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Zinc in PDB 6q2y: Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3

Enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3

All present enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3, PDB code: 6q2y was solved by L.Maso, A.Quotadamo, P.Bellio, M.Montanari, A.Venturelli, G.Celenza, 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) 53.62 / 1.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.425, 73.950, 77.687, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 17.6

Other elements in 6q2y:

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3 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 Broad Spectrum Boronic Inhibitor CPD3 (pdb code 6q2y). 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 CPD3, PDB code: 6q2y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6q2y

Go back to Zinc Binding Sites List in 6q2y
Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3


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 CPD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:7.0
occ:1.00
 O09 A:HCQ305 1.9 7.5 1.0
NE2 A:HIS189 2.0 6.8 1.0
ND1 A:HIS122 2.0 6.9 1.0
NE2 A:HIS120 2.1 6.6 1.0
O07 A:HCQ305 2.7 9.2 1.0
B06 A:HCQ305 2.9 7.8 1.0
CG A:HIS122 3.0 6.4 1.0
CD2 A:HIS189 3.0 6.3 1.0
CE1 A:HIS120 3.0 7.3 1.0
CE1 A:HIS189 3.0 6.6 1.0
CE1 A:HIS122 3.0 7.5 1.0
CD2 A:HIS120 3.0 6.7 1.0
CB A:HIS122 3.3 6.3 1.0
O08 A:HCQ305 3.6 9.1 1.0
OD1 A:ASP124 4.1 6.9 1.0
NE2 A:HIS122 4.1 7.9 1.0
CD2 A:HIS122 4.1 7.8 1.0
ND1 A:HIS189 4.1 6.3 1.0
ND1 A:HIS120 4.2 6.9 1.0
CG A:HIS189 4.2 5.8 1.0
CG A:HIS120 4.2 6.0 1.0
C05 A:HCQ305 4.2 8.9 1.0
SG A:CYS208 4.2 6.5 1.0
ZN A:ZN302 4.2 5.8 0.8
CG2 A:THR190 4.4 7.5 1.0
CB A:CYS208 4.4 6.6 1.0
C04 A:HCQ305 4.6 8.7 1.0
CA A:HIS122 4.8 5.8 1.0
CG A:ASP124 5.0 6.2 1.0

Zinc binding site 2 out of 4 in 6q2y

Go back to Zinc Binding Sites List in 6q2y
Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3


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 CPD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:5.8
occ:0.80
 O08 A:HCQ305 1.9 9.1 1.0
OD2 A:ASP124 2.0 7.4 1.0
NE2 A:HIS250 2.0 7.0 1.0
SG A:CYS208 2.3 6.5 1.0
CE1 A:HIS250 2.9 8.0 1.0
B06 A:HCQ305 3.0 7.8 1.0
CG A:ASP124 3.0 6.2 1.0
O09 A:HCQ305 3.0 7.5 1.0
CD2 A:HIS250 3.1 7.4 1.0
CB A:CYS208 3.4 6.6 1.0
OD1 A:ASP124 3.4 6.9 1.0
C05 A:HCQ305 3.9 8.9 1.0
O A:HOH508 4.0 6.7 1.0
ND1 A:HIS250 4.1 7.7 1.0
O07 A:HCQ305 4.1 9.2 1.0
CB A:SER249 4.1 6.7 1.0
CG A:HIS250 4.2 7.6 1.0
ZN A:ZN301 4.2 7.0 1.0
CB A:ASP124 4.3 5.8 1.0
S10 A:HCQ305 4.4 10.8 0.8
OG A:SER249 4.4 6.9 1.0
CA A:CYS208 4.5 7.0 1.0
NE2 A:HIS189 4.6 6.8 1.0
CE1 A:HIS189 4.7 6.6 1.0
CE1 A:HIS120 4.9 7.3 1.0
CE A:LYS125 5.0 7.3 1.0

Zinc binding site 3 out of 4 in 6q2y

Go back to Zinc Binding Sites List in 6q2y
Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3


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 CPD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:6.8
occ:1.00
 NE2 B:HIS189 2.0 6.5 1.0
ND1 B:HIS122 2.0 6.5 1.0
O08 B:HCQ305 2.0 7.3 1.0
NE2 B:HIS120 2.0 6.2 1.0
O07 B:HCQ305 2.6 9.2 1.0
B06 B:HCQ305 2.8 8.1 1.0
CE1 B:HIS122 3.0 7.7 1.0
CD2 B:HIS189 3.0 5.7 1.0
CE1 B:HIS189 3.0 6.9 1.0
CG B:HIS122 3.0 5.7 1.0
CE1 B:HIS120 3.0 7.3 1.0
CD2 B:HIS120 3.0 5.6 1.0
CB B:HIS122 3.3 6.0 1.0
O09 B:HCQ305 3.8 9.0 1.0
OD1 B:ASP124 4.1 7.2 1.0
NE2 B:HIS122 4.1 7.8 1.0
ND1 B:HIS189 4.1 6.6 1.0
CD2 B:HIS122 4.1 7.1 1.0
C05 B:HCQ305 4.1 9.6 1.0
ND1 B:HIS120 4.2 6.8 1.0
CG B:HIS189 4.2 5.8 1.0
CG B:HIS120 4.2 5.6 1.0
SG B:CYS208 4.2 6.6 1.0
ZN B:ZN302 4.3 5.9 0.8
CG2 B:THR190 4.4 7.2 1.0
CB B:CYS208 4.4 7.2 1.0
S10 B:HCQ305 4.7 11.9 0.8
CA B:HIS122 4.8 5.2 1.0
CG B:ASP124 5.0 6.1 1.0
OD2 B:ASP124 5.0 7.7 1.0

Zinc binding site 4 out of 4 in 6q2y

Go back to Zinc Binding Sites List in 6q2y
Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Broad Spectrum Boronic Inhibitor CPD3


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 CPD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:5.9
occ:0.80
 O09 B:HCQ305 1.9 9.0 1.0
OD2 B:ASP124 2.0 7.7 1.0
NE2 B:HIS250 2.0 7.0 1.0
SG B:CYS208 2.3 6.6 1.0
CE1 B:HIS250 3.0 6.8 1.0
B06 B:HCQ305 3.0 8.1 1.0
CG B:ASP124 3.0 6.1 1.0
CD2 B:HIS250 3.1 7.3 1.0
O08 B:HCQ305 3.1 7.3 1.0
CB B:CYS208 3.4 7.2 1.0
OD1 B:ASP124 3.4 7.2 1.0
O B:HOH518 4.0 6.4 1.0
C05 B:HCQ305 4.1 9.6 1.0
ND1 B:HIS250 4.1 7.8 1.0
CB B:SER249 4.1 7.4 1.0
CG B:HIS250 4.2 7.5 1.0
ZN B:ZN301 4.3 6.8 1.0
O07 B:HCQ305 4.3 9.2 1.0
CB B:ASP124 4.3 6.2 1.0
OG B:SER249 4.4 6.8 1.0
CA B:CYS208 4.5 6.7 1.0
C04 B:HCQ305 4.6 10.1 1.0
NE2 B:HIS189 4.7 6.5 1.0
CE1 B:HIS189 4.8 6.9 1.0
CE1 B:HIS120 4.9 7.3 1.0
CE B:LYS125 5.0 7.6 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 05:30:15 2024

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