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Bromine in PDB 6ibv: Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1

Enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1

All present enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1, PDB code: 6ibv was solved by L.Maso, A.Quotadamo, P.Bellio, M.Montanari, G.Celenza, A.Venturelli, M.P.Costi, D.Tondi, L.Cendron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.67 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.407, 73.824, 77.868, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25.2

Other elements in 6ibv:

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 4 atoms
Calcium (Ca) 3 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1 (pdb code 6ibv). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1, PDB code: 6ibv:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in 6ibv

Go back to Bromine Binding Sites List in 6ibv
Bromine binding site 1 out of 2 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br301

b:30.0
occ:1.00
BR A:H9E301 0.0 30.0 1.0
C14 A:H9E301 1.5 30.0 1.0
C01 A:H9E301 2.4 30.0 1.0
C02 A:H9E301 2.9 30.0 1.0
C13 A:H9E301 3.7 30.0 1.0
CD2 A:LEU65 3.8 26.4 1.0
O A:ASP66 4.2 32.1 1.0
CG2 A:VAL73 4.2 21.1 1.0
C03 A:H9E301 4.4 30.0 1.0
O A:LEU65 4.5 26.8 1.0
CG A:LEU65 4.7 24.9 1.0
CB A:VAL73 4.8 18.8 1.0
C A:ASP66 4.8 32.7 1.0
C12 A:H9E301 5.0 30.0 1.0
CH2 A:TRP93 5.0 10.3 1.0

Bromine binding site 2 out of 2 in 6ibv

Go back to Bromine Binding Sites List in 6ibv
Bromine binding site 2 out of 2 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor Cpd 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br302

b:30.0
occ:1.00
BR B:H9E302 0.0 30.0 1.0
C14 B:H9E302 1.5 30.0 1.0
C01 B:H9E302 2.4 30.0 1.0
C02 B:H9E302 3.0 30.0 1.0
OD2 B:ASP66 3.6 37.7 1.0
C13 B:H9E302 3.6 30.0 1.0
OD1 B:ASP66 3.7 36.8 1.0
CG B:ASP66 3.9 35.1 1.0
C03 B:H9E302 4.5 30.0 1.0
O B:LEU65 4.5 20.1 1.0
CD2 B:LEU65 4.6 22.3 1.0
CG2 B:VAL73 4.6 21.5 1.0
CH2 B:TRP93 4.8 9.6 1.0
CG B:LEU65 4.8 20.2 1.0
CZ3 B:TRP93 4.8 9.8 1.0
O B:HOH401 4.9 44.8 1.0
C12 B:H9E302 4.9 30.0 1.0
CB B:LEU65 5.0 17.0 1.0
CB B:VAL73 5.0 20.5 1.0

Reference:

L.Cendron, A.Quotadamo, L.Maso, P.Bellio, M.Montanari, G.Celenza, A.Venturelli, M.P.Costi, D.Tondi. X-Ray Crystallography Deciphers the Activity of Broad-Spectrum Boronic Acid Beta-Lactamase Inhibitors. Acs Med.Chem.Lett. V. 10 650 2019.
ISSN: ISSN 1948-5875
PubMed: 30996812
DOI: 10.1021/ACSMEDCHEMLETT.8B00607
Page generated: Sat Dec 12 02:34:14 2020

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