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Zinc in PDB 5lm6: Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35)

Protein crystallography data

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35), PDB code: 5lm6 was solved by G.-B.Li, J.Brem, H.Someya, 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) 52.01 / 1.17
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 102.983, 80.251, 68.319, 90.00, 130.00, 90.00
R / Rfree (%) 19 / 21.2

Other elements in 5lm6:

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35) also contains other interesting chemical elements:

Fluorine (F) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35) (pdb code 5lm6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35), PDB code: 5lm6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5lm6

Go back to Zinc Binding Sites List in 5lm6
Zinc binding site 1 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:15.6
occ:1.00
ND1 B:HIS116 1.9 17.7 1.0
O B:HOH632 1.9 19.2 1.0
NE2 B:HIS179 2.0 11.3 1.0
NE2 B:HIS114 2.0 13.8 1.0
CE1 B:HIS116 2.9 18.3 1.0
CE1 B:HIS114 2.9 12.7 1.0
CG B:HIS116 3.0 17.1 1.0
CD2 B:HIS179 3.0 11.4 1.0
CE1 B:HIS179 3.0 11.6 1.0
CD2 B:HIS114 3.1 11.4 1.0
O B:HOH617 3.3 36.5 1.0
CB B:HIS116 3.4 14.0 1.0
ZN B:ZN502 3.8 17.8 1.0
OD1 B:ASP118 3.9 17.5 1.0
NE2 B:HIS116 4.0 19.3 1.0
CD2 B:HIS116 4.1 17.6 1.0
ND1 B:HIS114 4.1 12.0 1.0
ND1 B:HIS179 4.1 12.0 1.0
CG B:HIS179 4.1 10.4 1.0
CB B:CYS198 4.2 11.6 1.0
CG B:HIS114 4.2 10.6 1.0
SG B:CYS198 4.3 13.6 1.0
O B:HOH774 4.4 18.9 0.5
OD2 B:ASP118 4.7 21.0 1.0
CG B:ASP118 4.8 15.4 1.0
CA B:HIS116 4.8 13.0 1.0

Zinc binding site 2 out of 6 in 5lm6

Go back to Zinc Binding Sites List in 5lm6
Zinc binding site 2 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:17.8
occ:1.00
NE2 B:HIS240 2.1 13.5 1.0
OD2 B:ASP118 2.1 21.0 1.0
SG B:CYS198 2.3 13.6 1.0
O B:HOH632 2.4 19.2 1.0
O B:HOH774 2.7 18.9 0.5
CE1 B:HIS240 3.1 12.2 1.0
CD2 B:HIS240 3.1 11.3 1.0
CG B:ASP118 3.2 15.4 1.0
CB B:CYS198 3.4 11.6 1.0
NH2 B:ARG119 3.4 19.2 0.2
OD1 B:ASP118 3.6 17.5 1.0
NH2 B:ARG119 3.8 20.3 0.8
ZN B:ZN501 3.8 15.6 1.0
NE B:ARG119 4.1 16.8 0.2
CZ B:ARG119 4.1 17.7 0.2
NE B:ARG119 4.2 16.2 0.8
ND1 B:HIS240 4.2 13.4 1.0
CG B:HIS240 4.2 12.0 1.0
CZ B:ARG119 4.5 17.6 0.8
CB B:ASP118 4.5 16.2 1.0
CE1 B:HIS114 4.5 12.7 1.0
O B:HOH699 4.5 16.0 1.0
NE2 B:HIS179 4.6 11.3 1.0
CA B:CYS198 4.6 10.5 1.0
NE2 B:HIS114 4.7 13.8 1.0
O B:HOH617 4.7 36.5 1.0
CE1 B:HIS179 4.7 11.6 1.0

Zinc binding site 3 out of 6 in 5lm6

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Zinc binding site 3 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:15.2
occ:1.00
O1 B:FMT505 1.8 20.3 1.0
O2 B:FMT504 1.9 17.2 1.0
ND1 B:HIS251 2.1 14.5 1.0
C B:FMT504 2.6 15.2 1.0
O1 B:FMT504 2.8 16.9 1.0
C B:FMT505 2.9 21.9 1.0
CE1 B:HIS251 3.0 14.2 1.0
CG B:HIS251 3.1 12.4 1.0
O2 B:FMT505 3.2 18.0 1.0
CB B:HIS251 3.5 12.8 1.0
CA B:HIS251 3.8 12.6 1.0
NE2 B:HIS251 4.1 14.4 1.0
CD2 B:HIS251 4.2 13.1 1.0
ND2 B:ASN254 4.5 19.7 1.0
O B:HIS251 4.6 13.1 1.0
C B:HIS251 4.7 12.4 1.0
CD2 B:LEU203 4.8 16.0 1.0
N B:HIS251 4.9 13.3 1.0

