4 45.7 0.1
ND1 X:HIS147 3.0 37.7 1.0
CG X:MET96 3.3 32.9 1.0
CB X:HIS147 3.4 30.8 1.0
CE2 X:PHE50 3.5 33.6 1.0
CG X:HIS147 3.6 32.9 1.0
CZ X:PHE50 3.9 34.8 1.0
CD2 X:PHE50 4.0 32.8 1.0
CE1 X:HIS147 4.1 33.5 1.0
CB X:MET96 4.1 28.6 1.0
CD1 X:ILE151 4.5 30.8 1.0
CE2 X:PHE166 4.6 30.8 1.0
CE1 X:PHE50 4.6 33.4 1.0
CZ X:PHE166 4.7 29.4 1.0
CG X:PHE50 4.7 30.6 1.0
CD2 X:LEU171 4.8 33.3 1.0
CD2 X:HIS147 4.8 30.0 1.0
CA X:HIS147 4.9 27.6 1.0
CA X:MET96 5.0 28.4 1.0
CD1 X:PHE50 5.0 32.6 1.0

Gold binding site 5 out of 10 in 5gu2

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Gold binding site 5 out of 10 in the Crystal Structure of Au(M).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(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au205

b:44.8
occ:0.15
 SG X:CYS52 2.1 31.1 0.5
SG X:CYS52 2.9 41.6 0.5
CB X:CYS52 2.9 32.2 0.5
AU X:AU206 3.2 38.3 0.6
CB X:CYS52 3.2 34.7 0.5
CE2 X:PHE35 3.8 33.5 1.0
CZ X:PHE35 4.0 35.8 1.0
CA X:CYS52 4.2 31.1 0.5
CA X:CYS52 4.3 29.5 0.5
CD2 X:PHE35 4.6 31.2 1.0
CE1 X:PHE35 5.0 31.2 1.0
CD1 X:LEU31 5.0 29.4 1.0

Gold binding site 6 out of 10 in 5gu2

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Gold binding site 6 out of 10 in the Crystal Structure of Au(M).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(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au206

b:38.3
occ:0.60
 SG X:CYS48 2.3 40.1 1.0
SG X:CYS52 2.3 31.1 0.5
O X:CYS48 3.0 27.8 1.0
AU X:AU205 3.2 44.8 0.1
CB X:CYS52 3.2 32.2 0.5
AU X:AU207 3.3 52.5 0.5
C X:CYS48 3.4 28.8 1.0
CB X:CYS52 3.4 34.7 0.5
CB X:CYS48 3.5 31.5 1.0
O X:GLY34 3.5 28.1 1.0
C X:GLY34 3.6 26.2 1.0
CA X:GLY34 3.6 28.6 1.0
CA X:CYS48 3.7 28.1 1.0
N X:PHE35 4.3 26.4 1.0
CA X:CYS52 4.3 31.1 0.5
N X:CYS52 4.4 28.6 1.0
N X:HIS49 4.4 32.6 1.0
CA X:CYS52 4.4 29.5 0.5
SG X:CYS52 4.5 41.6 0.5
CA X:HIS49 4.8 34.6 1.0
CA X:PHE35 5.0 25.6 1.0

Gold binding site 7 out of 10 in 5gu2

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Gold binding site 7 out of 10 in the Crystal Structure of Au(M).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(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au207

b:52.5
occ:0.45
 SG X:CYS48 2.1 40.1 1.0
CB X:CYS48 3.0 31.5 1.0
ND1 X:HIS49 3.1 69.3 1.0
AU X:AU206 3.3 38.3 0.6
N X:HIS49 3.3 32.6 1.0
C X:CYS48 3.3 28.8 1.0
CE1 X:HIS49 3.4 63.4 1.0
CG X:HIS49 3.5 62.0 1.0
CA X:HIS49 3.7 34.6 1.0
CA X:CYS48 3.7 28.1 1.0
O X:CYS45 3.8 23.0 1.0
NE2 X:HIS49 3.9 63.0 1.0
O X:CYS48 3.9 27.8 1.0
CD2 X:HIS49 3.9 57.9 1.0
CB X:HIS49 4.1 41.9 1.0
N X:CYS48 4.8 26.1 1.0
C X:CYS45 4.8 25.9 1.0
SG X:CYS45 4.8 41.5 1.0

Gold binding site 8 out of 10 in 5gu2

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Gold binding site 8 out of 10 in the Crystal Structure of Au(M).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(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au208

b:45.7
occ:0.15
 SD X:MET96 2.3 37.8 1.0
AU X:AU204 2.4 44.6 0.2
ND1 X:HIS147 2.7 37.7 1.0
CZ X:PHE50 3.0 34.8 1.0
CG X:MET144 3.2 34.2 1.0
CA X:MET144 3.3 27.2 1.0
CE2 X:PHE50 3.4 33.6 1.0
CG X:HIS147 3.5 32.9 1.0
CB X:HIS147 3.5 30.8 1.0
CE X:MET96 3.5 36.0 1.0
CB X:MET144 3.6 31.1 1.0
CG X:MET96 3.7 32.9 1.0
CE1 X:HIS147 3.7 33.5 1.0
CE1 X:PHE50 3.9 33.4 1.0
N X:MET144 4.0 29.1 1.0
O X:MET144 4.2 28.4 1.0
O X:LYS143 4.2 27.0 1.0
C X:MET144 4.2 30.1 1.0
C X:LYS143 4.4 29.7 1.0
CD2 X:PHE50 4.5 32.8 1.0
CD2 X:HIS147 4.6 30.0 1.0
SD X:MET144 4.7 37.4 1.0
NE2 X:HIS147 4.8 36.8 1.0
CE X:MET144 4.8 36.3 1.0
CA X:HIS147 4.9 27.6 1.0
CD1 X:PHE50 4.9 32.6 1.0
CB X:MET96 5.0 28.6 1.0

Gold binding site 9 out of 10 in 5gu2

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Gold binding site 9 out of 10 in the Crystal Structure of Au(M).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(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au209

b:54.1
occ:0.15
 CE1 X:HIS147 2.7 33.5 1.0
NE2 X:HIS147 2.8 36.8 1.0
CD2 X:LEU171 3.7 33.3 1.0
ND1 X:HIS147 3.9 37.7 1.0
CD2 X:HIS147 4.2 30.0 1.0
CD1 X:PHE50 4.3 32.6 1.0
CD X:LYS143 4.3 64.7 1.0
CE1 X:PHE50 4.4 33.4 1.0
O X:THR170 4.5 26.6 1.0
CG2 X:THR170 4.6 29.7 1.0
CG X:HIS147 4.7 32.9 1.0
CG X:LYS143 4.7 51.9 1.0
CA X:LEU171 4.9 35.7 1.0
NZ X:LYS143 5.0 74.3 1.0

Gold binding site 10 out of 10 in 5gu2

Go back to Gold Binding Sites List in 5gu2
Gold binding site 10 out of 10 in the Crystal Structure of Au(M).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 10 of Crystal Structure of Au(M).Cl-Apo-E45C/R52C-Rhlfr within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Au210

b:82.2
occ:0.20
 AU X:AU203 2.6 76.6 0.2
CB X:CYS126 3.8 65.5 1.0
CD X:CD212 3.8 50.2 0.2
AU X:AU201 4.0 89.1 0.3
OE2 X:GLU130 4.0 74.1 1.0
SG X:CYS126 4.2 86.0 1.0
CD X:GLU130 4.9 55.9 1.0
OE1 X:GLU130 4.9 62.1 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 14:29:46 2024

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