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Chlorine 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:

Cadmium (Cd) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6ex7

Go back to Chlorine Binding Sites List in 6ex7
Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl304

b:44.0
occ:1.00
 N A:LYS242 2.9 42.4 1.0
C A:PHE240 3.1 32.2 1.0
CA A:PHE240 3.3 29.7 1.0
N A:ALA243 3.3 40.6 1.0
N A:PRO241 3.4 33.3 1.0
O A:PHE240 3.5 34.5 1.0
CB A:LYS242 3.5 51.8 1.0
CA A:LYS242 3.5 49.9 1.0
CD A:PRO241 3.6 35.2 1.0
CB A:PHE240 3.7 30.3 1.0
C A:LYS242 3.9 48.4 1.0
C A:PRO241 3.9 40.6 1.0
O A:HOH421 4.1 37.8 1.0
CA A:PRO241 4.2 37.7 1.0
CG A:PRO241 4.3 36.1 1.0
CG A:LYS242 4.3 50.4 1.0
CA A:ALA243 4.3 39.2 1.0
CB A:ALA243 4.3 35.4 1.0
N A:PHE240 4.6 27.2 1.0
CD1 A:PHE240 4.7 27.9 1.0
CG A:PHE240 4.8 28.4 1.0
O A:ALA239 4.8 26.2 1.0
CB A:PRO241 4.9 38.3 1.0

Chlorine binding site 2 out of 3 in 6ex7

Go back to Chlorine Binding Sites List in 6ex7
Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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
B:Cl303

b:39.3
occ:1.00
 N B:LYS242 3.1 28.2 1.0
O B:HOH472 3.2 39.9 1.0
C B:PHE240 3.2 20.4 1.0
CA B:PHE240 3.3 19.4 1.0
N B:PRO241 3.5 23.2 1.0
N B:ALA243 3.5 26.4 1.0
CB B:LYS242 3.6 34.8 1.0
O B:PHE240 3.6 21.2 1.0
CD B:PRO241 3.7 24.8 1.0
CA B:LYS242 3.7 31.8 1.0
CB B:PHE240 3.8 18.4 1.0
C B:LYS242 4.0 35.4 1.0
C B:PRO241 4.1 28.6 1.0
CA B:PRO241 4.3 25.5 1.0
CG B:PRO241 4.4 27.2 1.0
O B:HOH434 4.4 32.8 1.0
CG B:LYS242 4.4 37.2 1.0
CB B:ALA243 4.4 22.1 1.0
CA B:ALA243 4.4 24.6 1.0
O B:HOH460 4.5 39.9 1.0
CD1 B:PHE240 4.6 17.5 1.0
N B:PHE240 4.6 18.7 1.0
CG B:PHE240 4.7 17.0 1.0
O B:ALA239 4.8 17.1 1.0

Chlorine binding site 3 out of 3 in 6ex7

Go back to Chlorine Binding Sites List in 6ex7
Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl 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
B:Cl304

b:50.5
occ:1.00
 N B:LYS216 3.5 31.6 1.0
CE B:LYS216 3.8 55.8 1.0
N B:SER217 4.2 29.5 1.0
OG B:SER217 4.2 32.4 1.0
CB B:LYS216 4.2 38.0 1.0
CA B:ALA215 4.3 34.7 1.0
CB B:ALA215 4.3 33.1 1.0
CA B:LYS216 4.3 34.1 1.0
C B:ALA215 4.4 34.9 1.0
NZ B:LYS216 4.5 63.5 1.0
C B:LYS216 4.6 32.2 1.0
O B:SER217 4.8 26.4 1.0
CG B:LYS216 4.9 42.0 1.0
CD B:LYS216 4.9 49.4 0.6

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: Sat Jul 27 22:42:10 2024

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