Zinc binding site 4 out of 6 in 5lm6

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Zinc binding site 4 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:13.0
occ:1.00
O A:HOH696 1.9 15.2 1.0
ND1 A:HIS116 2.0 16.7 1.0
NE2 A:HIS179 2.0 12.1 1.0
NE2 A:HIS114 2.1 13.0 1.0
CE1 A:HIS116 2.9 16.1 1.0
CE1 A:HIS114 3.0 11.4 1.0
CD2 A:HIS179 3.0 11.9 1.0
CE1 A:HIS179 3.0 12.3 1.0
CG A:HIS116 3.1 14.4 1.0
CD2 A:HIS114 3.1 11.8 1.0
CB A:HIS116 3.5 13.5 1.0
ZN A:ZN502 3.6 16.8 1.0
OD1 A:ASP118 3.9 18.7 1.0
O A:HOH602 3.9 27.0 1.0
NE2 A:HIS116 4.1 16.2 1.0
CB A:CYS198 4.1 12.7 1.0
ND1 A:HIS179 4.1 12.1 1.0
ND1 A:HIS114 4.1 11.2 1.0
CD2 A:HIS116 4.1 14.5 1.0
CG A:HIS179 4.2 10.7 1.0
O11 A:H32504 4.2 29.9 0.8
CG A:HIS114 4.2 10.7 1.0
SG A:CYS198 4.3 13.7 1.0
C19 A:H32504 4.4 35.8 0.8
OD2 A:ASP118 4.5 19.9 1.0
C14 A:H32504 4.7 35.1 0.8
CG A:ASP118 4.7 17.8 1.0
C10 A:H32504 4.7 30.3 0.8
C18 A:H32504 4.8 35.3 0.8
N12 A:H32504 4.9 35.5 0.8
CA A:HIS116 4.9 12.6 1.0

Zinc binding site 5 out of 6 in 5lm6

Go back to Zinc Binding Sites List in 5lm6
Zinc binding site 5 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:16.8
occ:1.00
O A:HOH696 2.0 15.2 1.0
OD2 A:ASP118 2.1 19.9 1.0
NE2 A:HIS240 2.1 13.6 1.0
SG A:CYS198 2.3 13.7 1.0
O A:HOH602 2.8 27.0 1.0
CD2 A:HIS240 3.1 11.5 1.0
CE1 A:HIS240 3.1 12.9 1.0
CG A:ASP118 3.1 17.8 1.0
CB A:CYS198 3.4 12.7 1.0
OD1 A:ASP118 3.5 18.7 1.0
NH2 A:ARG119 3.5 17.4 0.5
ZN A:ZN501 3.6 13.0 1.0
NH2 A:ARG119 3.9 15.4 0.5
C10 A:H32504 4.0 30.3 0.8
NE A:ARG119 4.0 14.8 0.5
NE A:ARG119 4.1 13.1 0.5
N12 A:H32504 4.2 35.5 0.8
CZ A:ARG119 4.2 15.9 0.5
ND1 A:HIS240 4.2 13.4 1.0
C04 A:H32504 4.2 29.6 0.8
CG A:HIS240 4.2 12.1 1.0
CE1 A:HIS114 4.3 11.4 1.0
C13 A:H32504 4.4 31.9 0.8
O11 A:H32504 4.4 29.9 0.8
CZ A:ARG119 4.4 15.3 0.5
C03 A:H32504 4.4 29.9 0.8
NE2 A:HIS179 4.4 12.1 1.0
CB A:ASP118 4.4 15.7 1.0
NE2 A:HIS114 4.5 13.0 1.0
O A:HOH692 4.6 14.1 1.0
CA A:CYS198 4.6 10.5 1.0
C14 A:H32504 4.7 35.1 0.8
CE1 A:HIS179 4.7 12.3 1.0
C05 A:H32504 4.8 32.3 0.8

Zinc binding site 6 out of 6 in 5lm6

Go back to Zinc Binding Sites List in 5lm6
Zinc binding site 6 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Vim-2 Metallo-Beta-Lactamase in Complex with 2-(3-Fluoro-4- Hydroxyphenyl)-3-Oxoisoindoline-4-Carboxylic Acid (Compound 35) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:12.6
occ:1.00
O2 A:FMT505 2.0 14.1 1.0
O1 A:FMT506 2.0 15.3 1.0
ND1 A:HIS251 2.1 13.8 1.0
C A:FMT505 2.7 12.1 1.0
O1 A:FMT505 2.8 14.2 1.0
C A:FMT506 2.9 15.0 1.0
CE1 A:HIS251 3.0 13.2 1.0
CG A:HIS251 3.1 11.3 1.0
O2 A:FMT506 3.2 15.2 1.0
CB A:HIS251 3.5 11.4 1.0
CA A:HIS251 3.8 11.4 1.0
NE2 A:HIS251 4.1 13.8 1.0
CD2 A:HIS251 4.2 12.0 1.0
ND2 A:ASN254 4.3 15.2 1.0
CD2 A:LEU203 4.5 15.5 1.0
O A:HIS251 4.7 12.0 1.0
C A:HIS251 4.7 10.9 1.0
N A:HIS251 4.9 11.2 1.0

Reference:

G.B.Li, M.I.Abboud, J.Brem, H.Someya, C.T.Lohans, S.Y.Yang, J.Spencer, D.W.Wareham, M.A.Mcdonough, C.J.Schofield. uc(Nmr)-Filtered Virtual Screening Leads to Non-Metal Chelating Metallo-Beta-Lactamase Inhibitors. Chem Sci V. 8 928 2017.
ISSN: ISSN 2041-6520
PubMed: 28451231
DOI: 10.1039/C6SC04524C
Page generated: Wed Dec 16 06:29:42 2020

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