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Zinc in PDB 5n4t: Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4)

Protein crystallography data

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4), PDB code: 5n4t 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) 56.29 / 1.16
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.903, 80.148, 79.085, 90.00, 139.49, 90.00
R / Rfree (%) 17.5 / 19.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4) (pdb code 5n4t). 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)-L-Tryptophan (Compound 4), PDB code: 5n4t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5n4t

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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)-L-Tryptophan (Compound 4)


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)-L-Tryptophan (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:10.9
occ:1.00
ND1 A:HIS116 2.0 13.0 1.0
NE2 A:HIS114 2.1 9.2 1.0
NE2 A:HIS179 2.1 9.8 1.0
S20 A:R59504 2.3 12.2 1.0
CE1 A:HIS116 3.0 12.1 1.0
CE1 A:HIS179 3.0 11.2 1.0
CE1 A:HIS114 3.0 9.1 1.0
CD2 A:HIS114 3.0 9.2 1.0
CG A:HIS116 3.1 11.0 1.0
CD2 A:HIS179 3.1 8.9 1.0
C19 A:R59504 3.4 13.8 1.0
CB A:HIS116 3.5 10.9 1.0
ZN A:ZN502 3.9 11.6 1.0
OD1 A:ASP118 4.1 12.1 1.0
NE2 A:HIS116 4.1 13.2 1.0
ND1 A:HIS114 4.1 9.3 1.0
ND1 A:HIS179 4.1 10.7 1.0
CB A:CYS198 4.2 9.7 1.0
CD2 A:HIS116 4.2 12.5 1.0
CG A:HIS114 4.2 9.6 1.0
CG A:HIS179 4.2 9.1 1.0
SG A:CYS198 4.5 10.3 1.0
C18 A:R59504 4.7 18.9 1.0
OD2 A:ASP118 4.8 11.7 1.0
CG A:ASP118 4.9 10.7 1.0
CA A:HIS116 4.9 10.2 1.0
O A:HOH817 4.9 31.8 1.0

Zinc binding site 2 out of 6 in 5n4t

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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)-L-Tryptophan (Compound 4)


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)-L-Tryptophan (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:11.6
occ:1.00
OD2 A:ASP118 2.0 11.7 1.0
NE2 A:HIS240 2.1 10.4 1.0
SG A:CYS198 2.3 10.3 1.0
S20 A:R59504 2.3 12.2 1.0
CG A:ASP118 3.0 10.7 1.0
CE1 A:HIS240 3.1 10.5 1.0
CD2 A:HIS240 3.1 10.2 1.0
C19 A:R59504 3.4 13.8 1.0
OD1 A:ASP118 3.4 12.1 1.0
CB A:CYS198 3.4 9.7 1.0
NH2 A:ARG119 3.7 13.8 1.0
ZN A:ZN501 3.9 10.9 1.0
C18 A:R59504 3.9 18.9 1.0
NE A:ARG119 4.0 11.8 1.0
ND1 A:HIS240 4.2 11.0 1.0
CG A:HIS240 4.2 9.5 1.0
CZ A:ARG119 4.2 10.1 1.0
CE1 A:HIS114 4.3 9.1 1.0
CB A:ASP118 4.3 12.9 1.0
C02 A:R59504 4.4 29.1 1.0
NE2 A:HIS114 4.5 9.2 1.0
CA A:CYS198 4.7 9.3 1.0
O A:HOH612 4.8 13.1 1.0
O05 A:R59504 4.8 32.1 1.0
NE2 A:HIS179 4.8 9.8 1.0
C16 A:R59504 4.8 22.9 1.0
C03 A:R59504 4.9 29.5 1.0
CE1 A:HIS179 5.0 11.2 1.0

Zinc binding site 3 out of 6 in 5n4t

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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)-L-Tryptophan (Compound 4)


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)-L-Tryptophan (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:11.4
occ:1.00
O2 A:FMT505 1.9 8.2 0.5
O1 A:BEZ507 1.9 11.3 1.0
ND1 A:HIS251 2.1 9.5 1.0
O1 A:FMT505 2.1 20.1 0.5
C A:BEZ507 2.7 13.3 1.0
O2 A:BEZ507 2.8 13.8 1.0
C A:FMT505 2.8 8.6 0.5
CE1 A:HIS251 3.0 11.0 1.0
C A:FMT505 3.0 21.4 0.5
O1 A:FMT505 3.2 7.0 0.5
CG A:HIS251 3.2 8.3 1.0
CB A:HIS251 3.5 10.5 1.0
CA A:HIS251 3.8 9.7 1.0
C1 A:BEZ507 4.2 19.8 1.0
NE2 A:HIS251 4.2 11.1 1.0
O2 A:FMT505 4.2 21.2 0.5
CD2 A:HIS251 4.3 10.7 1.0
ND2 A:ASN254 4.3 13.4 1.0
CD2 A:LEU203 4.6 13.1 1.0
O A:HIS251 4.6 9.3 1.0
C A:HIS251 4.7 9.6 1.0
C2 A:BEZ507 4.9 21.5 1.0
N A:HIS251 4.9 9.1 1.0

