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Zinc 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:

Chlorine (Cl) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Vim-2 Metallo-Beta-Lactamase in Complex with ML302 and ML302F, PDB code: 4pvo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4pvo

Go back to Zinc Binding Sites List in 4pvo
Zinc binding site 1 out of 6 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 Zinc with other atoms in the Zn 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:Zn401

b:8.5
occ:1.00
ND1 A:HIS118 2.0 7.2 1.0
NE2 A:HIS196 2.0 8.0 1.0
NE2 A:HIS116 2.1 7.1 1.0
S9 A:S3C403 2.3 7.1 0.7
CE1 A:HIS118 3.0 7.6 1.0
CE1 A:HIS116 3.0 7.0 1.0
CD2 A:HIS196 3.0 7.4 1.0
CG A:HIS118 3.0 7.6 1.0
CE1 A:HIS196 3.1 8.9 1.0
CD2 A:HIS116 3.1 6.8 1.0
C5 A:S3C403 3.1 9.0 0.7
CB A:HIS118 3.4 6.9 1.0
ZN A:ZN402 3.7 10.1 1.0
C6 A:S3C403 3.9 8.3 0.7
OD1 A:ASP120 4.0 9.3 1.0
C4 A:S3C403 4.0 9.4 0.7
O7 A:S3C403 4.0 6.8 0.7
NE2 A:HIS118 4.1 10.2 1.0
C3 A:S3C403 4.1 11.5 0.7
ND1 A:HIS116 4.1 7.6 1.0
CD2 A:HIS118 4.1 9.2 1.0
ND1 A:HIS196 4.2 7.7 1.0
CG A:HIS196 4.2 8.8 1.0
CG A:HIS116 4.2 5.0 1.0
CB A:CYS221 4.2 7.6 1.0
C2 A:S3C403 4.3 11.5 0.7
SG A:CYS221 4.4 8.5 1.0
CL1 A:S3C403 4.5 16.8 0.7
OD2 A:ASP120 4.7 10.3 1.0
C10 A:S3C403 4.7 13.8 0.7
CG A:ASP120 4.7 10.3 1.0
CA A:HIS118 4.8 7.0 1.0
O8 A:S3C403 5.0 10.7 0.7
C15 A:S3C403 5.0 11.9 0.7

Zinc binding site 2 out of 6 in 4pvo

Go back to Zinc Binding Sites List in 4pvo
Zinc binding site 2 out of 6 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 Zinc with other atoms in the Zn 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:Zn402

b:10.1
occ:1.00
NE2 A:HIS263 2.0 7.5 1.0
OD2 A:ASP120 2.2 10.3 1.0
O7 A:S3C403 2.2 6.8 0.7
SG A:CYS221 2.3 8.5 1.0
S9 A:S3C403 2.3 7.1 0.7
C6 A:S3C403 2.9 8.3 0.7
C5 A:S3C403 2.9 9.0 0.7
CD2 A:HIS263 3.0 7.7 1.0
CE1 A:HIS263 3.1 6.8 1.0
CG A:ASP120 3.2 10.3 1.0
CB A:CYS221 3.3 7.6 1.0
OD1 A:ASP120 3.6 9.3 1.0
ZN A:ZN401 3.7 8.5 1.0
NH2 A:ARG121 3.9 14.4 1.0
O8 A:S3C403 4.1 10.7 0.7
NE A:ARG121 4.1 9.5 1.0
CG A:HIS263 4.2 8.3 1.0
ND1 A:HIS263 4.2 8.0 1.0
CE1 A:HIS116 4.2 7.0 1.0
O A:HOH501 4.3 9.9 1.0
C4 A:S3C403 4.4 9.4 0.7
CZ A:ARG121 4.4 11.1 1.0
CB A:ASP120 4.4 9.3 1.0
NE2 A:HIS196 4.5 8.0 1.0
NE2 A:HIS116 4.5 7.1 1.0
CA A:CYS221 4.6 8.2 1.0
CL2 A:S3C403 4.7 15.0 0.7
CL2 A:SVB404 4.7 47.8 0.8
CE1 A:HIS196 4.8 8.9 1.0

Zinc binding site 3 out of 6 in 4pvo

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Zinc binding site 3 out of 6 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 Zinc with other atoms in the Zn 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:Zn405

b:11.7
occ:1.00
O2 A:FMT406 1.4 12.9 1.0
O2 A:FMT407 1.9 15.2 1.0
ND1 A:HIS285 2.0 8.4 1.0
C A:FMT406 2.6 20.0 1.0
C A:FMT407 2.7 15.4 1.0
O1 A:FMT407 2.9 16.8 1.0
CE1 A:HIS285 2.9 9.8 1.0
CG A:HIS285 3.2 8.1 1.0
O1 A:FMT406 3.5 28.0 1.0
CB A:HIS285 3.6 10.0 1.0
CA A:HIS285 3.8 9.6 1.0
NE2 A:HIS285 4.1 10.0 1.0
CD2 A:HIS285 4.2 10.6 1.0
O A:HIS285 4.5 10.2 1.0
ND2 A:ASN288 4.5 10.0 0.5
C A:HIS285 4.6 9.7 1.0
CD2 A:LEU226 4.8 13.3 1.0
N A:HIS285 4.9 10.4 1.0

Zinc binding site 4 out of 6 in 4pvo

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Zinc binding site 4 out of 6 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 Zinc with other atoms in the Zn 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
B:Zn401

b:9.5
occ:1.00
ND1 B:HIS118 2.0 9.5 1.0
NE2 B:HIS196 2.0 8.0 1.0
NE2 B:HIS116 2.0 7.5 1.0
S9 B:S3C406 2.2 13.6 0.7
CE1 B:HIS118 2.9 11.1 1.0
CD2 B:HIS196 3.0 7.6 1.0
CG B:HIS118 3.0 10.7 1.0
CE1 B:HIS116 3.0 8.2 1.0
CE1 B:HIS196 3.0 12.7 1.0
CD2 B:HIS116 3.0 7.6 1.0
C5 B:S3C406 3.2 17.3 0.7
CB B:HIS118 3.4 9.7 1.0
ZN B:ZN402 3.7 11.7 1.0
OD1 B:ASP120 4.0 12.7 1.0
C6 B:S3C406 4.0 14.1 0.7
O8 B:S3C406 4.0 8.3 0.7
NE2 B:HIS118 4.1 12.0 1.0
ND1 B:HIS116 4.1 8.3 1.0
ND1 B:HIS196 4.1 8.3 1.0
CD2 B:HIS118 4.1 11.4 1.0
C4 B:S3C406 4.1 24.6 0.7
CG B:HIS196 4.1 7.3 1.0
CG B:HIS116 4.1 8.0 1.0
C3 B:S3C406 4.2 28.5 0.7
CB B:CYS221 4.2 7.8 1.0
C2 B:S3C406 4.3 29.7 0.7
SG B:CYS221 4.4 9.6 1.0
CL1 B:S3C406 4.5 30.9 0.7
OD2 B:ASP120 4.6 13.5 1.0
CG B:ASP120 4.7 10.3 1.0
C10 B:S3C406 4.7 32.0 0.7
CA B:HIS118 4.8 7.8 1.0

Zinc binding site 5 out of 6 in 4pvo

Go back to Zinc Binding Sites List in 4pvo
Zinc binding site 5 out of 6 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 Zinc with other atoms in the Zn 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
B:Zn402

b:11.7
occ:1.00
NE2 B:HIS263 2.0 9.0 1.0
OD2 B:ASP120 2.1 13.5 1.0
S9 B:S3C406 2.2 13.6 0.7
O8 B:S3C406 2.3 8.3 0.7
SG B:CYS221 2.3 9.6 1.0
C5 B:S3C406 2.9 17.3 0.7
C6 B:S3C406 3.0 14.1 0.7
CD2 B:HIS263 3.0 10.7 1.0
CE1 B:HIS263 3.0 8.0 1.0
CG B:ASP120 3.2 10.3 1.0
CB B:CYS221 3.3 7.8 1.0
OD1 B:ASP120 3.6 12.7 1.0
ZN B:ZN401 3.7 9.5 1.0
NH2 B:ARG121 3.9 13.9 1.0
ND1 B:HIS263 4.1 9.5 1.0
NE B:ARG121 4.1 10.7 1.0
CG B:HIS263 4.1 7.3 1.0
O7 B:S3C406 4.2 17.4 0.7
CE1 B:HIS116 4.3 8.2 1.0
O B:HOH506 4.3 10.8 1.0
C4 B:S3C406 4.3 24.6 0.7
NE2 B:HIS116 4.4 7.5 1.0
CB B:ASP120 4.4 11.4 1.0
CZ B:ARG121 4.4 12.1 1.0
NE2 B:HIS196 4.5 8.0 1.0
CL2 B:S3C406 4.6 34.0 0.7
CA B:CYS221 4.6 8.1 1.0
CE1 B:HIS196 4.7 12.7 1.0

Zinc binding site 6 out of 6 in 4pvo

Go back to Zinc Binding Sites List in 4pvo
Zinc binding site 6 out of 6 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 Zinc with other atoms in the Zn 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
B:Zn403

b:9.8
occ:1.00
O2 B:FMT405 1.9 14.1 1.0
O2 B:FMT404 1.9 11.3 1.0
NE2 B:HIS170 2.0 11.2 1.0
C B:FMT404 2.7 11.6 1.0
O1 B:FMT404 2.8 12.1 1.0
CE1 B:HIS170 2.8 12.0 1.0
C B:FMT405 2.8 14.7 1.0
O1 B:FMT405 3.1 13.1 1.0
CD2 B:HIS170 3.2 10.3 1.0
ND1 B:HIS170 4.0 12.6 1.0
CG B:HIS170 4.2 12.1 1.0
CB B:ALA135 4.2 10.0 1.0
O B:HOH545 4.8 20.2 1.0
CA B:ALA135 4.9 9.9 1.0
CG2 B:THR169 4.9 12.8 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: Wed Dec 16 05:42:00 2020

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