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Zinc in PDB 5y6d: Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)

Protein crystallography data

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11), PDB code: 5y6d was solved by G.-B.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.74 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 189.030, 39.832, 133.841, 90.00, 124.56, 90.00
R / Rfree (%) 16.2 / 21.9

Other elements in 5y6d:

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) (pdb code 5y6d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11), PDB code: 5y6d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5y6d

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Zinc binding site 1 out of 9 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


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 (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:14.2
occ:1.00
OD2 A:ASP118 2.0 13.4 1.0
NE2 A:HIS240 2.2 13.6 1.0
S14 A:8PL304 2.2 15.2 1.0
SG A:CYS198 2.3 11.8 1.0
CG A:ASP118 3.1 13.7 1.0
CE1 A:HIS240 3.1 13.3 1.0
CD2 A:HIS240 3.1 14.0 1.0
C13 A:8PL304 3.3 24.4 1.0
CB A:CYS198 3.4 14.5 1.0
O17 A:8PL304 3.4 17.0 1.0
OD1 A:ASP118 3.4 9.3 1.0
ZN A:ZN302 3.7 11.8 1.0
NH2 A:ARG119 3.7 15.1 1.0
C12 A:8PL304 3.7 16.1 1.0
N09 A:8PL304 3.7 17.6 1.0
NE A:ARG119 4.1 13.0 1.0
C10 A:8PL304 4.1 19.7 1.0
ND1 A:HIS240 4.2 9.6 1.0
CE1 A:HIS114 4.2 10.9 1.0
CG A:HIS240 4.3 10.6 1.0
CZ A:ARG119 4.3 13.5 1.0
C16 A:8PL304 4.4 20.2 1.0
CB A:ASP118 4.4 13.8 1.0
NE2 A:HIS114 4.4 11.4 1.0
NE2 A:HIS179 4.5 12.5 1.0
CE1 A:HIS179 4.6 13.4 1.0
CA A:CYS198 4.7 11.7 1.0
O A:HOH420 4.7 13.0 1.0
C01 A:8PL304 4.7 22.1 1.0

Zinc binding site 2 out of 9 in 5y6d

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Zinc binding site 2 out of 9 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


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 (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.8
occ:1.00
NE2 A:HIS114 2.0 11.4 1.0
ND1 A:HIS116 2.0 9.4 1.0
NE2 A:HIS179 2.0 12.5 1.0
S14 A:8PL304 2.3 15.2 1.0
CE1 A:HIS179 2.9 13.4 1.0
CE1 A:HIS116 2.9 17.1 1.0
CE1 A:HIS114 2.9 10.9 1.0
CD2 A:HIS114 3.0 11.1 1.0
CG A:HIS116 3.0 12.9 1.0
CD2 A:HIS179 3.1 12.4 1.0
C13 A:8PL304 3.4 24.4 1.0
CB A:HIS116 3.4 10.0 1.0
ZN A:ZN301 3.7 14.2 1.0
OD1 A:ASP118 4.0 9.3 1.0
ND1 A:HIS114 4.0 13.3 1.0
ND1 A:HIS179 4.0 13.7 1.0
NE2 A:HIS116 4.1 13.1 1.0
CG A:HIS114 4.1 12.1 1.0
CD2 A:HIS116 4.1 15.2 1.0
CG A:HIS179 4.1 12.9 1.0
CB A:CYS198 4.2 14.5 1.0
SG A:CYS198 4.3 11.8 1.0
OD2 A:ASP118 4.7 13.4 1.0
CG A:ASP118 4.8 13.7 1.0
C12 A:8PL304 4.8 16.1 1.0
CA A:HIS116 4.8 12.4 1.0
O17 A:8PL304 5.0 17.0 1.0

Zinc binding site 3 out of 9 in 5y6d

Go back to Zinc Binding Sites List in 5y6d
Zinc binding site 3 out of 9 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


