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:
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
|