Chlorine in PDB 4pvt: Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F, PDB code: 4pvt was solved by W.S.Aik, J.Brem, M.A.Mcdonough, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.93 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.391, 78.909, 67.742, 90.00, 130.32, 90.00
R / Rfree (%)	16.6 / 21.9

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Chlorine atom in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F (pdb code 4pvt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F, PDB code: 4pvt:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F


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 Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:53.8 occ:0.70 CL1 A:S3C403 0.0 53.8 0.7 C2 A:S3C403 1.7 42.2 0.7 C15 A:S3C403 2.7 41.5 0.7 C3 A:S3C403 2.7 40.0 0.7 OD1 A:ASN233 2.7 40.9 1.0 CE1 A:HIS118 3.1 13.8 1.0 C4 A:S3C403 3.1 34.0 0.7 CG A:ASN233 3.2 43.3 1.0 CB A:ASN233 3.2 42.4 1.0 O A:HOH556 3.4 22.9 1.0 O A:ASN233 3.5 35.1 1.0 ND1 A:HIS118 3.6 13.5 1.0 NE2 A:HIS118 3.8 15.2 1.0 CE1 A:HIS196 3.8 11.2 1.0 C A:ASN233 3.9 35.0 1.0 C14 A:S3C403 4.0 40.9 0.7 C5 A:S3C403 4.0 27.5 0.7 C10 A:S3C403 4.0 41.9 0.7 ZN A:ZN401 4.1 15.9 1.0 CA A:ASN233 4.2 40.3 1.0 NE2 A:HIS196 4.2 10.3 1.0 O A:HOH592 4.4 36.6 1.0 ND2 A:ASN233 4.4 46.0 1.0 C12 A:S3C403 4.5 41.2 0.7 CG A:HIS118 4.5 13.9 1.0 S9 A:S3C403 4.6 11.2 0.7 CD2 A:HIS118 4.6 15.3 1.0 OD2 A:ASP236 4.8 18.7 1.0 N A:VAL234 4.8 27.2 1.0 N A:ASN233 4.9 40.5 1.0 ND1 A:HIS196 4.9 11.4 1.0 C6 A:S3C403 4.9 22.6 0.7 O7 A:S3C403 5.0 20.1 0.7

Chlorine binding site 2 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F


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 Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:37.5 occ:0.70 CL2 A:S3C403 0.0 37.5 0.7 C10 A:S3C403 1.7 41.9 0.7 C12 A:S3C403 2.7 41.2 0.7 C3 A:S3C403 2.7 40.0 0.7 C4 A:S3C403 3.0 34.0 0.7 CL3 A:S3C403 3.0 61.2 0.7 C5 A:S3C403 3.2 27.5 0.7 S9 A:S3C403 3.4 11.2 0.7 CZ2 A:TRP87 3.4 25.1 1.0 CH2 A:TRP87 3.7 26.8 1.0 C14 A:S3C403 4.0 40.9 0.7 C2 A:S3C403 4.0 42.2 0.7 O A:HOH659 4.0 28.3 1.0 CG A:ASP120 4.2 16.4 1.0 CE2 A:TRP87 4.3 22.4 1.0 OD2 A:ASP120 4.4 16.5 1.0 C6 A:S3C403 4.4 22.6 0.7 OD1 A:ASP120 4.4 15.7 1.0 ZN A:ZN402 4.4 15.6 1.0 CB A:ASP120 4.5 17.4 1.0 C15 A:S3C403 4.5 41.5 0.7 CE1 A:HIS263 4.6 14.8 1.0 CZ3 A:TRP87 4.6 26.3 1.0 O A:HOH658 4.7 27.1 1.0 NE2 A:HIS263 4.8 13.7 1.0 NE1 A:TRP87 4.9 20.9 1.0

Chlorine binding site 3 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F


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 Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:61.2 occ:0.70 CL3 A:S3C403 0.0 61.2 0.7 C12 A:S3C403 1.7 41.2 0.7 C10 A:S3C403 2.7 41.9 0.7 C14 A:S3C403 2.7 40.9 0.7 CL2 A:S3C403 3.0 37.5 0.7 O A:HOH507 3.4 26.2 1.0 O A:HOH560 3.7 21.3 1.0 CB A:ASP119 3.8 22.3 1.0 NE1 A:TRP87 3.8 20.9 1.0 C3 A:S3C403 4.0 40.0 0.7 CZ2 A:TRP87 4.0 25.1 1.0 C15 A:S3C403 4.0 41.5 0.7 N A:ASP119 4.1 18.3 1.0 CE2 A:TRP87 4.2 22.4 1.0 N A:ASP120 4.3 15.9 1.0 CA A:ASP119 4.4 19.5 1.0 C2 A:S3C403 4.5 42.2 0.7 C A:ASP119 4.7 17.8 1.0 OD1 A:ASP120 4.8 15.7 1.0 CB A:HIS118 4.8 13.8 1.0 CB A:ASP120 4.9 17.4 1.0 CD1 A:TRP87 4.9 19.3 1.0 CG A:ASP119 5.0 25.1 1.0