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 (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:0.0
occ:1.00
O A:HOH481 1.8 35.0 1.0
OD2 A:ASP78 2.0 40.7 1.0
O A:HOH421 2.1 43.4 1.0
O A:HOH445 2.6 36.1 1.0
CG A:ASP78 3.1 34.1 1.0
OD1 A:ASP78 3.5 35.6 1.0
CG A:GLU79 4.1 25.5 1.0
N A:ASP78 4.1 20.8 1.0
CD A:GLU79 4.2 30.6 1.0
O A:ASP76 4.2 22.4 1.0
CB A:ASP78 4.4 31.6 1.0
OE2 A:GLU79 4.5 39.2 1.0
OE1 A:GLU79 4.6 23.1 1.0
CA A:ASP78 4.6 25.3 1.0
N A:GLU79 4.7 17.8 1.0
C A:ASP78 4.7 16.9 1.0
CB A:GLU79 4.9 16.7 1.0

Zinc binding site 4 out of 9 in 5y6d

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Zinc binding site 4 out of 9 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


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 (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:10.5
occ:1.00
ND1 B:HIS116 2.0 9.8 1.0
NE2 B:HIS114 2.1 8.9 1.0
NE2 B:HIS179 2.1 9.3 1.0
S14 B:8PL303 2.4 13.4 1.0
CG B:HIS116 2.9 12.4 1.0
CE1 B:HIS116 3.0 12.8 1.0
CE1 B:HIS179 3.0 10.5 1.0
CD2 B:HIS114 3.0 9.8 1.0
CE1 B:HIS114 3.1 10.5 1.0
CD2 B:HIS179 3.2 11.8 1.0
CB B:HIS116 3.3 12.2 1.0
C13 B:8PL303 3.3 13.4 1.0
ZN B:ZN302 3.7 13.8 1.0
OD1 B:ASP118 4.0 13.5 1.0
NE2 B:HIS116 4.0 12.5 1.0
CD2 B:HIS116 4.1 14.4 1.0
ND1 B:HIS114 4.2 13.1 1.0
ND1 B:HIS179 4.2 12.4 1.0
CG B:HIS114 4.2 10.1 1.0
CB B:CYS198 4.2 8.5 1.0
CG B:HIS179 4.3 8.2 1.0
SG B:CYS198 4.4 13.2 1.0
OD2 B:ASP118 4.7 13.5 1.0
CA B:HIS116 4.7 10.9 1.0
C12 B:8PL303 4.8 17.6 1.0
CG B:ASP118 4.8 13.8 1.0

Zinc binding site 5 out of 9 in 5y6d

Go back to Zinc Binding Sites List in 5y6d
Zinc binding site 5 out of 9 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


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 (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:13.8
occ:1.00
OD2 B:ASP118 2.0 13.5 1.0
NE2 B:HIS240 2.1 10.9 1.0
S14 B:8PL303 2.2 13.4 1.0
SG B:CYS198 2.3 13.2 1.0
CE1 B:HIS240 3.0 12.3 1.0
CG B:ASP118 3.1 13.8 1.0
CD2 B:HIS240 3.1 15.9 1.0
C13 B:8PL303 3.3 13.4 1.0
OD1 B:ASP118 3.4 13.5 1.0
CB B:CYS198 3.4 8.5 1.0
O17 B:8PL303 3.6 14.5 1.0
NH2 B:ARG119 3.6 14.9 1.0
C12 B:8PL303 3.7 17.6 1.0
ZN B:ZN301 3.7 10.5 1.0
N09 B:8PL303 3.9 15.0 1.0
NE B:ARG119 4.0 12.8 1.0
ND1 B:HIS240 4.1 10.2 1.0
C10 B:8PL303 4.2 17.8 1.0
CG B:HIS240 4.2 10.7 1.0
CE1 B:HIS114 4.3 10.5 1.0
CZ B:ARG119 4.3 12.8 1.0
CB B:ASP118 4.4 15.7 1.0
NE2 B:HIS114 4.4 8.9 1.0
NE2 B:HIS179 4.6 9.3 1.0
C16 B:8PL303 4.6 18.7 1.0
CE1 B:HIS179 4.6 10.5 1.0
CA B:CYS198 4.7 11.4 1.0
O B:HOH438 4.9 7.3 1.0
C01 B:8PL303 4.9 22.1 1.0

