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Cadmium in PDB 4raw: Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin

Enzymatic activity of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin

All present enzymatic activity of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin, PDB code: 4raw was solved by Y.Kim, C.Tesar, R.Jedrzejczak, G.Babnigg, J.Sacchettini, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtbproteins Conferring Susceptibility To Known Mtb Inhibitors (Mtbi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.41 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.114, 78.769, 133.815, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 16.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin (pdb code 4raw). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin, PDB code: 4raw:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 4raw

Go back to Cadmium Binding Sites List in 4raw
Cadmium binding site 1 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:8.6
occ:0.62
 O A:HOH570 2.1 8.8 1.0
ND1 A:HIS122 2.1 8.9 1.0
NE2 A:HIS189 2.1 8.3 1.0
NE2 A:HIS120 2.2 8.1 1.0
OXT A:ZZ7301 2.4 10.0 1.0
CE1 A:HIS122 3.0 8.6 1.0
CD2 A:HIS189 3.1 7.7 1.0
CG A:HIS122 3.1 8.4 1.0
CE1 A:HIS189 3.1 7.2 1.0
CE1 A:HIS120 3.2 7.9 1.0
CD2 A:HIS120 3.2 7.4 1.0
C15 A:ZZ7301 3.3 9.7 1.0
CB A:HIS122 3.4 7.3 1.0
C14 A:ZZ7301 3.9 9.7 1.0
N3 A:ZZ7301 4.0 8.9 1.0
O4 A:ZZ7301 4.1 11.7 1.0
NE2 A:HIS122 4.1 9.4 1.0
ND1 A:HIS189 4.2 7.8 1.0
CD2 A:HIS122 4.2 8.6 1.0
CG A:HIS189 4.2 7.5 1.0
OD1 A:ASP124 4.2 8.7 1.0
CG2 A:THR190 4.3 8.1 1.0
ND1 A:HIS120 4.3 7.3 1.0
CG A:HIS120 4.3 6.5 1.0
SG A:CYS208 4.4 8.0 1.0
CB A:CYS208 4.4 8.0 1.0
CD A:CD303 4.6 9.9 0.7
C13 A:ZZ7301 4.6 8.7 1.0
O A:HOH585 4.8 30.2 1.0
CA A:HIS122 4.8 7.9 1.0
C12 A:ZZ7301 4.9 8.4 1.0

Cadmium binding site 2 out of 4 in 4raw

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Cadmium binding site 2 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:9.9
occ:0.69
 NE2 A:HIS250 2.1 8.0 1.0
OD2 A:ASP124 2.2 9.2 1.0
O1 A:ZZ7301 2.2 9.1 1.0
N3 A:ZZ7301 2.2 8.9 1.0
SG A:CYS208 2.4 8.0 1.0
O A:HOH570 3.0 8.8 1.0
C2 A:ZZ7301 3.0 8.5 1.0
C12 A:ZZ7301 3.1 8.4 1.0
CD2 A:HIS250 3.1 7.7 1.0
CE1 A:HIS250 3.1 9.2 1.0
C13 A:ZZ7301 3.3 8.7 1.0
CG A:ASP124 3.3 8.2 1.0
CB A:CYS208 3.4 8.0 1.0
C16 A:ZZ7301 3.6 10.3 1.0
OD1 A:ASP124 3.8 8.7 1.0
C6 A:ZZ7301 3.9 9.2 1.0
CB A:SER249 4.2 8.1 1.0
ND1 A:HIS250 4.2 9.8 1.0
O2 A:ZZ7301 4.2 9.7 1.0
CG A:HIS250 4.2 9.1 1.0
C14 A:ZZ7301 4.3 9.7 1.0
OXT A:ZZ7301 4.3 10.0 1.0
S1 A:ZZ7301 4.5 10.5 1.0
CA A:CYS208 4.5 6.9 1.0
CB A:ASP124 4.5 8.4 1.0
CD A:CD302 4.6 8.6 0.6
OG A:SER249 4.6 8.0 1.0
C15 A:ZZ7301 4.8 9.7 1.0
NE2 A:HIS189 4.9 8.3 1.0
CE1 A:HIS189 4.9 7.2 1.0

