Atomistry » Zinc » PDB 5lbt-5ll9 » 5lcf
Atomistry »
  Zinc »
    PDB 5lbt-5ll9 »
      5lcf »

Zinc in PDB 5lcf: Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30)

Protein crystallography data

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30), PDB code: 5lcf 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) 24.06 / 1.86
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.460, 65.637, 70.721, 90.00, 90.00, 90.00
R / Rfree (%) 12.7 / 16.4

Other elements in 5lcf:

The structure of Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30) (pdb code 5lcf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30), PDB code: 5lcf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5lcf

Go back to Zinc Binding Sites List in 5lcf
Zinc binding site 1 out of 2 in the Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30)


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 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:9.8
occ:1.00
O A:HOH712 1.9 7.4 1.0
ND1 A:HIS116 2.0 7.2 1.0
NE2 A:HIS114 2.1 6.9 1.0
NE2 A:HIS179 2.1 8.0 1.0
CE1 A:HIS116 3.0 10.0 1.0
CD2 A:HIS179 3.0 10.1 1.0
CE1 A:HIS114 3.0 7.8 1.0
CG A:HIS116 3.0 7.3 1.0
CD2 A:HIS114 3.1 6.3 1.0
CE1 A:HIS179 3.1 7.0 1.0
CB A:HIS116 3.4 6.9 1.0
ZN A:ZN502 3.5 11.1 1.0
OD1 A:ASP118 3.9 10.3 1.0
CB A:CYS198 4.0 8.3 1.0
C19 A:6TJ504 4.0 17.7 1.0
NE2 A:HIS116 4.1 11.1 1.0
O12 A:6TJ504 4.1 11.6 1.0
ND1 A:HIS114 4.1 7.8 1.0
CD2 A:HIS116 4.2 9.4 1.0
CG A:HIS179 4.2 10.0 1.0
ND1 A:HIS179 4.2 7.0 1.0
CG A:HIS114 4.2 6.7 1.0
SG A:CYS198 4.3 7.3 1.0
C14 A:6TJ504 4.4 11.6 1.0
C18 A:6TJ504 4.5 22.9 1.0
OD2 A:ASP118 4.5 7.8 1.0
C11 A:6TJ504 4.6 10.2 1.0
CG A:ASP118 4.6 7.3 1.0
N10 A:6TJ504 4.7 12.6 1.0
CA A:HIS116 4.8 7.1 1.0

Zinc binding site 2 out of 2 in 5lcf

Go back to Zinc Binding Sites List in 5lcf
Zinc binding site 2 out of 2 in the Vim-2 Metallo-Beta-Lactamase in Complex with 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30)


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 3-Oxo-2- Phenylisoindoline-4-Carboxylic Acid (Compound 30) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:11.1
occ:1.00
O A:HOH712 2.0 7.4 1.0
OD2 A:ASP118 2.0 7.8 1.0
NE2 A:HIS240 2.1 7.2 1.0
SG A:CYS198 2.3 7.3 1.0
CG A:ASP118 3.0 7.3 1.0
CE1 A:HIS240 3.0 8.2 1.0
CD2 A:HIS240 3.0 6.2 1.0
OD1 A:ASP118 3.3 10.3 1.0
CB A:CYS198 3.4 8.3 1.0
ZN A:ZN501 3.5 9.8 1.0
NH2 A:ARG119 3.9 15.0 1.0
NE A:ARG119 3.9 10.3 1.0
ND1 A:HIS240 4.1 8.3 1.0
N10 A:6TJ504 4.1 12.6 1.0
CG A:HIS240 4.2 7.5 1.0
CE1 A:HIS114 4.2 7.8 1.0
CZ A:ARG119 4.2 11.0 1.0
C11 A:6TJ504 4.2 10.2 1.0
CB A:ASP118 4.3 11.3 1.0
NE2 A:HIS114 4.3 6.9 1.0
C09 A:6TJ504 4.3 12.4 1.0
C13 A:6TJ504 4.5 8.1 1.0
NE2 A:HIS179 4.5 8.0 1.0
C08 A:6TJ504 4.5 12.4 1.0
C14 A:6TJ504 4.6 11.6 1.0
O12 A:6TJ504 4.6 11.6 1.0
CA A:CYS198 4.6 6.4 1.0
O A:HOH665 4.7 7.9 1.0
CD A:ARG119 4.8 7.8 1.0
CE1 A:HIS179 4.9 7.0 1.0
OG A:SER69 5.0 11.6 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 06:28:46 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy