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Zinc in PDB 5n4s: Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3)

Protein crystallography data

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3), PDB code: 5n4s was solved by G.-B.Li, 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) 52.21 / 1.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.845, 80.308, 68.732, 90.00, 130.34, 90.00
R / Rfree (%) 18.4 / 20

Zinc Binding Sites:

The binding sites of Zinc atom in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3) (pdb code 5n4s). 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 ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3), PDB code: 5n4s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5n4s

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Zinc binding site 1 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:10.2
occ:1.00
OD2 A:ASP118 2.0 11.8 1.0
NE2 A:HIS240 2.1 9.5 1.0
SG A:CYS198 2.3 9.9 1.0
S20 A:R38504 2.4 10.8 1.0
CG A:ASP118 3.1 9.5 1.0
CE1 A:HIS240 3.1 10.3 1.0
CD2 A:HIS240 3.1 9.7 1.0
C19 A:R38504 3.4 11.8 1.0
OD1 A:ASP118 3.5 10.3 1.0
CB A:CYS198 3.5 8.5 1.0
O04 A:R38504 3.7 29.4 1.0
NH2 A:ARG119 3.8 16.2 1.0
C18 A:R38504 3.8 13.8 1.0
ZN A:ZN502 3.8 9.3 1.0
N01 A:R38504 3.9 18.5 1.0
NE A:ARG119 4.1 11.5 1.0
ND1 A:HIS240 4.2 10.1 1.0
CG A:HIS240 4.2 8.8 1.0
C16 A:R38504 4.3 17.7 1.0
CE1 A:HIS114 4.3 8.5 1.0
CZ A:ARG119 4.4 15.0 1.0
CB A:ASP118 4.4 10.1 1.0
NE2 A:HIS114 4.5 8.7 1.0
C03 A:R38504 4.7 33.2 1.0
NE2 A:HIS179 4.7 8.1 1.0
CA A:CYS198 4.8 7.6 1.0
O A:HOH687 4.8 15.7 1.0
C02 A:R38504 4.9 23.9 1.0
CE1 A:HIS179 4.9 8.2 1.0

Zinc binding site 2 out of 6 in 5n4s

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Zinc binding site 2 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:9.3
occ:1.00
ND1 A:HIS116 2.0 10.0 1.0
NE2 A:HIS179 2.0 8.1 1.0
NE2 A:HIS114 2.1 8.7 1.0
S20 A:R38504 2.3 10.8 1.0
CE1 A:HIS116 2.9 10.7 1.0
CE1 A:HIS179 3.0 8.2 1.0
CE1 A:HIS114 3.0 8.5 1.0
CD2 A:HIS179 3.1 7.8 1.0
CG A:HIS116 3.1 9.6 1.0
CD2 A:HIS114 3.1 8.3 1.0
C19 A:R38504 3.3 11.8 1.0
CB A:HIS116 3.5 10.0 1.0
ZN A:ZN501 3.8 10.2 1.0
NE2 A:HIS116 4.1 12.7 1.0
OD1 A:ASP118 4.1 10.3 1.0
ND1 A:HIS179 4.1 9.2 1.0
CD2 A:HIS116 4.1 11.2 1.0
ND1 A:HIS114 4.1 8.8 1.0
CG A:HIS179 4.2 8.3 1.0
CG A:HIS114 4.2 8.1 1.0
CB A:CYS198 4.2 8.5 1.0
SG A:CYS198 4.5 9.9 1.0
C18 A:R38504 4.7 13.8 1.0
OD2 A:ASP118 4.8 11.8 1.0
CA A:HIS116 4.9 9.2 1.0
CG A:ASP118 4.9 9.5 1.0

Zinc binding site 3 out of 6 in 5n4s

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Zinc binding site 3 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:12.1
occ:1.00
O2 A:FMT506 2.0 12.3 1.0
O1 A:FMT505 2.0 15.8 1.0
ND1 A:HIS251 2.1 9.0 1.0
C A:FMT506 2.7 11.7 1.0
O1 A:FMT506 2.9 15.5 1.0
C A:FMT505 3.0 17.9 1.0
CE1 A:HIS251 3.0 9.5 1.0
CG A:HIS251 3.1 8.8 1.0
O2 A:FMT505 3.2 17.1 1.0
CB A:HIS251 3.5 10.3 1.0
CA A:HIS251 3.8 10.1 1.0
NE2 A:HIS251 4.1 9.6 1.0
CD2 A:HIS251 4.2 9.4 1.0
ND2 A:ASN254 4.4 13.6 1.0
O A:HIS251 4.6 11.8 1.0
C A:HIS251 4.7 10.8 1.0
CD2 A:LEU203 4.8 16.0 1.0
N A:HIS251 4.9 9.9 1.0

Zinc binding site 4 out of 6 in 5n4s

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Zinc binding site 4 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:10.7
occ:1.00
OD2 B:ASP118 2.0 12.5 1.0
NE2 B:HIS240 2.1 9.5 1.0
SG B:CYS198 2.3 9.8 1.0
S20 B:R38504 2.4 10.9 1.0
CG B:ASP118 3.1 8.9 1.0
CE1 B:HIS240 3.1 10.1 1.0
CD2 B:HIS240 3.1 10.2 1.0
C19 B:R38504 3.4 10.9 1.0
CB B:CYS198 3.4 8.7 1.0
OD1 B:ASP118 3.5 11.8 1.0
O05 B:R38504 3.7 20.9 1.0
NH2 B:ARG119 3.8 13.5 1.0
C18 B:R38504 3.8 14.9 1.0
ZN B:ZN502 3.8 9.6 1.0
N01 B:R38504 3.9 17.1 1.0
NE B:ARG119 4.0 12.0 1.0
ND1 B:HIS240 4.2 12.9 1.0
CG B:HIS240 4.2 9.4 1.0
C16 B:R38504 4.3 20.9 1.0
CZ B:ARG119 4.3 9.3 1.0
CE1 B:HIS114 4.4 7.8 1.0
CB B:ASP118 4.4 12.8 1.0
NE2 B:HIS114 4.5 8.4 1.0
C03 B:R38504 4.7 24.2 1.0
NE2 B:HIS179 4.7 8.2 1.0
CA B:CYS198 4.7 7.3 1.0
O B:HOH678 4.9 12.6 1.0
CE1 B:HIS179 4.9 8.9 1.0
C02 B:R38504 4.9 18.5 1.0

Zinc binding site 5 out of 6 in 5n4s

Go back to Zinc Binding Sites List in 5n4s
Zinc binding site 5 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:9.6
occ:1.00
ND1 B:HIS116 2.0 11.4 1.0
NE2 B:HIS179 2.1 8.2 1.0
NE2 B:HIS114 2.1 8.4 1.0
S20 B:R38504 2.3 10.9 1.0
CE1 B:HIS116 3.0 10.6 1.0
CE1 B:HIS179 3.0 8.9 1.0
CE1 B:HIS114 3.0 7.8 1.0
CD2 B:HIS114 3.1 7.6 1.0
CG B:HIS116 3.1 9.2 1.0
CD2 B:HIS179 3.1 8.7 1.0
C19 B:R38504 3.3 10.9 1.0
CB B:HIS116 3.4 9.7 1.0
ZN B:ZN501 3.8 10.7 1.0
NE2 B:HIS116 4.1 11.8 1.0
ND1 B:HIS114 4.1 7.4 1.0
ND1 B:HIS179 4.1 8.9 1.0
OD1 B:ASP118 4.1 11.8 1.0
CD2 B:HIS116 4.2 10.6 1.0
CG B:HIS114 4.2 8.2 1.0
CB B:CYS198 4.2 8.7 1.0
CG B:HIS179 4.2 8.6 1.0
SG B:CYS198 4.4 9.8 1.0
C18 B:R38504 4.7 14.9 1.0
OD2 B:ASP118 4.8 12.5 1.0
CA B:HIS116 4.9 9.3 1.0
CG B:ASP118 4.9 8.9 1.0

Zinc binding site 6 out of 6 in 5n4s

Go back to Zinc Binding Sites List in 5n4s
Zinc binding site 6 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3)


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 ((S)-3-Mercapto-2- Methylpropanoyl)-D-Tryptophan (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:10.4
occ:1.00
O2 B:FMT505 1.9 11.7 1.0
O1 B:FMT506 2.0 14.2 1.0
NE2 B:HIS153 2.1 12.0 1.0
C B:FMT505 2.7 13.3 1.0
O1 B:FMT505 2.8 13.9 1.0
CE1 B:HIS153 2.9 12.1 1.0
C B:FMT506 2.9 14.5 1.0
O2 B:FMT506 3.1 14.1 1.0
CD2 B:HIS153 3.2 11.3 1.0
ND1 B:HIS153 4.1 13.1 1.0
CG B:HIS153 4.3 10.9 1.0
CB B:ALA132 4.3 12.1 1.0
CA B:ALA132 4.9 12.4 1.0
O B:HOH646 4.9 19.8 1.0
CG2 B:THR152 4.9 12.8 1.0

Reference:

G.B.Li, J.Brem, R.Lesniak, M.I.Abboud, C.T.Lohans, I.J.Clifton, S.Y.Yang, J.C.Jimenez-Castellanos, M.B.Avison, J.Spencer, M.A.Mcdonough, C.J.Schofield. Crystallographic Analyses of Isoquinoline Complexes Reveal A New Mode of Metallo-Beta-Lactamase Inhibition. Chem. Commun. (Camb.) V. 53 5806 2017.
ISSN: ESSN 1364-548X
PubMed: 28470248
DOI: 10.1039/C7CC02394D
Page generated: Wed Dec 16 06:34:21 2020

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