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

Protein crystallography data

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

Other elements in 4pvt:

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

Chlorine (Cl) 6 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 4pvt

Go back to Zinc Binding Sites List in 4pvt
Zinc 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 Zinc with other atoms in the Zn 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:Zn401

b:15.9
occ:1.00
ND1 A:HIS118 1.9 13.5 1.0
NE2 A:HIS196 2.1 10.3 1.0
S9 A:S3C403 2.2 11.2 0.7
NE2 A:HIS116 2.2 13.7 1.0
CE1 A:HIS118 2.9 13.8 1.0
CG A:HIS118 2.9 13.9 1.0
CE1 A:HIS196 3.0 11.2 1.0
CD2 A:HIS196 3.1 10.0 1.0
CD2 A:HIS116 3.2 13.5 1.0
CE1 A:HIS116 3.2 13.1 1.0
C5 A:S3C403 3.2 27.5 0.7
CB A:HIS118 3.3 13.8 1.0
C3 A:S3C403 3.8 40.0 0.7
ZN A:ZN402 3.9 15.6 1.0
C2 A:S3C403 3.9 42.2 0.7
C4 A:S3C403 3.9 34.0 0.7
NE2 A:HIS118 4.0 15.2 1.0
C6 A:S3C403 4.0 22.6 0.7
CD2 A:HIS118 4.1 15.3 1.0
OD1 A:ASP120 4.1 15.7 1.0
CL1 A:S3C403 4.1 53.8 0.7
ND1 A:HIS196 4.2 11.4 1.0
O8 A:S3C403 4.2 21.5 0.7
CG A:HIS196 4.2 11.4 1.0
ND1 A:HIS116 4.3 12.6 1.0
CG A:HIS116 4.3 13.5 1.0
CB A:CYS221 4.3 13.2 1.0
C10 A:S3C403 4.4 41.9 0.7
C15 A:S3C403 4.5 41.5 0.7
SG A:CYS221 4.5 16.7 1.0
OD2 A:ASP120 4.7 16.5 1.0
CA A:HIS118 4.8 14.6 1.0
CG A:ASP120 4.8 16.4 1.0
O7 A:S3C403 5.0 20.1 0.7
C12 A:S3C403 5.0 41.2 0.7

Zinc binding site 2 out of 6 in 4pvt

Go back to Zinc Binding Sites List in 4pvt
Zinc 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 Zinc with other atoms in the Zn 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:Zn402

b:15.6
occ:1.00
OD2 A:ASP120 2.0 16.5 1.0
NE2 A:HIS263 2.1 13.7 1.0
S9 A:S3C403 2.2 11.2 0.7
SG A:CYS221 2.2 16.7 1.0
O8 A:S3C403 2.4 21.5 0.7
C5 A:S3C403 3.0 27.5 0.7
CE1 A:HIS263 3.0 14.8 1.0
CG A:ASP120 3.1 16.4 1.0
C6 A:S3C403 3.1 22.6 0.7
CD2 A:HIS263 3.1 14.2 1.0
CB A:CYS221 3.4 13.2 1.0
OD1 A:ASP120 3.5 15.7 1.0
ZN A:ZN401 3.9 15.9 1.0
NH2 A:ARG121 3.9 16.3 1.0
NE A:ARG121 4.1 13.5 1.0
ND1 A:HIS263 4.1 14.8 1.0
CG A:HIS263 4.2 14.4 1.0
CE1 A:HIS116 4.2 13.1 1.0
O7 A:S3C403 4.3 20.1 0.7
CB A:ASP120 4.3 17.4 1.0
CZ A:ARG121 4.4 14.4 1.0
CL2 A:S3C403 4.4 37.5 0.7
NE2 A:HIS116 4.5 13.7 1.0
C4 A:S3C403 4.5 34.0 0.7
CA A:CYS221 4.6 12.9 1.0
O A:HOH501 4.6 16.4 1.0
NE2 A:HIS196 4.7 10.3 1.0
O A:HOH658 4.9 27.1 1.0

Zinc binding site 3 out of 6 in 4pvt

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Zinc 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 Zinc with other atoms in the Zn 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:Zn404

b:20.0
occ:1.00
O1 A:FMT405 1.8 21.1 1.0
O2 A:FMT406 2.0 14.2 1.0
ND1 A:HIS285 2.2 18.3 1.0
C A:FMT406 2.6 14.8 1.0
O1 A:FMT406 2.7 15.6 1.0
C A:FMT405 2.8 23.3 1.0
O2 A:FMT405 3.2 24.7 1.0
CG A:HIS285 3.2 17.1 1.0
CE1 A:HIS285 3.2 18.6 1.0
CB A:HIS285 3.4 16.4 1.0
CA A:HIS285 3.7 16.9 1.0
ND2 A:ASN288 4.3 19.8 1.0
NE2 A:HIS285 4.3 18.0 1.0
CD2 A:HIS285 4.3 17.5 1.0
O A:HIS285 4.4 17.6 1.0
C A:HIS285 4.5 16.4 1.0
CD2 A:LEU226 4.8 16.8 1.0
N A:HIS285 4.8 17.3 1.0
CB A:ASN288 5.0 16.1 1.0

