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Gold in PDB 6lhe: Crystal Structure of Gold-Bound Ndm-1

Enzymatic activity of Crystal Structure of Gold-Bound Ndm-1

All present enzymatic activity of Crystal Structure of Gold-Bound Ndm-1:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Gold-Bound Ndm-1, PDB code: 6lhe was solved by H.Wang, H.Sun, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.95 / 1.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.470, 73.760, 77.720, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19

Gold Binding Sites:

The binding sites of Gold atom in the Crystal Structure of Gold-Bound Ndm-1 (pdb code 6lhe). 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 Gold-Bound Ndm-1, PDB code: 6lhe:
Jump to Gold binding site number: 1; 2; 3; 4; 5; 6;

Gold binding site 1 out of 6 in 6lhe

Go back to Gold Binding Sites List in 6lhe
Gold binding site 1 out of 6 in the Crystal Structure of Gold-Bound Ndm-1


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 Gold-Bound Ndm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au301

b:17.3
occ:0.55
 OD2 A:ASP223 2.2 17.5 1.0
O A:HOH557 2.3 46.8 1.0
OE2 A:GLU152 2.3 16.3 1.0
OE2 B:GLU227 2.4 24.3 1.0
OE1 A:GLU152 2.4 17.4 1.0
OE1 B:GLU227 2.5 20.8 1.0
CD A:GLU152 2.7 15.6 1.0
CD B:GLU227 2.8 19.9 1.0
CG A:ASP223 2.9 17.3 1.0
OD1 A:ASP223 3.0 20.2 1.0
O A:HOH563 3.8 35.9 1.0
O A:HOH491 4.2 17.8 1.0
NE2 A:HIS122 4.2 17.1 1.0
CG A:GLU152 4.3 14.0 1.0
NE2 B:HIS228 4.3 15.2 1.0
CG B:GLU227 4.3 18.6 1.0
CB A:ASP223 4.4 17.6 1.0
O A:HOH525 4.5 34.0 1.0
O B:HOH414 4.5 37.2 1.0
CE1 B:HIS228 4.5 16.5 1.0
O A:HOH439 4.6 19.1 1.0
O B:HOH483 4.8 25.7 1.0
CD2 A:HIS122 4.8 15.0 1.0

Gold binding site 2 out of 6 in 6lhe

Go back to Gold Binding Sites List in 6lhe
Gold binding site 2 out of 6 in the Crystal Structure of Gold-Bound Ndm-1


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 Gold-Bound Ndm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au302

b:17.5
occ:0.53
 OD2 A:ASP124 2.2 18.6 1.0
NE2 A:HIS250 2.3 17.2 1.0
O A:HOH568 2.4 20.2 1.0
SG A:CYS208 2.5 15.3 1.0
CE1 A:HIS250 3.2 17.1 1.0
CD2 A:HIS250 3.2 16.0 1.0
CG A:ASP124 3.3 17.0 1.0
CB A:CYS208 3.5 14.8 1.0
O A:HOH436 3.6 50.0 1.0
OD1 A:ASP124 3.6 17.1 1.0
AU A:AU303 3.8 30.1 0.4
NE2 A:HIS189 4.2 19.5 1.0
O A:HOH569 4.3 32.2 1.0
ND1 A:HIS250 4.4 15.8 1.0
CG A:HIS250 4.4 17.9 1.0
CE1 A:HIS189 4.4 16.1 1.0
CB A:SER249 4.4 14.8 1.0
CB A:ASP124 4.6 16.3 1.0
CA A:CYS208 4.7 14.2 1.0
OG A:SER249 4.7 15.1 1.0
NE2 A:HIS120 4.8 18.0 1.0
CE1 A:HIS120 4.9 13.1 1.0
O A:HOH596 5.0 45.6 1.0

Gold binding site 3 out of 6 in 6lhe

Go back to Gold Binding Sites List in 6lhe
Gold binding site 3 out of 6 in the Crystal Structure of Gold-Bound Ndm-1


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 Gold-Bound Ndm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au303

b:30.1
occ:0.41
 O A:HOH436 1.9 50.0 1.0
ND1 A:HIS122 2.0 17.7 1.0
NE2 A:HIS189 2.0 19.5 1.0
NE2 A:HIS120 2.5 18.0 1.0
CE1 A:HIS122 3.0 16.6 1.0
CD2 A:HIS189 3.0 16.4 1.0
CG A:HIS122 3.0 14.3 1.0
CE1 A:HIS189 3.1 16.1 1.0
CD2 A:HIS120 3.4 12.1 1.0
CB A:HIS122 3.4 14.8 1.0
CE1 A:HIS120 3.5 13.1 1.0
O A:HOH569 3.5 32.2 1.0
O A:HOH568 3.6 20.2 1.0
AU A:AU302 3.8 17.5 0.5
OD1 A:ASP124 4.1 17.1 1.0
NE2 A:HIS122 4.1 17.1 1.0
CD2 A:HIS122 4.1 15.0 1.0
CG A:HIS189 4.1 15.5 1.0
ND1 A:HIS189 4.2 16.1 1.0
SG A:CYS208 4.2 15.3 1.0
CB A:CYS208 4.5 14.8 1.0
CG A:HIS120 4.5 13.8 1.0
ND1 A:HIS120 4.6 14.6 1.0
CG2 A:THR190 4.6 15.2 1.0
OD2 A:ASP124 4.7 18.6 1.0
O A:HOH565 4.8 35.7 1.0
CG A:ASP124 4.8 17.0 1.0
CA A:HIS122 4.9 13.6 1.0

Gold binding site 4 out of 6 in 6lhe

Go back to Gold Binding Sites List in 6lhe
Gold binding site 4 out of 6 in the Crystal Structure of Gold-Bound Ndm-1


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 Gold-Bound Ndm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au301

b:20.8
occ:0.53
 O B:HOH548 2.2 51.4 1.0
OD2 B:ASP223 2.2 19.6 1.0
OE2 B:GLU152 2.4 20.7 1.0
OE2 A:GLU227 2.4 29.0 1.0
OE1 B:GLU152 2.5 20.2 1.0
OE1 A:GLU227 2.5 25.2 1.0
CD B:GLU152 2.8 17.5 1.0
CD A:GLU227 2.8 21.6 1.0
CG B:ASP223 2.9 19.9 1.0
OD1 B:ASP223 3.0 23.4 1.0
O B:HOH567 4.1 40.6 1.0
O B:HOH507 4.2 19.0 1.0
NE2 B:HIS122 4.2 20.1 1.0
CG B:GLU152 4.3 18.4 1.0
CG A:GLU227 4.3 21.2 1.0
NE2 A:HIS228 4.3 17.9 1.0
O B:HOH480 4.3 40.4 1.0
CB B:ASP223 4.4 20.2 1.0
CE1 A:HIS228 4.5 19.5 1.0
O B:HOH435 4.7 22.0 1.0
CD2 B:HIS122 4.9 20.1 1.0

Gold binding site 5 out of 6 in 6lhe

Go back to Gold Binding Sites List in 6lhe
Gold binding site 5 out of 6 in the Crystal Structure of Gold-Bound Ndm-1


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 Gold-Bound Ndm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au302

b:19.7
occ:0.53
 NE2 B:HIS250 2.3 18.8 1.0
OD2 B:ASP124 2.3 21.5 1.0
O B:HOH560 2.4 20.2 1.0
SG B:CYS208 2.4 15.9 1.0
CE1 B:HIS250 3.2 18.6 1.0
CD2 B:HIS250 3.2 18.9 1.0
CG B:ASP124 3.3 18.3 1.0
CB B:CYS208 3.5 15.2 1.0
O B:HOH557 3.5 26.3 1.0
OD1 B:ASP124 3.7 20.4 1.0
AU B:AU303 3.8 29.2 0.5
O B:HOH559 4.1 33.3 1.0
NE2 B:HIS189 4.3 19.7 1.0
ND1 B:HIS250 4.3 17.3 1.0
CG B:HIS250 4.4 18.2 1.0
CB B:SER249 4.4 16.3 1.0
CE1 B:HIS189 4.5 16.3 1.0
CB B:ASP124 4.6 18.9 1.0
CA B:CYS208 4.7 13.8 1.0
OG B:SER249 4.7 15.5 1.0
NE2 B:HIS120 4.8 19.2 1.0
CE1 B:HIS120 4.9 15.5 1.0

Gold binding site 6 out of 6 in 6lhe

Go back to Gold Binding Sites List in 6lhe
Gold binding site 6 out of 6 in the Crystal Structure of Gold-Bound Ndm-1


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 Gold-Bound Ndm-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au303

b:29.2
occ:0.45
 ND1 B:HIS122 2.0 18.4 1.0
NE2 B:HIS189 2.1 19.7 1.0
NE2 B:HIS120 2.8 19.2 1.0
CE1 B:HIS122 2.9 19.5 1.0
CG B:HIS122 3.1 16.7 1.0
CE1 B:HIS189 3.1 16.3 1.0
CD2 B:HIS189 3.1 14.9 1.0
O B:HOH559 3.2 33.3 1.0
O B:HOH560 3.3 20.2 1.0
CB B:HIS122 3.4 18.0 1.0
CD2 B:HIS120 3.6 15.6 1.0
CE1 B:HIS120 3.8 15.5 1.0
AU B:AU302 3.8 19.7 0.5
O B:HOH555 3.9 42.7 1.0
NE2 B:HIS122 4.1 20.1 1.0
CD2 B:HIS122 4.2 20.1 1.0
OD1 B:ASP124 4.2 20.4 1.0
ND1 B:HIS189 4.2 15.9 1.0
CG B:HIS189 4.3 14.8 1.0
SG B:CYS208 4.3 15.9 1.0
CB B:CYS208 4.6 15.2 1.0
CG2 B:THR190 4.6 17.0 1.0
O B:HOH563 4.7 35.4 1.0
CG B:HIS120 4.8 15.6 1.0
OD2 B:ASP124 4.8 21.5 1.0
ND1 B:HIS120 4.8 17.4 1.0
CG B:ASP124 4.9 18.3 1.0
CA B:HIS122 5.0 17.1 1.0

Reference:

H.Sun, Q.Zhang, R.Wang, H.Wang, Y.T.Wong, M.Wang, Q.Hao, A.Yan, R.Y.Kao, P.L.Ho, H.Li. Resensitizing Carbapenem- and Colistin-Resistant Bacteria to Antibiotics Using Auranofin. Nat Commun V. 11 5263 2020.
ISSN: ESSN 2041-1723
PubMed: 33067430
DOI: 10.1038/S41467-020-18939-Y
Page generated: Wed Jul 10 14:38:09 2024

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