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Gold in PDB 5jvx: X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound, PDB code: 5jvx was solved by G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.03 / 1.70
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.912, 57.912, 150.136, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 18.7

Other elements in 5jvx:

The structure of X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Gold Binding Sites:

The binding sites of Gold atom in the X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound (pdb code 5jvx). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 7 binding sites of Gold where determined in the X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound, PDB code: 5jvx:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6; 7;

Gold binding site 1 out of 7 in 5jvx

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Gold binding site 1 out of 7 in the X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au503

b:30.9
occ:0.65
AU A:6O0503 0.0 30.9 0.7
N A:ALA1 1.6 20.2 1.0
C1 A:6O0503 2.0 34.7 0.7
CA A:ALA1 2.8 24.0 1.0
H2A A:6O0503 3.0 37.1 0.7
N1 A:6O0503 3.0 36.3 0.7
H5B A:6O0503 3.0 36.5 0.7
N2 A:6O0503 3.0 35.5 0.7
HA A:ALA1 3.2 23.2 1.0
C A:ALA1 3.2 23.1 1.0
O A:ALA1 3.2 25.6 1.0
H6B A:6O0503 3.3 36.7 0.7
C2 A:6O0503 3.3 37.7 0.7
C5 A:6O0503 3.4 36.9 0.7
H2B A:6O0503 3.5 37.2 0.7
O A:VAL41 3.6 21.5 1.0
HD3 A:PRO43 3.6 22.7 1.0
O A:HOH856 3.7 62.0 1.0
HB3 A:ASN40 3.8 29.0 1.0
O A:HOH699 3.8 25.1 1.0
H A:VAL41 3.8 21.9 1.0
C6 A:6O0503 3.9 36.8 0.7
CB A:ALA1 4.0 24.6 1.0
N A:THR2 4.1 21.8 0.7
HB1 A:ALA1 4.2 24.4 1.0
C4 A:6O0503 4.2 36.9 0.7
C3 A:6O0503 4.2 36.9 0.7
N A:THR2 4.2 21.2 0.3
HA A:ASN40 4.2 24.9 1.0
HB3 A:ALA1 4.3 24.4 1.0
H2C A:6O0503 4.3 37.2 0.7
H5A A:6O0503 4.3 36.6 0.7
HG3 A:PRO43 4.4 22.9 1.0
N A:VAL41 4.5 21.3 1.0
C A:VAL41 4.5 21.5 1.0
H7A A:6O0503 4.5 36.9 0.7
H A:THR2 4.5 22.1 0.7
CD A:PRO43 4.5 22.9 1.0
HG23 A:THR2 4.6 22.6 0.7
H6A A:6O0503 4.6 36.8 0.7
CB A:ASN40 4.6 28.8 1.0
H A:THR2 4.7 21.4 0.3
HA A:GLU42 4.7 24.2 1.0
HB2 A:ALA1 4.8 24.5 1.0
CA A:ASN40 4.8 25.1 1.0
C7 A:6O0503 4.8 36.6 0.7
HG21 A:THR2 4.9 22.7 0.7
HA A:THR2 4.9 21.4 0.7
OD1 A:ASN40 4.9 37.9 1.0
CG A:PRO43 4.9 23.0 1.0
HA A:THR2 4.9 20.1 0.3
OG1 A:THR2 5.0 18.9 0.3

Gold binding site 2 out of 7 in 5jvx

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Gold binding site 2 out of 7 in the X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au504

