Atomistry » Cadmium » PDB 4evc-4l1l » 4hky
Atomistry »
  Cadmium »
    PDB 4evc-4l1l »
      4hky »

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: Fri Jul 19 17:25:51 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy