Zinc 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
Bromine (Br) 2 atoms
Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6ibv

Go back to Zinc Binding Sites List in 6ibv
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn302

b:10.6
occ:1.00
 O09 A:H9E301 2.0 30.0 1.0
OD2 A:ASP124 2.0 8.7 1.0
NE2 A:HIS250 2.1 8.1 1.0
SG A:CYS208 2.3 10.1 1.0
CE1 A:HIS250 2.8 8.4 1.0
CG A:ASP124 3.1 9.7 1.0
B06 A:H9E301 3.1 30.0 1.0
CD2 A:HIS250 3.2 9.2 1.0
O08 A:H9E301 3.2 30.0 1.0
CB A:CYS208 3.4 10.5 1.0
OD1 A:ASP124 3.5 12.4 1.0
ND1 A:HIS250 4.0 9.8 1.0
C05 A:H9E301 4.0 30.0 1.0
O A:HOH496 4.1 8.8 1.0
CB A:SER249 4.1 10.1 1.0
CG A:HIS250 4.2 9.5 1.0
ZN A:ZN303 4.3 11.0 1.0
CB A:ASP124 4.3 9.5 1.0
OG A:SER249 4.4 8.7 1.0
O07 A:H9E301 4.4 30.0 1.0
C04 A:H9E301 4.5 30.0 1.0
CA A:CYS208 4.5 10.7 1.0
NE2 A:HIS189 4.6 7.6 1.0
CE1 A:HIS189 4.8 8.8 1.0
CE1 A:HIS120 4.9 8.7 1.0
CE A:LYS125 5.0 10.9 1.0

Zinc binding site 2 out of 4 in 6ibv

Go back to Zinc Binding Sites List in 6ibv
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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
A:Zn303

b:11.0
occ:1.00
 O08 A:H9E301 2.0 30.0 1.0
NE2 A:HIS189 2.0 7.6 1.0
ND1 A:HIS122 2.1 9.0 1.0
NE2 A:HIS120 2.2 8.5 1.0
O07 A:H9E301 2.4 30.0 1.0
B06 A:H9E301 2.6 30.0 1.0
CD2 A:HIS189 2.8 8.8 1.0
CE1 A:HIS122 3.0 9.0 1.0
CG A:HIS122 3.0 8.3 1.0
CE1 A:HIS120 3.1 8.7 1.0
CE1 A:HIS189 3.2 8.8 1.0
CD2 A:HIS120 3.2 8.5 1.0
CB A:HIS122 3.3 8.1 1.0
O09 A:H9E301 3.5 30.0 1.0
CG A:HIS189 4.0 9.2 1.0
C05 A:H9E301 4.0 30.0 1.0
ND1 A:HIS189 4.1 9.2 1.0
CD2 A:HIS122 4.1 9.6 1.0
NE2 A:HIS122 4.1 9.4 1.0
ND1 A:HIS120 4.2 9.2 1.0
SG A:CYS208 4.2 10.1 1.0
OD1 A:ASP124 4.3 12.4 1.0
ZN A:ZN302 4.3 10.6 1.0
CG A:HIS120 4.3 8.3 1.0
CG2 A:THR190 4.4 7.6 1.0
CB A:CYS208 4.5 10.5 1.0
S10 A:H9E301 4.6 30.0 1.0
O A:HOH445 4.6 24.1 1.0
CA A:HIS122 4.8 8.2 1.0
OD2 A:ASP124 4.9 8.7 1.0

Zinc binding site 3 out of 4 in 6ibv

Go back to Zinc Binding Sites List in 6ibv
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn binding site number 3 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:Zn303

b:10.8
occ:1.00
 ND1 B:HIS122 2.0 8.3 1.0
NE2 B:HIS189 2.1 9.5 1.0
NE2 B:HIS120 2.1 8.9 1.0
O07 B:H9E302 2.2 30.0 1.0
O08 B:H9E302 2.3 30.0 1.0
B06 B:H9E302 2.7 30.0 1.0
CE1 B:HIS122 2.9 8.8 1.0
CD2 B:HIS189 3.0 10.3 1.0
CG B:HIS122 3.0 7.9 1.0
CE1 B:HIS120 3.1 8.6 1.0
CE1 B:HIS189 3.1 9.6 1.0
CD2 B:HIS120 3.2 8.9 1.0
CB B:HIS122 3.4 8.1 1.0
O09 B:H9E302 3.8 30.0 1.0
C05 B:H9E302 4.0 30.0 1.0
NE2 B:HIS122 4.1 9.8 1.0
CG B:HIS189 4.1 9.3 1.0
CD2 B:HIS122 4.1 8.8 1.0
ND1 B:HIS189 4.1 10.6 1.0
OD1 B:ASP124 4.2 9.1 1.0
ND1 B:HIS120 4.2 8.6 1.0
SG B:CYS208 4.2 9.9 1.0
CG B:HIS120 4.3 8.7 1.0
ZN B:ZN304 4.3 10.4 1.0
CG2 B:THR190 4.4 8.3 1.0
CB B:CYS208 4.5 10.1 1.0
S10 B:H9E302 4.6 30.0 1.0
O B:HOH487 4.6 15.2 1.0
CA B:HIS122 4.9 8.2 1.0

Zinc binding site 4 out of 4 in 6ibv

Go back to Zinc Binding Sites List in 6ibv
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn binding site number 4 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:Zn304

b:10.4
occ:1.00
 O09 B:H9E302 2.0 30.0 1.0
NE2 B:HIS250 2.0 9.2 1.0
OD2 B:ASP124 2.0 10.9 1.0
SG B:CYS208 2.2 9.9 1.0
O08 B:H9E302 2.7 30.0 1.0
CE1 B:HIS250 2.8 8.9 1.0
B06 B:H9E302 2.9 30.0 1.0
CG B:ASP124 3.0 9.1 1.0
CD2 B:HIS250 3.1 9.0 1.0
CB B:CYS208 3.4 10.1 1.0
OD1 B:ASP124 3.4 9.1 1.0
C05 B:H9E302 3.9 30.0 1.0
ND1 B:HIS250 4.0 8.4 1.0
O B:HOH512 4.1 6.1 1.0
CB B:SER249 4.1 9.2 1.0
CG B:HIS250 4.2 9.6 1.0
O07 B:H9E302 4.2 30.0 1.0
ZN B:ZN303 4.3 10.8 1.0
CB B:ASP124 4.3 8.3 1.0
OG B:SER249 4.4 9.4 1.0
C04 B:H9E302 4.4 30.0 1.0
CA B:CYS208 4.6 10.2 1.0
NE2 B:HIS189 4.7 9.5 1.0
CE1 B:HIS189 4.8 9.6 1.0
CE1 B:HIS120 4.9 8.6 1.0
CE B:LYS125 4.9 9.3 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: Wed Dec 16 11:59:59 2020

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