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Cadmium in PDB 4hky: New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Faropenem

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

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

Protein crystallography data

The structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Faropenem, PDB code: 4hky was solved by Y.Kim, C.Tesar, R.Jedrzejczak, J.Babnigg, J.Mire, J.Sacchettini, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtb Proteins Conferring Susceptibility To Known Mtbinhibitors (Mtbi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.12 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.627, 39.324, 75.370, 90.00, 99.96, 90.00
R / Rfree (%) 20.4 / 25.1

Other elements in 4hky:

The structure of New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Faropenem 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 and Faropenem (pdb code 4hky). 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 and Faropenem, PDB code: 4hky:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 4hky

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


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 and Faropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:43.2
occ:1.00
 NE2 A:HIS120 2.4 26.1 1.0
ND1 A:HIS122 2.6 30.3 1.0
NE2 A:HIS189 2.6 35.1 1.0
O7 A:FPM301 2.8 57.0 0.5
O72 A:SFR302 2.9 60.6 0.5
CE1 A:HIS120 3.2 28.9 1.0
SG A:CYS208 3.2 44.6 1.0
CD2 A:HIS189 3.2 34.0 1.0
O71 A:SFR302 3.3 64.6 0.5
CG A:HIS122 3.4 31.2 1.0
CB A:HIS122 3.4 28.1 1.0
C7 A:SFR302 3.4 63.6 0.5
CD A:CD304 3.5 48.0 1.0
CD2 A:HIS120 3.5 25.4 1.0
CE1 A:HIS122 3.7 37.2 1.0
CB A:CYS208 3.7 39.1 1.0
CE1 A:HIS189 3.8 43.2 1.0
OD1 A:ASP124 3.8 62.0 1.0
C7 A:FPM301 3.9 62.5 0.5
OD2 A:ASP124 4.3 62.8 1.0
ND1 A:HIS120 4.4 28.4 1.0
CG A:HIS189 4.4 37.6 1.0
O31 A:FPM301 4.5 60.9 0.5
CG A:ASP124 4.5 59.5 1.0
CG A:HIS120 4.6 26.4 1.0
CD2 A:HIS122 4.6 38.0 1.0
N4 A:SFR302 4.6 62.3 0.5
ND1 A:HIS189 4.7 38.7 1.0
NE2 A:HIS122 4.7 41.3 1.0
N4 A:FPM301 4.7 63.3 0.5
C6 A:SFR302 4.9 64.8 0.5
C61 A:FPM301 4.9 66.1 0.5
CA A:HIS122 4.9 31.2 1.0
C31 A:FPM301 4.9 60.7 0.5

Cadmium binding site 2 out of 6 in 4hky

Go back to Cadmium Binding Sites List in 4hky
Cadmium binding site 2 out of 6 in the New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Faropenem


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 and Faropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:48.0
occ:1.00
 O31 A:FPM301 1.8 60.9 0.5
N4 A:SFR302 1.9 62.3 0.5
NE2 A:HIS250 2.4 44.7 1.0
C31 A:FPM301 2.6 60.7 0.5
O31 A:SFR302 2.7 59.8 0.5
N4 A:FPM301 2.7 63.3 0.5
C3 A:SFR302 2.7 61.2 0.5
SG A:CYS208 2.8 44.6 1.0
OD2 A:ASP124 2.8 62.8 1.0
C7 A:FPM301 2.9 62.5 0.5
C3 A:FPM301 2.9 61.7 0.5
C31 A:SFR302 3.0 60.6 0.5
C5 A:SFR302 3.0 63.8 0.5
O7 A:FPM301 3.0 57.0 0.5
O71 A:SFR302 3.0 64.6 0.5
C7 A:SFR302 3.0 63.6 0.5
CE1 A:HIS250 3.2 45.2 1.0
O72 A:SFR302 3.3 60.6 0.5
CD A:CD303 3.5 43.2 1.0
CB A:CYS208 3.5 39.1 1.0
CD2 A:HIS250 3.6 46.6 1.0
C6 A:SFR302 3.6 64.8 0.5
C5 A:FPM301 3.6 65.4 0.5
O32 A:FPM301 3.7 59.7 0.5
CG A:ASP124 3.8 59.5 1.0
C2 A:SFR302 3.9 61.8 0.5
C6 A:FPM301 4.0 65.0 0.5
O32 A:SFR302 4.0 60.2 0.5
OD1 A:ASP124 4.1 62.0 1.0
C2 A:FPM301 4.2 62.0 0.5
C61 A:FPM301 4.2 66.1 0.5
S1 A:SFR302 4.3 70.0 0.5
NE2 A:HIS189 4.3 35.1 1.0
ND1 A:HIS250 4.4 53.9 1.0
CE1 A:HIS189 4.5 43.2 1.0
CB A:SER249 4.6 43.5 1.0
CA A:CYS208 4.6 40.2 1.0
CG A:HIS250 4.6 48.4 1.0
C61 A:SFR302 4.8 66.2 0.5
S1 A:FPM301 4.8 72.8 0.5
O62 A:FPM301 4.9 67.9 0.5