b:28.3
occ:0.55
AU A:6O0504 0.0 28.3 0.6
NZ A:LYS49 1.6 23.0 1.0
C1 A:6O0504 1.9 26.5 0.6
CE A:LYS49 2.9 21.8 1.0
N1 A:6O0504 2.9 27.8 0.6
N2 A:6O0504 3.0 26.5 0.6
HD2 A:LYS49 3.0 20.8 1.0
H2C A:6O0504 3.1 28.4 0.6
HE3 A:LYS49 3.2 21.8 1.0
CD A:LYS49 3.3 20.9 1.0
HD3 A:LYS49 3.3 20.8 1.0
H2A A:6O0504 3.3 28.4 0.6
C2 A:6O0504 3.3 28.7 0.6
C5 A:6O0504 3.4 24.8 0.6
HD13 A:LEU87 3.5 16.3 1.0
HE2 A:LYS49 3.6 21.8 1.0
HG3 A:LYS106 3.6 21.6 0.6
HG3 A:LYS106 3.6 18.9 0.4
HD12 A:LEU87 3.7 16.3 1.0
H5B A:6O0504 3.8 24.7 0.6
CD2 A:PHE80 3.8 23.0 1.0
HD2 A:PHE80 3.9 22.8 1.0
H8A A:6O0504 3.9 21.8 0.6
HE3 A:LYS106 3.9 26.1 0.6
CD1 A:LEU87 4.0 16.3 1.0
CE2 A:PHE80 4.1 23.0 1.0
C4 A:6O0504 4.2 27.2 0.6
C3 A:6O0504 4.2 28.1 0.6
CG A:PHE80 4.2 22.0 1.0
HE2 A:PHE80 4.3 23.1 1.0
H2B A:6O0504 4.3 28.4 0.6
HB3 A:PHE80 4.3 22.3 1.0
HD22 A:LEU87 4.3 17.3 1.0
HG2 A:LYS106 4.5 21.5 0.6
CG A:LYS106 4.5 21.4 0.6
HD11 A:LEU87 4.6 16.3 1.0
CG A:LYS106 4.6 18.8 0.4
O A:HOH896 4.6 45.9 1.0
CZ A:PHE80 4.6 23.5 1.0
OE2 A:GLU89 4.7 17.8 1.0
CB A:PHE80 4.7 22.5 1.0
CD1 A:PHE80 4.8 22.8 1.0
C6 A:6O0504 4.8 22.8 0.6
CE A:LYS106 4.8 26.1 0.6
CG A:LYS49 4.8 19.5 1.0
HG2 A:LYS106 4.8 18.9 0.4
C8 A:6O0504 4.8 21.1 0.6
HD2 A:LYS106 4.9 19.9 0.4
HB2 A:PHE80 4.9 22.3 1.0
H6A A:6O0504 4.9 23.3 0.6
CE1 A:PHE80 5.0 23.4 1.0
HE2 A:LYS106 5.0 26.1 0.6

Gold binding site 3 out of 7 in 5jvx

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Gold binding site 3 out of 7 in the X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au505

b:42.6
occ:0.35
AU A:6O0505 0.0 42.6 0.3
C1 A:6O0505 1.9 38.1 0.3
NZ A:LYS106 2.4 28.8 0.6
H2A A:6O0505 2.8 38.3 0.3
H3 A:6O0504 2.9 27.8 0.6
HD3 A:LYS106 2.9 19.9 0.4
HE2 A:LYS106 2.9 20.9 0.4
N1 A:6O0505 3.0 38.4 0.3
N2 A:6O0505 3.0 38.0 0.3
HD2 A:LYS106 3.1 19.9 0.4
H5B A:6O0505 3.1 37.0 0.3
C3 A:6O0504 3.1 28.1 0.6
H4 A:6O0504 3.2 27.2 0.6
HG2 A:PRO83 3.2 20.1 1.0
CD A:LYS106 3.3 19.9 0.4
C2 A:6O0505 3.4 38.3 0.3
C5 A:6O0505 3.4 36.9 0.3
C4 A:6O0504 3.5 27.2 0.6
H5A A:6O0505 3.5 37.0 0.3
HE3 A:LYS106 3.5 26.1 0.6
CE A:LYS106 3.5 26.1 0.6
HD2 A:LYS106 3.6 23.7 0.6
HD3 A:PRO83 3.6 19.7 1.0
CE A:LYS106 3.6 20.9 0.4
CG A:PRO83 3.8 20.4 1.0
HG3 A:PRO83 3.8 20.1 1.0
HD2 A:PRO83 3.9 19.8 1.0
CD A:PRO83 4.0 19.9 1.0
H2B A:6O0505 4.0 38.3 0.3
H2C A:6O0505 4.1 38.3 0.3
H2A A:6O0505 4.1 26.6 0.3
CD A:LYS106 4.1 23.9 0.6
N1 A:6O0504 4.1 27.8 0.6
C4 A:6O0505 4.2 38.0 0.3
C3 A:6O0505 4.2 38.3 0.3
HE3 A:LYS106 4.2 20.9 0.4
HE2 A:LYS106 4.3 26.1 0.6
N2 A:6O0504 4.5 26.5 0.6
H2B A:6O0504 4.6 28.4 0.6
NZ A:LYS106 4.7 22.0 0.4
H2B A:6O0505 4.7 26.6 0.3
AU A:6O0505 4.8 27.8 0.3
HD3 A:LYS106 4.8 23.8 0.6
CG A:LYS106 4.8 18.8 0.4
C2 A:6O0504 4.8 28.7 0.6
HG3 A:LYS106 4.8 21.6 0.6
C2 A:6O0505 4.8 26.7 0.3
H2A A:6O0504 4.9 28.4 0.6
C1 A:6O0504 4.9 26.5 0.6
C6 A:6O0505 4.9 36.1 0.3
HG3 A:LYS106 5.0 18.9 0.4