Cadmium binding site 3 out of 4 in 4raw

Go back to Cadmium Binding Sites List in 4raw
Cadmium binding site 3 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd302

b:8.2
occ:0.61
 ND1 B:HIS122 2.1 7.3 1.0
O B:HOH401 2.1 8.2 1.0
NE2 B:HIS189 2.1 6.9 1.0
NE2 B:HIS120 2.2 7.9 1.0
OXT B:ZZ7301 2.4 9.2 1.0
CE1 B:HIS122 3.0 8.1 1.0
CG B:HIS122 3.1 7.3 1.0
CD2 B:HIS189 3.1 6.9 1.0
CE1 B:HIS189 3.1 7.8 1.0
CE1 B:HIS120 3.1 8.5 1.0
CD2 B:HIS120 3.2 7.3 1.0
C15 B:ZZ7301 3.3 8.7 1.0
CB B:HIS122 3.4 7.9 1.0
C14 B:ZZ7301 3.9 8.5 1.0
N3 B:ZZ7301 4.0 9.1 1.0
NE2 B:HIS122 4.1 8.9 1.0
O4 B:ZZ7301 4.2 12.2 1.0
CD2 B:HIS122 4.2 8.9 1.0
CG2 B:THR190 4.2 7.8 1.0
ND1 B:HIS189 4.2 8.4 1.0
CG B:HIS189 4.2 7.1 1.0
OD1 B:ASP124 4.2 8.0 1.0
ND1 B:HIS120 4.3 8.4 1.0
CG B:HIS120 4.3 7.0 1.0
SG B:CYS208 4.4 7.5 1.0
CB B:CYS208 4.5 6.9 1.0
C13 B:ZZ7301 4.6 8.3 1.0
CD B:CD303 4.6 8.0 0.6
O B:HOH488 4.7 16.9 1.0
CA B:HIS122 4.9 7.5 1.0
C12 B:ZZ7301 4.9 8.7 1.0

Cadmium binding site 4 out of 4 in 4raw

Go back to Cadmium Binding Sites List in 4raw
Cadmium binding site 4 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin


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 New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd303

b:8.0
occ:0.61
 NE2 B:HIS250 2.1 8.8 1.0
OD2 B:ASP124 2.2 8.3 1.0
O1 B:ZZ7301 2.2 9.0 1.0
N3 B:ZZ7301 2.2 9.1 1.0
SG B:CYS208 2.4 7.5 1.0
O B:HOH401 3.0 8.2 1.0
C2 B:ZZ7301 3.0 8.4 1.0
CD2 B:HIS250 3.0 9.5 1.0
C12 B:ZZ7301 3.0 8.7 1.0
CE1 B:HIS250 3.1 8.7 1.0
C13 B:ZZ7301 3.3 8.3 1.0
CG B:ASP124 3.3 7.4 1.0
CB B:CYS208 3.4 6.9 1.0
C16 B:ZZ7301 3.6 11.0 1.0
OD1 B:ASP124 3.8 8.0 1.0
C6 B:ZZ7301 3.9 9.5 1.0
CG B:HIS250 4.2 9.7 1.0
CB B:SER249 4.2 8.1 1.0
ND1 B:HIS250 4.2 8.7 1.0
O2 B:ZZ7301 4.2 10.0 1.0
C14 B:ZZ7301 4.3 8.5 1.0
OXT B:ZZ7301 4.4 9.2 1.0
CA B:CYS208 4.5 7.8 1.0
S1 B:ZZ7301 4.5 10.9 1.0
CB B:ASP124 4.5 7.3 1.0
OG B:SER249 4.6 8.0 1.0
CD B:CD302 4.6 8.2 0.6
C15 B:ZZ7301 4.8 8.7 1.0
NE2 B:HIS189 4.9 6.9 1.0
CE1 B:HIS189 4.9 7.8 1.0

Reference:

Y.Kim, C.Tesar, R.Jedrzejczak, G.Babnigg, J.Sacchettini, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtb Proteins Conferring Susceptibility Toknown Mtb Inhibitors (Mtbi). Crystal Structure of New Delhi Metallo-Beta-Lactamase-1 Mutant M67V Complexed with Hydrolyzed Ampicillin To Be Published.
Page generated: Thu Jul 10 13:59:32 2025

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