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Cadmium in PDB 6ex7: Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement

Enzymatic activity of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement

All present enzymatic activity of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement, PDB code: 6ex7 was solved by Y.Kim, J.E.Raczynska, I.G.Shabalin, M.Jaskolski, W.Minor, A.Wlodawer, C.Tesar, R.Jedrzejczak, J.Babnigg, J.Mire, J.Sacchettini, A.Joachimiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.20 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.062, 39.220, 75.233, 90.00, 99.99, 90.00
R / Rfree (%) 19.5 / 22.6

Other elements in 6ex7:

The structure of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement (pdb code 6ex7). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement, PDB code: 6ex7:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 6ex7

Go back to Cadmium Binding Sites List in 6ex7
Cadmium binding site 1 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:34.9
occ:1.00
 O71 A:UNL305 2.2 35.1 1.0
NE2 A:HIS120 2.2 20.9 1.0
NE2 A:HIS189 2.3 24.6 1.0
ND1 A:HIS122 2.3 21.1 1.0
CE1 A:HIS120 3.0 23.1 1.0
C7 A:UNL305 3.0 48.0 1.0
CD2 A:HIS189 3.2 22.4 1.0
SG A:CYS208 3.2 27.1 1.0
O72 A:UNL305 3.2 52.3 1.0
CE1 A:HIS122 3.3 20.6 1.0
CG A:HIS122 3.3 19.5 1.0
CD2 A:HIS120 3.3 19.4 1.0
CE1 A:HIS189 3.4 23.7 1.0
CD A:CD302 3.5 38.8 1.0
OD1 A:ASP124 3.5 34.2 1.0
CB A:HIS122 3.5 19.6 1.0
CB A:CYS208 3.7 27.7 1.0
OD2 A:ASP124 4.0 39.8 1.0
ND1 A:HIS120 4.2 21.0 1.0
CG A:ASP124 4.2 36.2 1.0
CG A:HIS189 4.4 23.0 1.0
CG A:HIS120 4.4 18.0 1.0
ND1 A:HIS189 4.4 23.8 1.0
NE2 A:HIS122 4.4 21.3 1.0
O31 A:UNL305 4.4 36.4 1.0
CD2 A:HIS122 4.4 20.9 1.0
C6 A:UNL305 4.5 64.1 1.0
N4 A:UNL305 4.7 51.0 1.0
CG2 A:THR190 4.9 21.2 1.0

Cadmium binding site 2 out of 6 in 6ex7

Go back to Cadmium Binding Sites List in 6ex7
Cadmium binding site 2 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:38.8
occ:1.00
 O31 A:UNL305 2.2 36.4 1.0
O71 A:UNL305 2.2 35.1 1.0
NE2 A:HIS250 2.2 32.6 1.0
N4 A:UNL305 2.2 51.0 1.0
OD2 A:ASP124 2.2 39.8 1.0
SG A:CYS208 2.5 27.1 1.0
C7 A:UNL305 3.0 48.0 1.0
CE1 A:HIS250 3.0 33.4 1.0
C3 A:UNL305 3.0 54.9 1.0
C31 A:UNL305 3.1 45.5 1.0
C5 A:UNL305 3.3 52.9 1.0
CD2 A:HIS250 3.3 33.3 1.0
CG A:ASP124 3.4 36.2 1.0
CD A:CD301 3.5 34.9 1.0
CB A:CYS208 3.5 27.7 1.0
C6 A:UNL305 3.6 64.1 1.0
OD1 A:ASP124 3.9 34.2 1.0
O72 A:UNL305 4.0 52.3 1.0
ND1 A:HIS250 4.2 36.7 1.0
O32 A:UNL305 4.2 42.4 1.0
NE2 A:HIS189 4.3 24.6 1.0
C2 A:UNL305 4.3 67.0 1.0
CG A:HIS250 4.4 37.1 1.0
CB A:SER249 4.4 28.6 1.0
CE1 A:HIS189 4.4 23.7 1.0
CA A:CYS208 4.5 26.9 1.0
S1 A:UNL305 4.7 60.4 1.0
CB A:ASP124 4.7 38.0 1.0
OG A:SER249 4.8 29.6 1.0

Cadmium binding site 3 out of 6 in 6ex7

Go back to Cadmium Binding Sites List in 6ex7
Cadmium binding site 3 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:33.6
occ:0.72
 OD2 A:ASP223 2.1 29.2 1.0
O A:HOH411 2.2 45.8 1.0
OE1 B:GLU227 2.4 49.5 1.0
OE1 A:GLU152 2.4 28.7 1.0
OE2 B:GLU227 2.5 48.3 1.0
OE2 A:GLU152 2.6 30.0 1.0
OD1 A:ASP223 2.8 43.5 1.0
CD B:GLU227 2.8 39.1 1.0
CG A:ASP223 2.8 35.4 1.0
O A:HOH455 2.9 40.5 1.0
CD A:GLU152 2.9 30.2 1.0
NE2 A:HIS122 4.1 21.3 1.0
O A:HOH457 4.1 26.9 1.0
NE2 B:HIS228 4.2 25.2 1.0
CG B:GLU227 4.3 34.9 1.0
CB A:ASP223 4.3 32.2 1.0
CE1 B:HIS228 4.4 25.3 1.0
CG A:GLU152 4.4 26.8 1.0
CD2 A:HIS122 4.6 20.9 1.0
O A:HOH431 4.7 44.1 1.0

Cadmium binding site 4 out of 6 in 6ex7

Go back to Cadmium Binding Sites List in 6ex7
Cadmium binding site 4 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd307

b:31.0
occ:0.63
 O A:HOH451 2.2 39.2 1.0
OD2 B:ASP223 2.2 38.9 1.0
OE2 A:GLU227 2.3 52.6 1.0
OE1 A:GLU227 2.4 54.6 1.0
OE1 B:GLU152 2.4 27.0 1.0
OE2 B:GLU152 2.6 32.2 1.0
CD A:GLU227 2.6 44.3 1.0
OD1 B:ASP223 2.8 37.8 1.0
CG B:ASP223 2.9 29.9 1.0
CD B:GLU152 2.9 27.0 1.0
CG A:GLU227 4.0 46.1 1.0
O B:HOH481 4.1 27.3 1.0
NE2 A:HIS228 4.1 24.6 1.0
NE2 B:HIS122 4.2 29.7 1.0
CE1 A:HIS228 4.3 25.6 1.0
CB B:ASP223 4.4 27.9 1.0
CG B:GLU152 4.4 25.6 1.0
CD2 B:HIS122 4.7 21.9 1.0
CB A:GLU227 4.8 36.9 1.0

Cadmium binding site 5 out of 6 in 6ex7

Go back to Cadmium Binding Sites List in 6ex7
Cadmium binding site 5 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:32.6
occ:1.00
 O72 B:UNL305 2.2 35.0 1.0
NE2 B:HIS120 2.2 17.8 1.0
ND1 B:HIS122 2.3 20.1 1.0
NE2 B:HIS189 2.3 20.2 1.0
C7 B:UNL305 3.0 54.4 1.0
CE1 B:HIS120 3.0 18.6 1.0
CD2 B:HIS189 3.2 18.6 1.0
CE1 B:HIS122 3.2 27.9 1.0
O71 B:UNL305 3.2 51.1 1.0
CG B:HIS122 3.2 19.7 1.0
SG B:CYS208 3.3 21.7 1.0
CD2 B:HIS120 3.3 16.5 1.0
CE1 B:HIS189 3.4 20.3 1.0
OD1 B:ASP124 3.5 25.9 1.0
CB B:HIS122 3.5 20.4 1.0
CD B:CD302 3.5 30.2 1.0
CB B:CYS208 3.8 19.8 1.0
OD2 B:ASP124 4.0 43.8 1.0
ND1 B:HIS120 4.2 16.6 1.0
CG B:ASP124 4.2 29.5 1.0
NE2 B:HIS122 4.3 29.7 1.0
CG B:HIS120 4.4 15.2 1.0
CG B:HIS189 4.4 18.6 1.0
CD2 B:HIS122 4.4 21.9 1.0
ND1 B:HIS189 4.4 19.3 1.0
C6 B:UNL305 4.5 69.3 1.0
O32 B:UNL305 4.5 29.3 1.0
N4 B:UNL305 4.7 50.9 1.0
CG2 B:THR190 4.9 17.3 1.0
CA B:HIS122 5.0 19.7 1.0

Cadmium binding site 6 out of 6 in 6ex7

Go back to Cadmium Binding Sites List in 6ex7
Cadmium binding site 6 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Cd Ions and A Hydrolyzed Beta-Lactam Ligand - New Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:30.2
occ:1.00
 O72 B:UNL305 2.2 35.0 1.0
OD2 B:ASP124 2.2 43.8 1.0
O32 B:UNL305 2.2 29.3 1.0
NE2 B:HIS250 2.2 21.5 1.0
N4 B:UNL305 2.2 50.9 1.0
SG B:CYS208 2.5 21.7 1.0
C7 B:UNL305 3.0 54.4 1.0
CE1 B:HIS250 3.0 23.4 1.0
C3 B:UNL305 3.0 46.6 1.0
C31 B:UNL305 3.1 30.4 1.0
C5 B:UNL305 3.2 56.1 1.0
CD2 B:HIS250 3.3 21.1 1.0
CG B:ASP124 3.4 29.5 1.0
CD B:CD301 3.5 32.6 1.0
C6 B:UNL305 3.5 69.3 1.0
CB B:CYS208 3.5 19.8 1.0
OD1 B:ASP124 3.8 25.9 1.0
O71 B:UNL305 4.0 51.1 1.0
ND1 B:HIS250 4.2 23.9 1.0
NE2 B:HIS189 4.2 20.2 1.0
O31 B:UNL305 4.2 36.9 1.0
C2 B:UNL305 4.3 42.9 1.0
CB B:SER249 4.4 22.4 1.0
CG B:HIS250 4.4 22.5 1.0
CE1 B:HIS189 4.4 20.3 1.0
CA B:CYS208 4.5 19.0 1.0
CB B:ASP124 4.6 29.4 1.0
S1 B:UNL305 4.7 50.3 1.0
OG B:SER249 4.8 24.2 1.0

Reference:

J.E.Raczynska, I.G.Shabalin, W.Minor, A.Wlodawer, M.Jaskolski. A Close Look Onto Structural Models and Primary Ligands of Metallo-Beta-Lactamases. Drug Resist. Updat. V. 40 1 2018.
ISSN: ESSN 1532-2084
PubMed: 30466711
DOI: 10.1016/J.DRUP.2018.08.001
Page generated: Sat Dec 12 08:28:20 2020

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