Zinc binding site 6 out of 9 in 5y6d

Go back to Zinc Binding Sites List in 5y6d
Zinc binding site 6 out of 9 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


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 (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:12.6
occ:1.00
ND1 C:HIS116 2.0 13.1 1.0
NE2 C:HIS114 2.1 12.0 1.0
NE2 C:HIS179 2.1 11.3 1.0
S14 C:8PL303 2.3 17.9 1.0
CE1 C:HIS179 3.0 12.9 1.0
CE1 C:HIS116 3.0 13.6 1.0
CE1 C:HIS114 3.0 11.4 1.0
CG C:HIS116 3.0 14.0 1.0
CD2 C:HIS114 3.1 10.3 1.0
CD2 C:HIS179 3.1 14.8 1.0
CB C:HIS116 3.4 13.7 1.0
C13 C:8PL303 3.4 18.6 1.0
ZN C:ZN302 3.7 16.9 1.0
OD1 C:ASP118 4.0 11.4 1.0
ND1 C:HIS179 4.1 14.5 1.0
NE2 C:HIS116 4.1 16.0 1.0
ND1 C:HIS114 4.1 11.8 1.0
CD2 C:HIS116 4.2 15.0 1.0
CG C:HIS114 4.2 9.8 1.0
CG C:HIS179 4.2 9.7 1.0
CB C:CYS198 4.2 11.8 1.0
SG C:CYS198 4.4 15.2 1.0
OD2 C:ASP118 4.7 16.9 1.0
CG C:ASP118 4.8 12.5 1.0
C12 C:8PL303 4.8 17.4 1.0
CA C:HIS116 4.8 13.2 1.0

Zinc binding site 7 out of 9 in 5y6d

Go back to Zinc Binding Sites List in 5y6d
Zinc binding site 7 out of 9 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:16.9
occ:1.00
OD2 C:ASP118 2.0 16.9 1.0
NE2 C:HIS240 2.1 17.5 1.0
SG C:CYS198 2.3 15.2 1.0
S14 C:8PL303 2.3 17.9 1.0
CD2 C:HIS240 3.0 15.1 1.0
CE1 C:HIS240 3.1 16.2 1.0
CG C:ASP118 3.1 12.5 1.0
C13 C:8PL303 3.3 18.6 1.0
CB C:CYS198 3.4 11.8 1.0
OD1 C:ASP118 3.4 11.4 1.0
O17 C:8PL303 3.7 19.8 1.0
C12 C:8PL303 3.7 17.4 1.0
ZN C:ZN301 3.7 12.6 1.0
NH2 C:ARG119 3.8 13.7 1.0
N09 C:8PL303 3.9 22.6 1.0
C10 C:8PL303 4.0 22.2 1.0
NE C:ARG119 4.1 14.9 1.0
ND1 C:HIS240 4.1 12.6 1.0
CG C:HIS240 4.1 14.9 1.0
CE1 C:HIS114 4.2 11.4 1.0
CB C:ASP118 4.4 20.0 1.0
CZ C:ARG119 4.4 16.2 1.0
NE2 C:HIS114 4.4 12.0 1.0
NE2 C:HIS179 4.6 11.3 1.0
C16 C:8PL303 4.7 21.2 1.0
CA C:CYS198 4.7 12.8 1.0
CE1 C:HIS179 4.7 12.9 1.0
C01 C:8PL303 4.9 25.9 1.0
O C:HOH437 5.0 13.7 1.0
O11 C:8PL303 5.0 23.2 1.0

Zinc binding site 8 out of 9 in 5y6d

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Zinc binding site 8 out of 9 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:25.5
occ:1.00
ND1 D:HIS116 1.9 26.0 1.0
S14 D:8PL303 2.0 36.1 1.0
NE2 D:HIS114 2.1 31.9 1.0
NE2 D:HIS179 2.2 33.6 1.0
CE1 D:HIS116 2.9 36.0 1.0
CE1 D:HIS114 2.9 29.7 1.0
CG D:HIS116 2.9 37.9 1.0
CD2 D:HIS179 3.0 30.9 1.0
C13 D:8PL303 3.2 39.3 1.0
CD2 D:HIS114 3.2 33.2 1.0
CE1 D:HIS179 3.2 29.8 1.0
CB D:HIS116 3.3 34.5 1.0
ZN D:ZN302 3.8 30.9 1.0
NE2 D:HIS116 4.0 37.0 1.0
OD1 D:ASP118 4.0 31.7 1.0
CD2 D:HIS116 4.0 36.0 1.0
ND1 D:HIS114 4.1 31.2 1.0
CG D:HIS179 4.2 27.2 1.0
ND1 D:HIS179 4.2 23.9 1.0
CG D:HIS114 4.2 29.0 1.0
CB D:CYS198 4.3 28.3 1.0
SG D:CYS198 4.3 30.4 1.0
C12 D:8PL303 4.6 37.3 1.0
OD2 D:ASP118 4.7 33.7 1.0
ND2 D:ASN210 4.7 40.7 1.0
CA D:HIS116 4.7 38.7 1.0
CG D:ASP118 4.8 32.4 1.0
C10 D:8PL303 4.9 43.9 1.0

Zinc binding site 9 out of 9 in 5y6d

Go back to Zinc Binding Sites List in 5y6d
Zinc binding site 9 out of 9 in the Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Vim-2 Metallo-Beta-Lactamase in Complex with (R)-2-(4-Fluorophenyl)-2- ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid (Compound 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:30.9
occ:1.00
NE2 D:HIS240 2.0 28.8 1.0
OD2 D:ASP118 2.1 33.7 1.0
S14 D:8PL303 2.1 36.1 1.0
SG D:CYS198 2.4 30.4 1.0
CE1 D:HIS240 2.9 27.5 1.0
CD2 D:HIS240 3.0 28.6 1.0
CG D:ASP118 3.1 32.4 1.0
C13 D:8PL303 3.2 39.3 1.0
O18 D:8PL303 3.3 32.9 1.0
CB D:CYS198 3.5 28.3 1.0
OD1 D:ASP118 3.5 31.7 1.0
C12 D:8PL303 3.5 37.3 1.0
N09 D:8PL303 3.7 33.9 1.0
NH2 D:ARG119 3.7 33.1 1.0
ZN D:ZN301 3.8 25.5 1.0
C10 D:8PL303 3.9 43.9 1.0
ND1 D:HIS240 4.1 21.2 1.0
NE D:ARG119 4.1 28.6 1.0
CG D:HIS240 4.1 21.4 1.0
CZ D:ARG119 4.3 27.2 1.0
C16 D:8PL303 4.3 39.5 1.0
CE1 D:HIS114 4.4 29.7 1.0
CB D:ASP118 4.4 35.0 1.0
NE2 D:HIS179 4.6 33.6 1.0
CE1 D:HIS179 4.6 29.8 1.0
CA D:CYS198 4.7 30.8 1.0
NE2 D:HIS114 4.7 31.9 1.0
C01 D:8PL303 4.7 32.8 1.0
O D:HOH428 4.8 21.4 1.0
O11 D:8PL303 4.9 51.5 1.0
C15 D:8PL303 5.0 34.9 1.0

Reference:

S.Liu, L.Jing, Z.-J.Yu, C.Wu, Y.Zheng, E.Zhang, Q.Chen, Y.Yu, L.Guo, Y.Wu, G.-B.Li. ((S)-3-Mercapto-2-Methylpropanamido)Acetic Acid Derivatives As Metallo-Beta-Lactamase Inhibitors: Synthesis, Kinetic and Crystallographic Studies. Eur J Med Chem V. 145 649 2018.
ISSN: ISSN 1768-3254
PubMed: 29353720
DOI: 10.1016/J.EJMECH.2018.01.032
Page generated: Wed Dec 16 11:22:19 2020

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