Zinc binding site 4 out of 6 in 5n4t

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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)-L-Tryptophan (Compound 4)


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)-L-Tryptophan (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:10.1
occ:1.00
ND1 B:HIS116 2.0 10.8 1.0
NE2 B:HIS179 2.0 8.8 1.0
NE2 B:HIS114 2.1 8.2 1.0
S20 B:R59304 2.3 11.2 1.0
CE1 B:HIS116 2.9 12.3 1.0
CE1 B:HIS179 3.0 9.8 1.0
CG B:HIS116 3.0 10.3 1.0
CE1 B:HIS114 3.1 8.9 1.0
CD2 B:HIS179 3.1 9.6 1.0
CD2 B:HIS114 3.1 8.1 1.0
C19 B:R59304 3.3 13.4 1.0
CB B:HIS116 3.4 10.6 1.0
ZN B:ZN302 3.9 10.8 1.0
NE2 B:HIS116 4.1 12.2 1.0
OD1 B:ASP118 4.1 10.9 1.0
ND1 B:HIS179 4.1 9.4 1.0
CD2 B:HIS116 4.1 11.1 1.0
ND1 B:HIS114 4.2 9.4 1.0
CB B:CYS198 4.2 10.3 1.0
CG B:HIS179 4.2 9.7 1.0
CG B:HIS114 4.2 9.3 1.0
SG B:CYS198 4.5 10.2 1.0
C18 B:R59304 4.7 20.6 1.0
OD2 B:ASP118 4.8 12.1 1.0
CG B:ASP118 4.9 11.6 1.0
CA B:HIS116 4.9 10.4 1.0

Zinc binding site 5 out of 6 in 5n4t

Go back to Zinc Binding Sites List in 5n4t
Zinc binding site 5 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4)


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)-L-Tryptophan (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:10.8
occ:1.00
OD2 B:ASP118 2.0 12.1 1.0
NE2 B:HIS240 2.1 10.4 1.0
SG B:CYS198 2.3 10.2 1.0
S20 B:R59304 2.4 11.2 1.0
CG B:ASP118 3.0 11.6 1.0
CE1 B:HIS240 3.1 9.4 1.0
CD2 B:HIS240 3.1 10.5 1.0
C19 B:R59304 3.3 13.4 1.0
OD1 B:ASP118 3.4 10.9 1.0
CB B:CYS198 3.4 10.3 1.0
NH2 B:ARG119 3.7 15.4 1.0
C18 B:R59304 3.9 20.6 1.0
ZN B:ZN301 3.9 10.1 1.0
NE B:ARG119 4.0 11.9 1.0
ND1 B:HIS240 4.2 10.2 1.0
CG B:HIS240 4.2 9.1 1.0
CZ B:ARG119 4.3 12.1 1.0
C02 B:R59304 4.3 33.1 1.0
CE1 B:HIS114 4.3 8.9 1.0
CB B:ASP118 4.4 11.9 1.0
NE2 B:HIS114 4.5 8.2 1.0
O04 B:R59304 4.7 34.6 1.0
O B:HOH420 4.7 13.6 1.0
CA B:CYS198 4.7 8.6 1.0
NE2 B:HIS179 4.8 8.8 1.0
C16 B:R59304 4.8 26.0 1.0
C03 B:R59304 4.9 34.1 1.0
CE1 B:HIS179 5.0 9.8 1.0
N01 B:R59304 5.0 30.4 1.0

Zinc binding site 6 out of 6 in 5n4t

Go back to Zinc Binding Sites List in 5n4t
Zinc binding site 6 out of 6 in the Vim-2 Metallo-Beta-Lactamase in Complex with ((S)-3-Mercapto-2- Methylpropanoyl)-L-Tryptophan (Compound 4)


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)-L-Tryptophan (Compound 4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:14.6
occ:1.00
O2 B:BEZ306 1.9 18.3 1.0
O1 B:FMT305 2.0 13.6 1.0
ND1 B:HIS251 2.1 11.8 1.0
C B:BEZ306 2.7 20.9 1.0
O1 B:BEZ306 2.8 18.9 1.0
C B:FMT305 3.0 17.0 1.0
CE1 B:HIS251 3.0 12.1 1.0
CG B:HIS251 3.1 12.0 1.0
O2 B:FMT305 3.3 16.5 1.0
CB B:HIS251 3.5 11.1 1.0
CA B:HIS251 3.8 10.4 1.0
C1 B:BEZ306 4.1 28.6 1.0
NE2 B:HIS251 4.2 11.7 1.0
CD2 B:HIS251 4.2 10.9 1.0
ND2 B:ASN254 4.4 16.6 1.0
O B:HIS251 4.6 11.9 1.0
C B:HIS251 4.7 10.5 1.0
CD2 B:LEU203 4.8 14.2 1.0
C6 B:BEZ306 4.8 29.5 1.0
N B:HIS251 4.9 11.6 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 06:34:23 2020

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