Gold binding site 4 out of 7 in 5jvx

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Gold binding site 4 out of 7 in the X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au505

b:27.8
occ:0.35
AU A:6O0505 0.0 27.8 0.3
C1 A:6O0505 1.9 26.3 0.3
NZ A:LYS106 2.1 22.0 0.4
H6B A:6O0505 2.1 23.8 0.3
HE2 A:LYS106 2.5 26.1 0.6
NZ A:LYS106 2.6 28.8 0.6
HD3 A:LYS106 2.6 23.8 0.6
CE A:LYS106 2.8 26.1 0.6
C6 A:6O0505 2.9 23.8 0.3
H2A A:6O0505 3.0 26.6 0.3
N2 A:6O0505 3.0 24.9 0.3
N1 A:6O0505 3.0 26.3 0.3
H6A A:6O0505 3.0 23.8 0.3
CE A:LYS106 3.1 20.9 0.4
CD A:LYS106 3.1 23.9 0.6
HE2 A:LYS106 3.1 20.9 0.4
HD2 A:LYS106 3.2 19.9 0.4
C5 A:6O0505 3.3 24.3 0.3
HD2 A:LYS106 3.3 23.7 0.6
H5B A:6O0505 3.5 24.3 0.3
C2 A:6O0505 3.5 26.7 0.3
SG A:CYS149 3.6 19.4 1.0
HB3 A:CYS149 3.6 18.2 1.0
CD A:LYS106 3.6 19.9 0.4
HE3 A:LYS106 3.7 26.1 0.6
HE3 A:LYS106 3.9 20.9 0.4
HG2 A:LYS106 3.9 18.9 0.4
H7A A:6O0505 4.0 23.3 0.3
H2C A:6O0505 4.1 26.6 0.3
H2B A:6O0505 4.1 26.6 0.3
C7 A:6O0505 4.1 23.5 0.3
CB A:CYS149 4.1 17.9 1.0
C4 A:6O0505 4.1 25.4 0.3
HG21 A:ILE105 4.2 17.6 1.0
C3 A:6O0505 4.2 25.5 0.3
H5A A:6O0505 4.2 24.3 0.3
OD2 A:ASP147 4.3 18.0 1.0
O A:ILE105 4.4 16.2 1.0
CG A:LYS106 4.4 18.8 0.4
HD3 A:LYS106 4.4 19.9 0.4
CG A:LYS106 4.5 21.4 0.6
HG23 A:ILE105 4.6 17.7 1.0
HG2 A:LYS106 4.6 21.5 0.6
HB2 A:CYS149 4.6 18.2 1.0
HA A:LYS106 4.6 17.3 0.4
H7B A:6O0505 4.6 23.4 0.3
HA A:LYS106 4.6 18.0 0.6
O A:HOH896 4.7 45.9 1.0
AU A:6O0505 4.8 42.6 0.3
CG2 A:ILE105 4.8 17.6 1.0
HA A:CYS158 4.9 17.8 1.0
OG1 A:THR150 4.9 18.5 1.0
H A:THR150 4.9 18.2 1.0
HG3 A:LYS106 5.0 21.6 0.6
H4 A:6O0505 5.0 25.4 0.3

Gold binding site 5 out of 7 in 5jvx

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Gold binding site 5 out of 7 in the X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 5 of X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au506

b:52.3
occ:0.15
NZ A:LYS97 2.1 29.2 0.5
HE3 A:LYS97 2.3 29.0 0.5
CE A:LYS97 2.7 29.1 0.5
HE3 A:LYS97 3.0 29.0 0.5
HG22 A:THR192 3.1 23.1 1.0
HE2 A:LYS97 3.5 29.0 0.5
HG3 A:LYS97 3.5 27.3 0.5
HD2 A:LYS97 3.5 28.2 0.5
HG3 A:LYS97 3.6 27.3 0.5
CD A:LYS97 3.6 28.5 0.5
CE A:LYS97 3.8 29.0 0.5
HD2 A:LYS97 3.9 28.4 0.5
O A:HOH649 3.9 42.5 1.0
CG2 A:THR192 3.9 23.1 1.0
HG23 A:THR192 3.9 23.1 1.0
CG A:LYS97 4.1 27.2 0.5
CD A:LYS97 4.2 28.6 0.5
NZ A:LYS97 4.2 29.6 0.5
CG A:LYS97 4.2 27.2 0.5
HD3 A:LYS97 4.4 28.3 0.5
HG21 A:THR192 4.5 23.1 1.0
HB A:THR192 4.6 22.9 1.0
HE2 A:LYS97 4.6 29.1 0.5
HG2 A:LYS97 4.7 27.3 0.5
O A:HOH708 4.7 33.0 0.7
HG2 A:LYS97 4.7 27.3 0.5
HG1 A:THR192 4.8 23.5 0.0
HH A:TYR99 4.8 29.9 0.0
CB A:THR192 4.8 23.0 1.0

Gold binding site 6 out of 7 in 5jvx

Go back to Gold Binding Sites List in 5jvx
Gold binding site 6 out of 7 in the X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 6 of X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au507

b:48.4
occ:0.35
O A:HOH835 2.2 19.4 0.3
NH1 A:ARG8 2.2 21.5 1.0
O A:HOH735 2.9 32.5 0.7
HH22 A:ARG8 3.0 21.3 1.0
CZ A:ARG8 3.2 21.0 1.0
NH2 A:ARG8 3.5 21.5 1.0
O A:PRO205 3.6 23.0 1.0
HG22 A:THR202 3.7 17.7 1.0
HH22 A:ARG125 3.7 34.5 1.0
HB2 A:PRO205 3.8 20.5 1.0
HA A:PRO205 3.8 21.0 1.0
HB3 A:PRO205 3.9 20.5 1.0
CB A:PRO205 4.1 20.5 1.0
HH21 A:ARG125 4.1 34.3 1.0
NH2 A:ARG125 4.1 35.3 1.0
HG1 A:THR202 4.1 17.5 0.0
O A:HOH622 4.2 51.0 1.0
CA A:PRO205 4.3 20.9 1.0
HH21 A:ARG8 4.3 21.3 1.0
O A:HOH606 4.3 38.5 1.0
C A:PRO205 4.4 23.6 1.0
NE A:ARG8 4.4 18.5 1.0
CG2 A:THR202 4.5 18.0 1.0
HG21 A:THR202 4.5 17.7 1.0
O A:HOH830 4.6 61.7 1.0
HD2 A:ARG8 4.6 18.5 1.0
HB A:THR202 4.6 17.2 1.0
OG1 A:THR202 4.9 17.1 1.0
CB A:THR202 4.9 17.2 1.0

Gold binding site 7 out of 7 in 5jvx

Go back to Gold Binding Sites List in 5jvx
Gold binding site 7 out of 7 in the X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 7 of X-Ray Structure of the Adduct Formed in the Reaction Between Thaumatin and A Gold Carbene Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au508

b:31.6
occ:0.20
NH2 A:ARG175 2.2 22.7 0.5
O A:HOH744 2.2 21.4 1.0
O A:HOH693 2.7 14.8 0.5
HA A:PHE172 2.9 17.2 1.0
CZ A:ARG175 3.0 21.1 0.5
NE A:ARG175 3.1 22.4 0.5
HB2 A:PHE172 3.2 17.5 1.0
NE A:ARG175 3.5 16.7 0.5
HD1 A:PHE172 3.6 17.6 1.0
NH2 A:ARG175 3.7 17.5 0.5
CA A:PHE172 3.7 17.3 1.0
CB A:PHE172 3.9 17.6 1.0
N A:PHE172 4.0 16.8 1.0
CZ A:ARG175 4.1 15.3 0.5
O A:HOH892 4.2 31.0 1.0
NH1 A:ARG175 4.3 23.3 0.5
H A:PHE172 4.3 16.9 1.0
CD1 A:PHE172 4.4 17.5 1.0
C A:ARG171 4.5 16.9 1.0
CD A:ARG175 4.5 22.8 0.5
O A:ARG171 4.6 18.5 1.0
HB3 A:PHE172 4.6 17.5 1.0
O A:GLU168 4.6 17.3 1.0
CD A:ARG175 4.6 15.7 0.5
CG A:PHE172 4.7 17.6 1.0
O A:HOH659 4.7 34.1 1.0
HB3 A:ARG171 4.8 17.8 1.0
O A:HOH833 4.9 45.0 1.0
HB2 A:ARG171 4.9 17.8 1.0
CB A:ARG175 4.9 20.1 0.5
C A:PHE172 5.0 16.9 1.0

Reference:

G.Ferraro, C.Gabbiani, A.Merlino. First Crystal Structure For A Gold Carbene-Protein Adduct. Bioconjug.Chem. V. 27 1584 2016.
ISSN: ISSN 1043-1802
PubMed: 27364343
DOI: 10.1021/ACS.BIOCONJCHEM.6B00298
Page generated: Sat Dec 12 01:54:22 2020

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