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

Enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 6

All present enzymatic activity of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 6:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ndm-1 Beta-Lactamase in Complex with Boronic Inhibitor Cpd 6, PDB code: 6ibs 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) 42.59 / 1.37
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.285, 73.737, 77.613, 90.00, 90.00, 90.00
R / Rfree (%) 13.2 / 16.3

Other elements in 6ibs:

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

Zinc binding site 1 out of 4 in 6ibs

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


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

b:12.3
occ:1.00
 O17 A:HB8303 1.8 17.3 1.0
OD2 A:ASP124 2.0 10.8 1.0
NE2 A:HIS250 2.1 10.5 1.0
SG A:CYS208 2.3 10.5 1.0
O16 A:HB8303 2.8 12.2 1.0
B15 A:HB8303 2.9 14.0 1.0
CE1 A:HIS250 3.0 10.8 1.0
CG A:ASP124 3.0 9.3 1.0
CD2 A:HIS250 3.1 10.6 1.0
CB A:CYS208 3.4 10.8 1.0
OD1 A:ASP124 3.5 10.2 1.0
C14 A:HB8303 3.9 15.1 1.0
O A:HOH526 4.1 10.4 1.0
O18 A:HB8303 4.1 15.9 1.0
CB A:SER249 4.2 9.7 1.0
ND1 A:HIS250 4.2 11.6 1.0
ZN A:ZN302 4.2 11.8 1.0
CG A:HIS250 4.2 10.2 1.0
CB A:ASP124 4.3 9.3 1.0
OG A:SER249 4.5 10.2 1.0
CA A:CYS208 4.5 9.8 1.0
S13 A:HB8303 4.5 22.1 1.0
NE2 A:HIS189 4.6 11.3 1.0
CE1 A:HIS189 4.8 10.5 1.0
CE1 A:HIS120 4.8 12.0 1.0
NE2 A:HIS120 5.0 10.5 1.0

Zinc binding site 2 out of 4 in 6ibs

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


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

b:11.8
occ:1.00
 NE2 A:HIS189 2.0 11.3 1.0
O16 A:HB8303 2.0 12.2 1.0
ND1 A:HIS122 2.0 11.0 1.0
NE2 A:HIS120 2.1 10.5 1.0
O18 A:HB8303 2.8 15.9 1.0
B15 A:HB8303 2.9 14.0 1.0
CD2 A:HIS189 3.0 10.2 1.0
CE1 A:HIS122 3.0 12.6 1.0
CG A:HIS122 3.0 10.1 1.0
CE1 A:HIS189 3.1 10.5 1.0
CD2 A:HIS120 3.1 9.3 1.0
CE1 A:HIS120 3.1 12.0 1.0
CB A:HIS122 3.3 9.6 1.0
O17 A:HB8303 4.0 17.3 1.0
OD1 A:ASP124 4.1 10.2 1.0
CG A:HIS189 4.1 9.6 1.0
CD2 A:HIS122 4.1 12.5 1.0
ND1 A:HIS189 4.1 10.2 1.0
NE2 A:HIS122 4.2 12.6 1.0
C14 A:HB8303 4.2 15.1 1.0
ND1 A:HIS120 4.2 10.6 1.0
ZN A:ZN301 4.2 12.3 1.0
SG A:CYS208 4.2 10.5 1.0
CG A:HIS120 4.2 9.2 1.0
CG2 A:THR190 4.3 9.8 1.0
CB A:CYS208 4.4 10.8 1.0
C19 A:HB8303 4.5 14.4 1.0
CA A:HIS122 4.8 8.9 1.0
CG A:ASP124 5.0 9.3 1.0
OD2 A:ASP124 5.0 10.8 1.0

Zinc binding site 3 out of 4 in 6ibs

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


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

b:12.0
occ:1.00
 O17 B:HB8303 1.8 13.1 1.0
OD2 B:ASP124 2.0 9.7 1.0
NE2 B:HIS250 2.0 10.0 1.0
SG B:CYS208 2.3 10.2 1.0
O16 B:HB8303 2.9 11.1 1.0
B15 B:HB8303 2.9 11.4 1.0
CD2 B:HIS250 3.0 10.6 1.0
CE1 B:HIS250 3.0 10.3 1.0
CG B:ASP124 3.0 9.7 1.0
CB B:CYS208 3.4 9.8 1.0
OD1 B:ASP124 3.5 10.0 1.0
C14 B:HB8303 3.9 13.3 1.0
O B:HOH510 4.0 9.2 1.0
ND1 B:HIS250 4.1 10.7 1.0
CB B:SER249 4.1 9.8 1.0
O18 B:HB8303 4.1 12.5 1.0
CG B:HIS250 4.1 10.3 1.0
ZN B:ZN302 4.2 10.7 1.0
CB B:ASP124 4.3 8.4 1.0
OG B:SER249 4.4 10.1 1.0
S13 B:HB8303 4.5 19.6 1.0
CA B:CYS208 4.5 9.2 1.0
NE2 B:HIS189 4.7 8.9 1.0
CE1 B:HIS189 4.8 9.9 1.0
CE1 B:HIS120 4.9 9.4 1.0
CE B:LYS125 5.0 9.5 1.0

Zinc binding site 4 out of 4 in 6ibs

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


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

b:10.7
occ:1.00
 O16 B:HB8303 1.9 11.1 1.0
NE2 B:HIS189 2.0 8.9 1.0
ND1 B:HIS122 2.0 10.3 1.0
NE2 B:HIS120 2.1 8.9 1.0
O18 B:HB8303 2.7 12.5 1.0
B15 B:HB8303 2.8 11.4 1.0
CE1 B:HIS189 3.0 9.9 1.0
CG B:HIS122 3.0 10.3 1.0
CD2 B:HIS189 3.0 9.9 1.0
CE1 B:HIS122 3.0 10.6 1.0
CE1 B:HIS120 3.1 9.4 1.0
CD2 B:HIS120 3.1 9.2 1.0
CB B:HIS122 3.3 10.1 1.0
O17 B:HB8303 3.9 13.1 1.0
OD1 B:ASP124 4.1 10.0 1.0
C14 B:HB8303 4.1 13.3 1.0
ND1 B:HIS189 4.1 9.8 1.0
NE2 B:HIS122 4.2 10.8 1.0
CD2 B:HIS122 4.2 10.7 1.0
CG B:HIS189 4.2 9.6 1.0
ND1 B:HIS120 4.2 9.9 1.0
ZN B:ZN301 4.2 12.0 1.0
CG B:HIS120 4.2 8.5 1.0
SG B:CYS208 4.2 10.2 1.0
CG2 B:THR190 4.4 10.3 1.0
CB B:CYS208 4.4 9.8 1.0
C19 B:HB8303 4.5 12.8 1.0
CA B:HIS122 4.8 9.7 1.0
CG B:ASP124 5.0 9.7 1.0
OD2 B:ASP124 5.0 9.7 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: Mon Oct 28 23:38:02 2024

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