Cadmium binding site 3 out of 6 in 4hky

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


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 and Faropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:45.6
occ:0.72
 OD2 A:ASP223 2.5 45.1 1.0
OE2 B:GLU227 2.5 60.2 1.0
O A:HOH431 2.7 46.0 1.0
OE1 B:GLU227 2.7 61.9 1.0
OE1 A:GLU152 2.7 45.5 1.0
OE2 A:GLU152 2.8 47.3 1.0
OD1 A:ASP223 2.9 51.7 1.0
CD B:GLU227 3.0 58.0 1.0
CG A:ASP223 3.0 48.0 1.0
CD A:GLU152 3.1 44.3 1.0
NE2 A:HIS122 3.9 41.3 1.0
NE2 B:HIS228 4.2 31.9 1.0
CG B:GLU227 4.4 51.4 1.0
CB A:ASP223 4.5 40.8 1.0
CE1 B:HIS228 4.5 37.6 1.0
CG A:GLU152 4.6 39.6 1.0
CD2 A:HIS122 4.6 38.0 1.0
CE1 A:HIS122 5.0 37.2 1.0

Cadmium binding site 4 out of 6 in 4hky

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


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 and Faropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd305

b:42.8
occ:1.00
 O71 B:SFR301 2.4 36.4 0.5
NE2 B:HIS120 2.5 30.5 1.0
ND1 B:HIS122 2.5 34.0 1.0
NE2 B:HIS189 2.6 32.4 1.0
O7 B:FPM302 2.7 49.8 0.5
O72 B:SFR301 3.1 51.1 0.5
C7 B:SFR301 3.1 50.1 0.5
CD2 B:HIS189 3.1 25.6 1.0
SG B:CYS208 3.2 35.5 1.0
CG B:HIS122 3.4 28.4 1.0
CD2 B:HIS120 3.4 28.1 1.0
OD1 B:ASP124 3.4 37.6 1.0
CE1 B:HIS120 3.5 28.7 1.0
CD B:CD306 3.5 42.3 1.0
CB B:HIS122 3.5 28.5 1.0
CE1 B:HIS122 3.5 44.7 1.0
CE1 B:HIS189 3.7 33.1 1.0
C7 B:FPM302 3.8 54.8 0.5
CB B:CYS208 3.9 34.0 1.0
OD2 B:ASP124 4.3 53.1 1.0
CG B:ASP124 4.3 44.6 1.0
CG B:HIS189 4.4 25.6 1.0
CD2 B:HIS122 4.6 32.9 1.0
C61 B:FPM302 4.6 59.0 0.5
ND1 B:HIS120 4.6 29.6 1.0
C6 B:SFR301 4.6 57.1 0.5
CG B:HIS120 4.6 23.4 1.0
NE2 B:HIS122 4.6 42.0 1.0
C62 B:FPM302 4.6 55.7 0.5
ND1 B:HIS189 4.6 28.1 1.0
N4 B:SFR301 4.7 61.0 0.5
C6 B:FPM302 4.8 58.8 0.5
N4 B:FPM302 4.8 60.5 0.5
O31 B:FPM302 4.9 59.8 0.5
CG2 B:THR190 4.9 28.5 1.0
CG B:LYS125 5.0 31.1 1.0

Cadmium binding site 5 out of 6 in 4hky

Go back to Cadmium Binding Sites List in 4hky
Cadmium binding site 5 out of 6 in the New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Faropenem


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 and Faropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd306

b:42.3
occ:1.00
 O31 B:FPM302 2.2 59.8 0.5
N4 B:SFR301 2.3 61.0 0.5
NE2 B:HIS250 2.4 33.8 1.0
O71 B:SFR301 2.7 36.4 0.5
SG B:CYS208 2.7 35.5 1.0
N4 B:FPM302 2.8 60.5 0.5
O31 B:SFR301 2.8 60.1 0.5
OD2 B:ASP124 2.8 53.1 1.0
C7 B:FPM302 2.8 54.8 0.5
O7 B:FPM302 2.9 49.8 0.5
C31 B:FPM302 3.0 60.0 0.5
C7 B:SFR301 3.1 50.1 0.5
C3 B:SFR301 3.2 61.3 0.5
C3 B:FPM302 3.2 61.5 0.5
CE1 B:HIS250 3.2 35.5 1.0
C5 B:SFR301 3.3 59.5 0.5
C31 B:SFR301 3.4 59.8 0.5
CD2 B:HIS250 3.4 33.7 1.0
CD B:CD305 3.5 42.8 1.0
CG B:ASP124 3.6 44.6 1.0
O72 B:SFR301 3.6 51.1 0.5
CB B:CYS208 3.6 34.0 1.0
C5 B:FPM302 3.7 61.2 0.5
C6 B:SFR301 3.7 57.1 0.5
OD1 B:ASP124 3.8 37.6 1.0
C6 B:FPM302 3.9 58.8 0.5
C61 B:FPM302 4.0 59.0 0.5
O32 B:FPM302 4.1 58.0 0.5
NE2 B:HIS189 4.2 32.4 1.0
C2 B:SFR301 4.4 62.6 0.5
CB B:SER249 4.4 31.7 1.0
ND1 B:HIS250 4.4 36.5 1.0
C2 B:FPM302 4.4 62.4 0.5
CE1 B:HIS189 4.5 33.1 1.0
CG B:HIS250 4.5 38.7 1.0
O32 B:SFR301 4.6 58.9 0.5
CA B:CYS208 4.6 32.5 1.0
S1 B:SFR301 4.7 68.0 0.5
O62 B:FPM302 4.7 62.5 0.5
OG B:SER249 4.8 31.9 1.0
CB B:ASP124 4.8 43.9 1.0
S1 B:FPM302 5.0 70.2 0.5

Cadmium binding site 6 out of 6 in 4hky

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


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 and Faropenem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd307

b:45.8
occ:0.63
 OD2 B:ASP223 2.6 47.8 1.0
OE1 B:GLU152 2.7 42.1 1.0
OE1 A:GLU227 2.8 73.5 1.0
OE2 A:GLU227 2.8 77.6 1.0
OD1 B:ASP223 2.8 50.4 1.0
O B:HOH465 2.8 59.7 1.0
CD A:GLU227 2.9 71.7 1.0
OE2 B:GLU152 2.9 44.0 1.0
CG B:ASP223 3.0 45.7 1.0
CD B:GLU152 3.2 41.1 1.0
CG A:GLU227 4.0 61.5 1.0
NE2 A:HIS228 4.1 38.6 1.0
NE2 B:HIS122 4.1 42.0 1.0
O B:HOH434 4.3 37.9 1.0
CE1 A:HIS228 4.3 42.5 1.0
CB B:ASP223 4.5 40.1 1.0
CG B:GLU152 4.7 39.6 1.0
CD2 B:HIS122 4.8 32.9 1.0
CB A:GLU227 4.9 55.7 1.0

Reference:

Y.Kim, C.Tesar, R.Jedrzejczak, J.Babnigg, J.Mire, J.Sacchettini, A.Joachimiak. New Delhi Metallo-Beta-Lactamase-1, Complexed with Cd and Faropenem To Be Published.
Page generated: Sat Dec 12 08:24:45 2020

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