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Cadmium in PDB 3srx: New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd

Enzymatic activity of New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd

All present enzymatic activity of New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd:
3.5.2.6;

Protein crystallography data

The structure of New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd, PDB code: 3srx was solved by Y.Kim, C.Tesar, R.Jedrzejczak, J.Babnigg, T.A.Binkowski, J.Mire, J.Sacchettini, A.Joachimiak, Midwest Center For Structural Genomics(Mcsg), Structures Of Mtb Proteins Conferring Susceptibility To Knownmtb Inhibitors (Mtbi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.53 / 2.50
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 108.945, 108.945, 237.883, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 21.2

Other elements in 3srx:

The structure of New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd (pdb code 3srx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd, PDB code: 3srx:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 3srx

Go back to Cadmium Binding Sites List in 3srx
Cadmium binding site 1 out of 6 in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd280

b:41.5
occ:1.00
 NE2 A:HIS250 2.2 50.4 1.0
CL A:CL284 2.4 35.1 1.0
OD2 A:ASP124 2.5 34.4 1.0
SG A:CYS208 2.5 45.4 1.0
CL A:CL285 2.5 46.1 1.0
CE1 A:HIS250 3.2 47.2 1.0
CD2 A:HIS250 3.2 48.6 1.0
CD A:CD281 3.4 43.1 1.0
CB A:CYS208 3.5 40.5 1.0
CG A:ASP124 3.6 58.1 1.0
CE1 A:HIS189 3.8 39.7 1.0
NE2 A:HIS189 3.9 37.7 1.0
OD1 A:ASP124 4.2 58.2 1.0
ND1 A:HIS250 4.3 49.0 1.0
CG A:HIS250 4.3 50.1 1.0
CB A:SER249 4.4 38.8 1.0
CA A:CYS208 4.4 41.7 1.0
OG A:SER249 4.6 38.8 1.0
CB A:ASP124 4.7 55.3 1.0
ND1 A:HIS189 4.7 41.5 1.0
NZ A:LYS211 4.9 48.5 1.0
CD2 A:HIS189 4.9 38.0 1.0

Cadmium binding site 2 out of 6 in 3srx

Go back to Cadmium Binding Sites List in 3srx
Cadmium binding site 2 out of 6 in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd281

b:43.1
occ:1.00
 NE2 A:HIS120 2.3 37.4 1.0
ND1 A:HIS122 2.4 44.4 1.0
NE2 A:HIS189 2.5 37.7 1.0
CL A:CL285 2.7 46.1 1.0
OD1 A:ASP124 2.8 58.2 1.0
SG A:CYS208 2.9 45.4 1.0
OD2 A:ASP124 3.1 34.4 1.0
CE1 A:HIS120 3.2 37.2 1.0
CD2 A:HIS189 3.3 38.0 1.0
CG A:ASP124 3.3 58.1 1.0
CE1 A:HIS122 3.3 41.5 1.0
CG A:HIS122 3.3 46.7 1.0
CD A:CD280 3.4 41.5 1.0
CD2 A:HIS120 3.4 37.1 1.0
CE1 A:HIS189 3.5 39.7 1.0
CB A:HIS122 3.6 47.4 1.0
CB A:CYS208 3.7 40.5 1.0
O A:HOH333 4.3 60.0 1.0
ND1 A:HIS120 4.3 35.8 1.0
NE2 A:HIS122 4.4 40.7 1.0
CG A:HIS189 4.5 38.9 1.0
CD2 A:HIS122 4.5 42.2 1.0
CG A:HIS120 4.5 34.6 1.0
ND1 A:HIS189 4.5 41.5 1.0
CG A:LYS125 4.7 48.2 1.0
CB A:ASP124 4.8 55.3 1.0

Cadmium binding site 3 out of 6 in 3srx

Go back to Cadmium Binding Sites List in 3srx
Cadmium binding site 3 out of 6 in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd282

b:47.1
occ:1.00
 OE2 A:GLU152 2.2 41.0 1.0
OD2 A:ASP223 2.5 43.6 1.0
O A:HOH320 2.5 32.0 1.0
OE1 A:GLU152 2.6 54.7 1.0
OD1 A:ASP223 2.6 40.2 1.0
CD A:GLU152 2.8 46.8 1.0
CG A:ASP223 2.9 41.1 1.0
O A:HOH338 3.2 64.1 1.0
O A:HOH321 3.8 55.4 1.0
O A:HOH15 4.1 37.5 1.0
CG A:GLU152 4.3 48.4 1.0
O A:HOH294 4.4 47.4 1.0
CB A:ASP223 4.5 37.4 1.0
NE2 A:HIS122 4.5 40.7 1.0
CD2 A:HIS122 4.8 42.2 1.0

Cadmium binding site 4 out of 6 in 3srx

Go back to Cadmium Binding Sites List in 3srx
Cadmium binding site 4 out of 6 in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd280

b:57.0
occ:1.00
 ND1 B:HIS122 2.2 63.0 1.0
NE2 B:HIS189 2.5 53.5 1.0
NE2 B:HIS120 2.5 66.7 1.0
SG B:CYS208 2.6 51.3 1.0
OD2 B:ASP124 2.7 69.8 1.0
CL B:CL271 2.7 46.8 1.0
CE1 B:HIS122 3.0 61.0 1.0
CG B:HIS122 3.2 68.5 1.0
CD B:CD281 3.2 50.5 1.0
CE1 B:HIS120 3.2 60.0 1.0
OD1 B:ASP124 3.3 85.1 1.0
CD2 B:HIS189 3.3 50.2 1.0
CG B:ASP124 3.4 79.3 1.0
CE1 B:HIS189 3.4 53.4 1.0
CB B:CYS208 3.5 42.8 1.0
CB B:HIS122 3.6 70.0 1.0
CD2 B:HIS120 3.7 68.2 1.0
NE2 B:HIS122 4.2 63.5 1.0
CD2 B:HIS122 4.3 67.3 1.0
CG B:LYS125 4.4 78.0 1.0
ND1 B:HIS120 4.5 60.3 1.0
CG B:HIS189 4.5 47.0 1.0
ND1 B:HIS189 4.5 50.4 1.0
CG B:HIS120 4.7 62.4 1.0
CB B:ASP124 4.8 82.0 1.0

Cadmium binding site 5 out of 6 in 3srx

Go back to Cadmium Binding Sites List in 3srx
Cadmium binding site 5 out of 6 in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd281

b:50.5
occ:1.00
 NE2 B:HIS250 2.2 55.2 1.0
CL B:CL271 2.3 46.8 1.0
SG B:CYS208 2.6 51.3 1.0
CL B:CL285 2.6 44.3 1.0
OD2 B:ASP124 2.9 69.8 1.0
CE1 B:HIS250 3.1 55.0 1.0
CD2 B:HIS250 3.2 55.6 1.0
CD B:CD280 3.2 57.0 1.0
CB B:CYS208 3.3 42.8 1.0
CG B:ASP124 3.7 79.3 1.0
CE1 B:HIS189 3.9 53.4 1.0
NE2 B:HIS189 4.0 53.5 1.0
OD1 B:ASP124 4.2 85.1 1.0
ND1 B:HIS250 4.2 61.1 1.0
CG B:HIS250 4.3 55.9 1.0
CA B:CYS208 4.3 48.1 1.0
CB B:SER249 4.6 54.9 1.0
CB B:ASP124 4.7 82.0 1.0
NZ B:LYS211 4.8 51.9 1.0
ND1 B:HIS189 4.8 50.4 1.0
OG B:SER249 4.9 53.7 1.0
CD2 B:HIS189 4.9 50.2 1.0

Cadmium binding site 6 out of 6 in 3srx

Go back to Cadmium Binding Sites List in 3srx
Cadmium binding site 6 out of 6 in the New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd282

b:0.5
occ:1.00
 O B:HOH277 2.4 53.1 1.0
OD1 B:ASP223 2.5 90.1 1.0
O B:HOH292 3.1 77.3 1.0
OD2 B:ASP223 3.1 85.2 1.0
OE2 B:GLU152 3.2 91.7 1.0
CG B:ASP223 3.2 83.3 1.0
OE1 B:GLU152 3.5 94.6 1.0
CD B:GLU152 3.7 94.3 1.0
CB B:ASP223 4.6 75.0 1.0

Reference:

Y.Kim, C.Tesar, R.Jedrzejczak, J.Babnigg, T.A.Binkowski, J.Mire, J.Sacchettini, A.Joachimiak. New Delhi Metallo-Beta-Lactamase-1 Complexed with Cd To Be Published.
Page generated: Thu Jul 10 12:58:36 2025

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