Chlorine binding site 4 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl406 b:47.1 occ:0.90 CL1 B:S3C406 0.0 47.1 0.9 C2 B:S3C406 1.7 35.9 0.9 C15 B:S3C406 2.7 36.9 0.9 C3 B:S3C406 2.7 33.3 0.9 OD1 B:ASN233 3.0 40.8 1.0 C4 B:S3C406 3.1 29.3 0.9 CE1 B:HIS118 3.2 14.9 1.0 CG B:ASN233 3.4 40.0 1.0 O B:ASN233 3.4 29.3 1.0 CB B:ASN233 3.4 36.1 1.0 O B:HOH502 3.5 20.0 1.0 ND1 B:HIS118 3.7 14.5 1.0 NE2 B:HIS118 3.8 16.1 1.0 C14 B:S3C406 4.0 36.3 0.9 C B:ASN233 4.0 28.4 1.0 C10 B:S3C406 4.0 34.3 0.9 C5 B:S3C406 4.1 25.0 0.9 CE1 B:HIS196 4.1 12.9 1.0 ND2 B:ASN233 4.3 42.6 1.0 CA B:ASN233 4.3 32.7 1.0 ZN B:ZN401 4.4 14.5 1.0 NE2 B:HIS196 4.5 11.4 1.0 C12 B:S3C406 4.5 35.2 0.9 CG B:HIS118 4.5 14.3 1.0 CD2 B:HIS118 4.6 15.7 1.0 OD2 B:ASP236 4.7 16.8 1.0 S9 B:S3C406 4.8 15.0 0.9 O8 B:S3C406 4.9 21.0 0.9 C6 B:S3C406 4.9 21.6 0.9 N B:VAL234 5.0 20.6 1.0 N B:ALA235 5.0 25.2 1.0

Chlorine binding site 5 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl406 b:39.5 occ:0.90 CL2 B:S3C406 0.0 39.5 0.9 C10 B:S3C406 1.8 34.3 0.9 C3 B:S3C406 2.7 33.3 0.9 C12 B:S3C406 2.8 35.2 0.9 C4 B:S3C406 2.9 29.3 0.9 C5 B:S3C406 3.1 25.0 0.9 CZ2 B:TRP87 3.3 21.0 1.0 S9 B:S3C406 3.3 15.0 0.9 CH2 B:TRP87 3.3 20.8 1.0 CL3 B:S3C406 3.4 56.7 0.9 O2 B:GOL407 3.4 49.4 1.0 C2 B:S3C406 4.0 35.9 0.9 C14 B:S3C406 4.1 36.3 0.9 CE2 B:TRP87 4.2 18.5 1.0 CZ3 B:TRP87 4.3 19.9 1.0 C3 B:GOL407 4.3 47.5 1.0 C6 B:S3C406 4.3 21.6 0.9 CG B:ASP120 4.4 15.3 1.0 C2 B:GOL407 4.4 48.3 1.0 ZN B:ZN402 4.5 15.5 1.0 OD1 B:ASP120 4.5 15.5 1.0 C15 B:S3C406 4.5 36.9 0.9 OD2 B:ASP120 4.6 15.5 1.0 CB B:ASP120 4.6 16.0 1.0 CE1 B:PHE61 4.7 26.2 0.5 CE1 B:HIS263 4.7 14.4 1.0 CD1 B:PHE61 4.7 26.3 0.5 NE2 B:HIS263 4.8 13.5 1.0 CZ B:PHE61 4.9 25.3 0.5 NE1 B:TRP87 4.9 17.9 1.0 O8 B:S3C406 4.9 21.0 0.9 CG B:PHE61 4.9 25.5 0.5 O7 B:S3C406 5.0 19.4 0.9 CD2 B:TRP87 5.0 17.7 1.0

Chlorine binding site 6 out of 6 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302F within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl406 b:56.7 occ:0.90 CL3 B:S3C406 0.0 56.7 0.9 C12 B:S3C406 1.7 35.2 0.9 C14 B:S3C406 2.7 36.3 0.9 C10 B:S3C406 2.8 34.3 0.9 O B:HOH558 3.2 22.8 1.0 CL2 B:S3C406 3.4 39.5 0.9 O B:HOH546 3.7 21.9 1.0 CE2 B:PHE61 3.8 24.5 0.5 NE1 B:TRP87 3.9 17.9 1.0 CZ2 B:TRP87 3.9 21.0 1.0 C15 B:S3C406 4.0 36.9 0.9 CB B:ASP119 4.0 27.6 1.0 C3 B:S3C406 4.0 33.3 0.9 CE2 B:TRP87 4.1 18.5 1.0 CD2 B:PHE61 4.2 24.6 0.5 N B:ASP119 4.2 15.4 1.0 CZ B:PHE61 4.3 25.3 0.5 C2 B:S3C406 4.5 35.9 0.9 N B:ASP120 4.6 15.4 1.0 CA B:ASP119 4.6 19.6 1.0 CB B:HIS118 4.9 13.0 1.0 CD1 B:TRP87 4.9 17.4 1.0 C B:ASP119 4.9 17.5 1.0 CG B:PHE61 5.0 25.5 0.5

J.Brem, S.S.Van Berkel, W.S.Aik, A.M.Rydzik, M.B.Avison, I.Pettinati, K.-D.Umland, A.Kawamura, J.Spencer, T.D.W.Claridge, M.A.Mcdonough, C.J.Schofield. Rhodanine Hydrolysis Leads to Potent Thioenolate Mediated Metallo-Beta-Lactamase Inhibition Nat.Chem. 2014.
ISSN: ESSN 1755-4349
DOI: 10.1038/NCHEM.2110