Zinc binding site 4 out of 6 in 4pvt

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Zinc 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 Zinc with other atoms in the Zn 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:Zn401

b:14.5
occ:1.00
NE2 B:HIS196 2.0 11.4 1.0
ND1 B:HIS118 2.0 14.5 1.0
NE2 B:HIS116 2.1 13.1 1.0
S9 B:S3C406 2.3 15.0 0.9
CE1 B:HIS196 2.9 12.9 1.0
CG B:HIS118 3.0 14.3 1.0
CE1 B:HIS118 3.0 14.9 1.0
CD2 B:HIS196 3.1 10.4 1.0
CE1 B:HIS116 3.1 13.1 1.0
CD2 B:HIS116 3.1 14.3 1.0
C5 B:S3C406 3.2 25.0 0.9
CB B:HIS118 3.3 13.0 1.0
ZN B:ZN402 3.8 15.5 1.0
C6 B:S3C406 3.9 21.6 0.9
OD1 B:ASP120 3.9 15.5 1.0
C4 B:S3C406 4.0 29.3 0.9
C3 B:S3C406 4.0 33.3 0.9
ND1 B:HIS196 4.1 12.8 1.0
O7 B:S3C406 4.1 19.4 0.9
NE2 B:HIS118 4.1 16.1 1.0
CG B:HIS196 4.1 11.3 1.0
CD2 B:HIS118 4.2 15.7 1.0
C2 B:S3C406 4.2 35.9 0.9
ND1 B:HIS116 4.2 12.8 1.0
CG B:HIS116 4.2 13.5 1.0
CB B:CYS221 4.3 11.3 1.0
CL1 B:S3C406 4.4 47.1 0.9
SG B:CYS221 4.5 13.9 1.0
OD2 B:ASP120 4.6 15.5 1.0
C10 B:S3C406 4.6 34.3 0.9
CG B:ASP120 4.7 15.3 1.0
CA B:HIS118 4.8 13.1 1.0
O8 B:S3C406 4.8 21.0 0.9
C15 B:S3C406 4.9 36.9 0.9

Zinc binding site 5 out of 6 in 4pvt

Go back to Zinc Binding Sites List in 4pvt
Zinc 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 Zinc with other atoms in the Zn 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:Zn402

b:15.5
occ:1.00
NE2 B:HIS263 2.1 13.5 1.0
OD2 B:ASP120 2.1 15.5 1.0
O7 B:S3C406 2.3 19.4 0.9
S9 B:S3C406 2.3 15.0 0.9
SG B:CYS221 2.3 13.9 1.0
CE1 B:HIS263 3.0 14.4 1.0
C6 B:S3C406 3.0 21.6 0.9
C5 B:S3C406 3.0 25.0 0.9
CG B:ASP120 3.1 15.3 1.0
CD2 B:HIS263 3.1 13.7 1.0
CB B:CYS221 3.4 11.3 1.0
OD1 B:ASP120 3.5 15.5 1.0
ZN B:ZN401 3.8 14.5 1.0
NH2 B:ARG121 4.0 16.0 1.0
ND1 B:HIS263 4.1 14.7 1.0
NE B:ARG121 4.2 15.2 1.0
O2 B:GOL407 4.2 49.4 1.0
CG B:HIS263 4.2 14.4 1.0
CE1 B:HIS116 4.2 13.1 1.0
O8 B:S3C406 4.2 21.0 0.9
CB B:ASP120 4.3 16.0 1.0
O B:HOH505 4.4 9.9 1.0
NE2 B:HIS116 4.4 13.1 1.0
CZ B:ARG121 4.5 16.2 1.0
C4 B:S3C406 4.5 29.3 0.9
CL2 B:S3C406 4.5 39.5 0.9
NE2 B:HIS196 4.6 11.4 1.0
CA B:CYS221 4.6 11.3 1.0
CE1 B:HIS196 4.8 12.9 1.0

Zinc binding site 6 out of 6 in 4pvt

Go back to Zinc Binding Sites List in 4pvt
Zinc 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 Zinc with other atoms in the Zn 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:Zn403

b:16.2
occ:1.00
O2 B:FMT404 1.9 17.1 1.0
NE2 B:HIS170 2.1 14.2 1.0
O1 B:FMT405 2.1 14.9 1.0
C B:FMT404 2.7 16.9 1.0
O1 B:FMT404 2.9 16.5 1.0
CE1 B:HIS170 2.9 14.5 1.0
C B:FMT405 3.0 17.0 1.0
O2 B:FMT405 3.1 18.7 1.0
CD2 B:HIS170 3.2 13.4 1.0
CB B:ALA135 4.1 14.1 1.0
ND1 B:HIS170 4.1 13.9 1.0
CG B:HIS170 4.2 13.3 1.0
CA B:ALA135 4.7 13.8 1.0
O B:HOH543 4.8 20.5 1.0
CG2 B:THR169 4.9 17.7 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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