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Chlorine in PDB 4pvo: Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F

Protein crystallography data

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F, PDB code: 4pvo 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) 39.10 / 1.48
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.570, 79.239, 67.967, 90.00, 131.57, 90.00
R / Rfree (%) 14.1 / 16.5

Other elements in 4pvo:

The structure of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F (pdb code 4pvo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F, PDB code: 4pvo:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4pvo

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Chlorine binding site 1 out of 9 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and 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 ML302 and ML302F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:16.8
occ:0.70
 CL1 A:S3C403 0.0 16.8 0.7
C2 A:S3C403 1.7 11.5 0.7
C3 A:S3C403 2.7 11.5 0.7
C15 A:S3C403 2.7 11.9 0.7
C4 A:S3C403 3.0 9.4 0.7
CE1 A:HIS118 3.4 7.6 1.0
O A:ASN233 3.5 26.1 1.0
O A:HOH562 3.5 18.6 1.0
CG A:ASN233 3.5 35.6 1.0
ND2 A:ASN233 3.5 35.8 1.0
CB A:ASN233 3.6 24.9 1.0
ND1 A:HIS118 3.9 7.2 1.0
C5 A:S3C403 3.9 9.0 0.7
OD1 A:ASN233 4.0 35.8 1.0
C14 A:S3C403 4.0 14.8 0.7
C10 A:S3C403 4.0 13.8 0.7
CE1 A:HIS196 4.0 8.9 1.0
O10 A:SVB404 4.0 34.6 0.8
NE2 A:HIS118 4.0 10.2 1.0
C A:ASN233 4.1 21.4 1.0
O A:HOH507 4.3 35.4 1.0
NE2 A:HIS196 4.4 8.0 1.0
C12 A:S3C403 4.5 14.2 0.7
ZN A:ZN401 4.5 8.5 1.0
CA A:ASN233 4.5 29.2 1.0
O A:HOH618 4.7 32.5 1.0
CG A:HIS118 4.7 7.6 1.0
S9 A:S3C403 4.7 7.1 0.7
CD2 A:HIS118 4.8 9.2 1.0
C6 A:S3C403 4.8 8.3 0.7
O8 A:S3C403 4.8 10.7 0.7
OD2 A:ASP236 4.8 14.9 1.0

Chlorine binding site 2 out of 9 in 4pvo

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Chlorine binding site 2 out of 9 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and 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 ML302 and ML302F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:15.0
occ:0.70
 CL2 A:S3C403 0.0 15.0 0.7
C10 A:S3C403 1.7 13.8 0.7
C12 A:S3C403 2.7 14.2 0.7
C3 A:S3C403 2.7 11.5 0.7
C4 A:S3C403 3.0 9.4 0.7
CL3 A:S3C403 3.1 19.8 0.7
C5 A:S3C403 3.4 9.0 0.7
S9 A:S3C403 3.4 7.1 0.7
CZ2 A:TRP87 3.5 16.1 1.0
C6 A:SVB404 3.7 30.3 0.8
N7 A:SVB404 3.7 33.3 0.8
CH2 A:TRP87 3.8 14.9 1.0
C9 A:SVB404 3.8 34.4 0.8
S5 A:SVB404 3.9 30.9 0.8
C4 A:SVB404 3.9 34.7 0.8
C14 A:S3C403 4.0 14.8 0.7
C2 A:S3C403 4.0 11.5 0.7
CL2 A:SVB404 4.2 47.8 0.8
CE2 A:TRP87 4.2 11.8 1.0
CG A:ASP120 4.3 10.3 1.0
C8 A:SVB404 4.4 35.9 0.8
OD1 A:ASP120 4.4 9.3 1.0
S11 A:SVB404 4.5 29.1 0.8
C6 A:S3C403 4.5 8.3 0.7
O10 A:SVB404 4.5 34.6 0.8
C15 A:S3C403 4.5 11.9 0.7
OD2 A:ASP120 4.5 10.3 1.0
CB A:ASP120 4.6 9.3 1.0
ZN A:ZN402 4.7 10.1 1.0
CZ3 A:TRP87 4.7 14.4 1.0
C3 A:SVB404 4.7 41.9 0.8
NE1 A:TRP87 4.8 13.2 1.0
CE1 A:HIS263 4.9 6.8 1.0
NE2 A:HIS263 5.0 7.5 1.0

Chlorine binding site 3 out of 9 in 4pvo

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Chlorine binding site 3 out of 9 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and 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 ML302 and ML302F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:19.8
occ:0.70
 CL3 A:S3C403 0.0 19.8 0.7
C12 A:S3C403 1.7 14.2 0.7
C10 A:S3C403 2.7 13.8 0.7
C14 A:S3C403 2.7 14.8 0.7
CL2 A:S3C403 3.1 15.0 0.7
O A:HOH508 3.3 24.1 1.0
CB A:ASP119 4.0 13.8 1.0
O A:HOH566 4.0 14.7 1.0
C15 A:S3C403 4.0 11.9 0.7
C3 A:S3C403 4.0 11.5 0.7
NE1 A:TRP87 4.1 13.2 1.0
C8 A:SVB404 4.2 35.9 0.8
CZ2 A:TRP87 4.3 16.1 1.0
N A:ASP119 4.3 8.8 1.0
C2 A:S3C403 4.5 11.5 0.7
CE2 A:TRP87 4.5 11.8 1.0
N7 A:SVB404 4.5 33.3 0.8
N A:ASP120 4.6 9.8 1.0
CA A:ASP119 4.6 9.6 1.0
S11 A:SVB404 4.8 29.1 0.8
C6 A:SVB404 4.9 30.3 0.8
CB A:HIS118 4.9 6.9 1.0
C A:ASP119 5.0 10.7 1.0
OD1 A:ASP119 5.0 25.2 1.0

Chlorine binding site 4 out of 9 in 4pvo

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Chlorine binding site 4 out of 9 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and 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 ML302 and ML302F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:54.4
occ:0.80
 CL1 A:SVB404 0.0 54.4 0.8
C1 A:SVB404 1.7 51.3 0.8
C2 A:SVB404 2.7 47.7 0.8
C15 A:SVB404 2.8 51.9 0.8
C3 A:SVB404 3.0 41.9 0.8
CA A:GLY232 3.6 48.0 1.0
C4 A:SVB404 3.9 34.7 0.8
C14 A:SVB404 4.0 52.4 0.8
N A:ASN233 4.0 32.1 1.0
C12 A:SVB404 4.1 48.3 0.8
C A:GLY232 4.1 43.7 1.0
O B:HOH593 4.1 28.9 1.0
O A:HOH588 4.3 35.1 1.0
O A:HOH507 4.4 35.4 1.0
C13 A:SVB404 4.5 52.4 0.8
C9 A:SVB404 4.6 34.4 0.8
CE2 A:TYR67 4.6 19.1 1.0
O10 A:SVB404 4.7 34.6 0.8
OH A:TYR67 4.7 30.4 1.0
NH2 A:ARG228 4.8 27.3 1.0
S5 A:SVB404 4.9 30.9 0.8
O A:GLY232 4.9 36.7 1.0
N A:GLY232 5.0 33.7 1.0

Chlorine binding site 5 out of 9 in 4pvo

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Chlorine binding site 5 out of 9 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and 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 ML302 and ML302F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:47.8
occ:0.80
 CL2 A:SVB404 0.0 47.8 0.8
C12 A:SVB404 1.8 48.3 0.8
C13 A:SVB404 2.8 52.4 0.8
C2 A:SVB404 2.8 47.7 0.8
C3 A:SVB404 3.1 41.9 0.8
CL3 A:SVB404 3.3 55.5 0.8
C4 A:SVB404 3.4 34.7 0.8
S5 A:SVB404 3.5 30.9 0.8
CE1 A:HIS263 3.5 6.8 1.0
NE2 A:HIS263 3.6 7.5 1.0
ND1 A:HIS263 3.7 8.0 1.0
CD2 A:HIS263 3.7 7.7 1.0
O8 A:S3C403 3.7 10.7 0.7
C6 A:S3C403 3.8 8.3 0.7
CG A:HIS263 3.8 8.3 1.0
C1 A:SVB404 4.1 51.3 0.8
O7 A:S3C403 4.2 6.8 0.7
C14 A:SVB404 4.2 52.4 0.8
C5 A:S3C403 4.2 9.0 0.7
CL2 A:S3C403 4.2 15.0 0.7
C4 A:S3C403 4.3 9.4 0.7
CD2 A:TYR67 4.4 16.8 1.0
CH2 A:TRP87 4.5 14.9 1.0
NH2 A:ARG228 4.6 27.3 1.0
CB A:HIS263 4.6 7.5 1.0
C9 A:SVB404 4.6 34.4 0.8
C15 A:SVB404 4.7 51.9 0.8
ZN A:ZN402 4.7 10.1 1.0
NH1 A:ARG228 4.7 20.6 1.0
CG A:TYR67 4.8 17.3 1.0
CB A:TYR67 4.8 12.9 1.0
CZ A:ARG228 4.8 29.6 1.0
CZ3 A:TRP87 4.8 14.4 1.0
C6 A:SVB404 4.9 30.3 0.8
CE2 A:TYR67 5.0 19.1 1.0

Chlorine binding site 6 out of 9 in 4pvo

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Chlorine binding site 6 out of 9 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and 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 ML302 and ML302F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:55.5
occ:0.80
 CL3 A:SVB404 0.0 55.5 0.8
C13 A:SVB404 1.7 52.4 0.8
C12 A:SVB404 2.7 48.3 0.8
C14 A:SVB404 2.7 52.4 0.8
O A:HOH725 3.2 33.2 1.0
CL2 A:SVB404 3.3 47.8 0.8
CB A:HIS263 3.3 7.5 1.0
O B:GLY63 3.5 37.5 1.0
CG A:HIS263 3.7 8.3 1.0
CD2 A:TYR67 3.9 16.8 1.0
C15 A:SVB404 4.0 51.9 0.8
ND1 A:HIS263 4.0 8.0 1.0
C2 A:SVB404 4.1 47.7 0.8
O A:PRO68 4.2 9.7 1.0
NH1 A:ARG228 4.3 20.6 1.0
CD A:PRO68 4.3 14.5 1.0
C B:GLY63 4.3 36.2 1.0
CD2 A:HIS263 4.4 7.7 1.0
CB A:TYR67 4.5 12.9 1.0
CZ A:ARG228 4.5 29.6 1.0
C1 A:SVB404 4.5 51.3 0.8
CG A:TYR67 4.7 17.3 1.0
NE A:ARG228 4.7 31.9 1.0
CD A:ARG228 4.7 25.6 1.0
CA A:HIS263 4.7 8.2 1.0
CA B:GLY63 4.8 36.7 1.0
CE2 A:TYR67 4.8 19.1 1.0
CG A:PRO68 4.8 16.4 1.0
CE1 A:HIS263 4.9 6.8 1.0
N A:PRO68 5.0 11.5 1.0

Chlorine binding site 7 out of 9 in 4pvo

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Chlorine binding site 7 out of 9 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:30.9
occ:0.70
 CL1 B:S3C406 0.0 30.9 0.7
C2 B:S3C406 1.7 29.7 0.7
ND2 B:ASN233 2.6 32.6 1.0
C15 B:S3C406 2.7 30.9 0.7
C3 B:S3C406 2.7 28.5 0.7
C4 B:S3C406 3.1 24.6 0.7
CG B:ASN233 3.2 37.1 1.0
CE1 B:HIS118 3.3 11.1 1.0
CB B:ASN233 3.4 40.8 1.0
O B:HOH503 3.4 18.1 1.0
O B:ASN233 3.5 21.8 1.0
ND1 B:HIS118 3.8 9.5 1.0
NE2 B:HIS118 3.9 12.0 1.0
C B:ASN233 3.9 21.9 1.0
C5 B:S3C406 4.0 17.3 0.7
C14 B:S3C406 4.0 31.4 0.7
C10 B:S3C406 4.0 32.0 0.7
CE1 B:HIS196 4.1 12.7 1.0
OD1 B:ASN233 4.1 54.2 1.0
CA B:ASN233 4.2 26.7 1.0
C12 B:S3C406 4.5 33.0 0.7
NE2 B:HIS196 4.5 8.0 1.0
ZN B:ZN401 4.5 9.5 1.0
CG B:HIS118 4.6 10.7 1.0
OD2 B:ASP236 4.6 19.6 1.0
CD2 B:HIS118 4.7 11.4 1.0
S9 B:S3C406 4.7 13.6 0.7
N B:ALA235 4.8 16.7 1.0
N B:VAL234 4.8 22.3 1.0
C6 B:S3C406 4.8 14.1 0.7
O7 B:S3C406 4.9 17.4 0.7

Chlorine binding site 8 out of 9 in 4pvo

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Chlorine binding site 8 out of 9 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:34.0
occ:0.70
 CL2 B:S3C406 0.0 34.0 0.7
C10 B:S3C406 1.7 32.0 0.7
C3 B:S3C406 2.7 28.5 0.7
C12 B:S3C406 2.7 33.0 0.7
C4 B:S3C406 2.9 24.6 0.7
CL3 B:S3C406 3.1 37.4 0.7
C5 B:S3C406 3.3 17.3 0.7
CZ2 B:TRP87 3.4 18.0 1.0
S9 B:S3C406 3.4 13.6 0.7
CH2 B:TRP87 3.6 18.7 1.0
O B:HOH732 3.9 43.2 1.0
C2 B:S3C406 4.0 29.7 0.7
C14 B:S3C406 4.0 31.4 0.7
CE2 B:TRP87 4.2 14.4 1.0
CG B:ASP120 4.2 10.3 1.0
OD1 B:ASP120 4.2 12.7 1.0
OD2 B:ASP120 4.4 13.5 1.0
C6 B:S3C406 4.4 14.1 0.7
C15 B:S3C406 4.5 30.9 0.7
CZ3 B:TRP87 4.5 17.9 1.0
ZN B:ZN402 4.6 11.7 1.0
CB B:ASP120 4.6 11.4 1.0
CE1 B:PHE61 4.7 34.5 0.5
CE1 B:HIS263 4.7 8.0 1.0
CZ B:PHE61 4.7 29.6 0.5
NE2 B:HIS263 4.8 9.0 1.0
NE1 B:TRP87 4.8 14.1 1.0
CD1 B:PHE61 4.9 35.4 0.5
CE2 B:PHE61 4.9 31.3 0.5
CD2 B:TRP87 5.0 12.2 1.0

Chlorine binding site 9 out of 9 in 4pvo

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Chlorine binding site 9 out of 9 in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:37.4
occ:0.70
 CL3 B:S3C406 0.0 37.4 0.7
C12 B:S3C406 1.7 33.0 0.7
C14 B:S3C406 2.7 31.4 0.7
C10 B:S3C406 2.7 32.0 0.7
CL2 B:S3C406 3.1 34.0 0.7
O B:HOH560 3.3 25.3 1.0
O B:HOH548 3.7 19.9 1.0
CE2 B:PHE61 3.8 31.3 0.5
CB B:ASP119 3.9 15.4 1.0
NE1 B:TRP87 3.9 14.1 1.0
C15 B:S3C406 4.0 30.9 0.7
C3 B:S3C406 4.0 28.5 0.7
CZ2 B:TRP87 4.0 18.0 1.0
CZ B:PHE61 4.1 29.6 0.5
CE2 B:TRP87 4.2 14.4 1.0
N B:ASP119 4.2 10.4 1.0
CD2 B:PHE61 4.3 32.6 0.5
C2 B:S3C406 4.5 29.7 0.7
N B:ASP120 4.5 9.4 1.0
CA B:ASP119 4.6 11.9 1.0
OD1 B:ASP120 4.9 12.7 1.0
C B:ASP119 4.9 10.2 1.0
CB B:HIS118 4.9 9.7 1.0
CE1 B:PHE61 4.9 34.5 0.5
CD1 B:TRP87 5.0 13.2 1.0

Reference:

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
Page generated: Fri Jul 26 00:09:45 2024

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