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Zinc in PDB 6q30: Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5

Enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5

All present enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5, PDB code: 6q30 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) 42.52 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.250, 73.748, 77.276, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 19.1

Other elements in 6q30:

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5 also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5 (pdb code 6q30). 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 Boronic Inhibitor Cpd 5, PDB code: 6q30:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6q30

Go back to Zinc Binding Sites List in 6q30
Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5


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 Boronic Inhibitor Cpd 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:13.8
occ:1.00
 O11 A:HCH305 1.7 17.8 1.0
OD2 A:ASP124 2.0 14.7 1.0
NE2 A:HIS250 2.1 13.6 1.0
SG A:CYS208 2.3 11.8 1.0
B08 A:HCH305 2.9 15.8 1.0
O10 A:HCH305 3.0 14.9 1.0
CE1 A:HIS250 3.0 13.0 1.0
CG A:ASP124 3.1 12.0 1.0
CD2 A:HIS250 3.1 13.5 1.0
CB A:CYS208 3.4 12.8 1.0
OD1 A:ASP124 3.5 13.9 1.0
C07 A:HCH305 3.9 19.2 1.0
O A:HOH528 4.0 12.6 1.0
CB A:SER249 4.1 12.4 1.0
ND1 A:HIS250 4.2 13.3 1.0
C12 A:HCH305 4.2 24.8 1.0
CG A:HIS250 4.2 12.8 1.0
ZN A:ZN302 4.2 14.0 1.0
O09 A:HCH305 4.3 23.0 1.0
CB A:ASP124 4.3 12.1 1.0
OG A:SER249 4.5 11.6 1.0
CA A:CYS208 4.5 9.9 1.0
NE2 A:HIS189 4.5 15.0 1.0
CE1 A:HIS189 4.7 12.5 1.0
CE1 A:HIS120 4.8 13.4 1.0
CE A:LYS125 5.0 11.9 1.0

Zinc binding site 2 out of 4 in 6q30

Go back to Zinc Binding Sites List in 6q30
Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5


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 Boronic Inhibitor Cpd 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:14.0
occ:1.00
 O10 A:HCH305 1.8 14.9 1.0
ND1 A:HIS122 2.0 13.8 1.0
NE2 A:HIS189 2.0 15.0 1.0
NE2 A:HIS120 2.1 13.6 1.0
O09 A:HCH305 2.6 23.0 1.0
B08 A:HCH305 2.8 15.8 1.0
CE1 A:HIS122 2.9 15.4 1.0
CD2 A:HIS189 3.0 13.4 1.0
CG A:HIS122 3.0 11.4 1.0
CE1 A:HIS120 3.0 13.4 1.0
CD2 A:HIS120 3.1 12.6 1.0
CE1 A:HIS189 3.1 12.5 1.0
CB A:HIS122 3.3 11.8 1.0
O11 A:HCH305 3.8 17.8 1.0
NE2 A:HIS122 4.1 14.2 1.0
CD2 A:HIS122 4.1 14.3 1.0
ND1 A:HIS120 4.1 11.4 1.0
OD1 A:ASP124 4.1 13.9 1.0
CG A:HIS189 4.2 12.9 1.0
C07 A:HCH305 4.2 19.2 1.0
ND1 A:HIS189 4.2 12.6 1.0
CG A:HIS120 4.2 10.0 1.0
ZN A:ZN301 4.2 13.8 1.0
SG A:CYS208 4.3 11.8 1.0
CG2 A:THR190 4.4 13.2 1.0
CB A:CYS208 4.4 12.8 1.0
S06 A:HCH305 4.7 26.1 1.0
CA A:HIS122 4.8 10.5 1.0

Zinc binding site 3 out of 4 in 6q30

Go back to Zinc Binding Sites List in 6q30
Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5


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 Boronic Inhibitor Cpd 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:14.3
occ:1.00
 O10 B:HCH305 1.8 24.3 1.0
NE2 B:HIS250 1.9 15.2 1.0
OD2 B:ASP124 2.2 15.5 1.0
SG B:CYS208 2.3 12.2 1.0
O11 B:HCH305 2.9 16.0 1.0
CE1 B:HIS250 2.9 14.6 1.0
B08 B:HCH305 2.9 22.4 1.0
CD2 B:HIS250 3.1 15.6 1.0
CG B:ASP124 3.2 11.6 1.0
CB B:CYS208 3.4 13.1 1.0
OD1 B:ASP124 3.5 15.4 1.0
C07 B:HCH305 4.0 25.6 1.0
O B:HOH519 4.0 15.2 1.0
CB B:SER249 4.1 12.5 1.0
ND1 B:HIS250 4.1 13.3 1.0
CG B:HIS250 4.2 13.5 1.0
ZN B:ZN302 4.2 13.5 1.0
O09 B:HCH305 4.2 22.2 1.0
CB B:ASP124 4.4 11.7 1.0
OG B:SER249 4.4 11.2 1.0
CA B:CYS208 4.5 11.7 1.0
NE2 B:HIS189 4.6 13.5 1.0
C12 B:HCH305 4.7 35.5 1.0
CE1 B:HIS189 4.7 15.0 1.0
CE1 B:HIS120 4.8 14.2 1.0
NE2 B:HIS120 5.0 12.0 1.0

Zinc binding site 4 out of 4 in 6q30

Go back to Zinc Binding Sites List in 6q30
Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 5


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 Boronic Inhibitor Cpd 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:13.5
occ:1.00
 O11 B:HCH305 1.9 16.0 1.0
ND1 B:HIS122 2.0 12.9 1.0
NE2 B:HIS189 2.0 13.5 1.0
NE2 B:HIS120 2.0 12.0 1.0
O09 B:HCH305 2.7 22.2 1.0
CE1 B:HIS122 3.0 13.5 1.0
B08 B:HCH305 3.0 22.4 1.0
CD2 B:HIS189 3.0 12.6 1.0
CE1 B:HIS120 3.0 14.2 1.0
CG B:HIS122 3.0 11.7 1.0
CD2 B:HIS120 3.0 12.2 1.0
CE1 B:HIS189 3.1 15.0 1.0
CB B:HIS122 3.3 9.6 1.0
O10 B:HCH305 4.0 24.3 1.0
ND1 B:HIS120 4.1 11.3 1.0
CD2 B:HIS122 4.1 13.1 1.0
CG B:HIS120 4.1 10.7 1.0
NE2 B:HIS122 4.1 13.7 1.0
CG B:HIS189 4.2 11.6 1.0
ND1 B:HIS189 4.2 13.5 1.0
OD1 B:ASP124 4.2 15.4 1.0
ZN B:ZN301 4.2 14.3 1.0
SG B:CYS208 4.2 12.2 1.0
C07 B:HCH305 4.2 25.6 1.0
CG2 B:THR190 4.4 11.3 1.0
CB B:CYS208 4.4 13.1 1.0
S06 B:HCH305 4.6 34.6 1.0
CA B:HIS122 4.8 8.9 1.0
O B:HOH551 4.9 45.0 1.0
O B:HOH457 5.0 17.8 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: Tue Oct 29 05:31:10 2024

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