Atomistry » Cadmium » PDB 5wgr-6fpc » 6ex7
Atomistry »
  Cadmium »
    PDB 5wgr-6fpc »
      6ex7 »

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: Thu Jul 10 14:53:11 2025

Last articles

Mg in 9GUR
Mg in 9GRE
Mg in 9GTK
Mg in 9GU5
Mg in 9GOB
Mg in 9GO5
Mg in 9GMZ
Mg in 9GQO
Mg in 9GMX
Mg in 9GMW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy