Zinc in PDB 2yz3: Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor
Enzymatic activity of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor
All present enzymatic activity of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor:
3.5.2.6;
Protein crystallography data
The structure of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor, PDB code: 2yz3
was solved by
Y.Yamaguchi,
Y.Yamagata,
Y.Arakawa,
H.Kurosaki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.80 /
2.30
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.184,
90.749,
128.977,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.2 /
24.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor
(pdb code 2yz3). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor, PDB code: 2yz3:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 2yz3
Go back to
Zinc Binding Sites List in 2yz3
Zinc binding site 1 out
of 4 in the Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:35.4
occ:1.00
|
ND1
|
A:HIS96
|
2.0
|
36.3
|
1.0
|
NE2
|
A:HIS159
|
2.2
|
37.6
|
1.0
|
NE2
|
A:HIS94
|
2.2
|
35.2
|
1.0
|
S1
|
A:M5P401
|
2.5
|
39.3
|
1.0
|
CE1
|
A:HIS96
|
2.9
|
33.9
|
1.0
|
CD2
|
A:HIS159
|
2.9
|
37.9
|
1.0
|
CG
|
A:HIS96
|
3.0
|
36.1
|
1.0
|
CD2
|
A:HIS94
|
3.1
|
34.8
|
1.0
|
CE1
|
A:HIS94
|
3.1
|
34.2
|
1.0
|
CE1
|
A:HIS159
|
3.3
|
37.2
|
1.0
|
C11
|
A:M5P401
|
3.3
|
40.2
|
1.0
|
CB
|
A:HIS96
|
3.4
|
35.0
|
1.0
|
ZN
|
A:ZN302
|
3.8
|
24.9
|
0.8
|
NE2
|
A:HIS96
|
4.0
|
35.2
|
1.0
|
CB
|
A:CYS178
|
4.0
|
34.3
|
1.0
|
CG
|
A:HIS159
|
4.1
|
36.1
|
1.0
|
CD2
|
A:HIS96
|
4.1
|
34.7
|
1.0
|
OD2
|
A:ASP98
|
4.1
|
35.2
|
1.0
|
ND1
|
A:HIS94
|
4.2
|
33.3
|
1.0
|
CG
|
A:HIS94
|
4.2
|
33.6
|
1.0
|
C10
|
A:M5P401
|
4.2
|
44.6
|
1.0
|
ND1
|
A:HIS159
|
4.2
|
37.5
|
1.0
|
SG
|
A:CYS178
|
4.4
|
31.4
|
1.0
|
OD1
|
A:ASP98
|
4.5
|
31.2
|
1.0
|
C12
|
A:M5P401
|
4.5
|
46.6
|
1.0
|
CG
|
A:ASP98
|
4.7
|
33.9
|
1.0
|
O1
|
A:M5P401
|
4.8
|
48.8
|
1.0
|
CA
|
A:HIS96
|
4.8
|
34.9
|
1.0
|
O2
|
A:M5P401
|
4.9
|
49.7
|
1.0
|
|
Zinc binding site 2 out
of 4 in 2yz3
Go back to
Zinc Binding Sites List in 2yz3
Zinc binding site 2 out
of 4 in the Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:24.9
occ:0.80
|
OD1
|
A:ASP98
|
1.9
|
31.2
|
1.0
|
S1
|
A:M5P401
|
2.1
|
39.3
|
1.0
|
NE2
|
A:HIS220
|
2.1
|
35.8
|
1.0
|
SG
|
A:CYS178
|
2.2
|
31.4
|
1.0
|
CD2
|
A:HIS220
|
3.0
|
33.5
|
1.0
|
CG
|
A:ASP98
|
3.1
|
33.9
|
1.0
|
CE1
|
A:HIS220
|
3.2
|
32.4
|
1.0
|
CB
|
A:CYS178
|
3.3
|
34.3
|
1.0
|
C11
|
A:M5P401
|
3.5
|
40.2
|
1.0
|
NH2
|
A:ARG99
|
3.6
|
30.8
|
1.0
|
OD2
|
A:ASP98
|
3.6
|
35.2
|
1.0
|
ZN
|
A:ZN301
|
3.8
|
35.4
|
1.0
|
NE
|
A:ARG99
|
4.0
|
27.6
|
1.0
|
CZ
|
A:ARG99
|
4.2
|
28.5
|
1.0
|
CE1
|
A:HIS94
|
4.2
|
34.2
|
1.0
|
CG
|
A:HIS220
|
4.2
|
33.8
|
1.0
|
ND1
|
A:HIS220
|
4.2
|
31.6
|
1.0
|
NE2
|
A:HIS94
|
4.3
|
35.2
|
1.0
|
CB
|
A:ASP98
|
4.3
|
29.9
|
1.0
|
O
|
A:HOH531
|
4.3
|
29.4
|
1.0
|
C8
|
A:M5P401
|
4.5
|
38.9
|
1.0
|
CA
|
A:CYS178
|
4.6
|
36.9
|
1.0
|
C10
|
A:M5P401
|
4.6
|
44.6
|
1.0
|
O
|
A:HOH538
|
4.7
|
45.7
|
1.0
|
O
|
A:GLY219
|
4.9
|
34.2
|
1.0
|
NE2
|
A:HIS159
|
5.0
|
37.6
|
1.0
|
|
Zinc binding site 3 out
of 4 in 2yz3
Go back to
Zinc Binding Sites List in 2yz3
Zinc binding site 3 out
of 4 in the Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn303
b:27.2
occ:1.00
|
NE2
|
B:HIS94
|
2.1
|
25.0
|
1.0
|
ND1
|
B:HIS96
|
2.2
|
29.5
|
1.0
|
NE2
|
B:HIS159
|
2.2
|
28.5
|
1.0
|
S1
|
B:M5P402
|
2.2
|
32.7
|
1.0
|
CE1
|
B:HIS94
|
3.0
|
24.8
|
1.0
|
CD2
|
B:HIS159
|
3.0
|
29.0
|
1.0
|
CG
|
B:HIS96
|
3.1
|
27.7
|
1.0
|
CE1
|
B:HIS96
|
3.1
|
28.2
|
1.0
|
CD2
|
B:HIS94
|
3.2
|
25.9
|
1.0
|
CE1
|
B:HIS159
|
3.2
|
28.9
|
1.0
|
CB
|
B:HIS96
|
3.4
|
25.5
|
1.0
|
C11
|
B:M5P402
|
3.4
|
39.7
|
1.0
|
ZN
|
B:ZN304
|
3.7
|
19.5
|
0.8
|
OD2
|
B:ASP98
|
4.1
|
26.2
|
1.0
|
ND1
|
B:HIS94
|
4.1
|
26.1
|
1.0
|
CB
|
B:CYS178
|
4.1
|
28.2
|
1.0
|
NE2
|
B:HIS96
|
4.1
|
29.1
|
1.0
|
CD2
|
B:HIS96
|
4.2
|
26.4
|
1.0
|
CG
|
B:HIS94
|
4.2
|
26.7
|
1.0
|
CG
|
B:HIS159
|
4.2
|
30.2
|
1.0
|
C10
|
B:M5P402
|
4.2
|
43.9
|
1.0
|
ND1
|
B:HIS159
|
4.3
|
29.2
|
1.0
|
C12
|
B:M5P402
|
4.3
|
45.9
|
1.0
|
SG
|
B:CYS178
|
4.3
|
27.5
|
1.0
|
O1
|
B:M5P402
|
4.5
|
49.5
|
1.0
|
OD1
|
B:ASP98
|
4.5
|
22.4
|
1.0
|
O2
|
B:M5P402
|
4.7
|
50.8
|
1.0
|
CG
|
B:ASP98
|
4.7
|
26.3
|
1.0
|
CA
|
B:HIS96
|
4.8
|
27.5
|
1.0
|
|
Zinc binding site 4 out
of 4 in 2yz3
Go back to
Zinc Binding Sites List in 2yz3
Zinc binding site 4 out
of 4 in the Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor
 Mono view
 Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystallographic Investigation of Inhibition Mode of the Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa with Mercaptocarboxylate Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn304
b:19.5
occ:0.80
|
OD1
|
B:ASP98
|
2.0
|
22.4
|
1.0
|
NE2
|
B:HIS220
|
2.1
|
24.7
|
1.0
|
S1
|
B:M5P402
|
2.2
|
32.7
|
1.0
|
SG
|
B:CYS178
|
2.3
|
27.5
|
1.0
|
CE1
|
B:HIS220
|
3.0
|
25.5
|
1.0
|
CD2
|
B:HIS220
|
3.1
|
25.1
|
1.0
|
CG
|
B:ASP98
|
3.1
|
26.3
|
1.0
|
C11
|
B:M5P402
|
3.3
|
39.7
|
1.0
|
CB
|
B:CYS178
|
3.4
|
28.2
|
1.0
|
NH2
|
B:ARG99
|
3.5
|
26.6
|
1.0
|
OD2
|
B:ASP98
|
3.6
|
26.2
|
1.0
|
ZN
|
B:ZN303
|
3.7
|
27.2
|
1.0
|
NE
|
B:ARG99
|
3.9
|
26.4
|
1.0
|
CZ
|
B:ARG99
|
4.1
|
29.3
|
1.0
|
ND1
|
B:HIS220
|
4.1
|
25.0
|
1.0
|
CG
|
B:HIS220
|
4.2
|
26.4
|
1.0
|
CE1
|
B:HIS94
|
4.2
|
24.8
|
1.0
|
CB
|
B:ASP98
|
4.3
|
23.9
|
1.0
|
C10
|
B:M5P402
|
4.4
|
43.9
|
1.0
|
NE2
|
B:HIS94
|
4.5
|
25.0
|
1.0
|
O
|
B:HOH612
|
4.5
|
56.9
|
1.0
|
CA
|
B:CYS178
|
4.6
|
29.3
|
1.0
|
C8
|
B:M5P402
|
4.6
|
39.8
|
1.0
|
O
|
B:HOH523
|
4.6
|
29.0
|
1.0
|
NE2
|
B:HIS159
|
4.7
|
28.5
|
1.0
|
OG
|
B:SER49
|
4.8
|
24.1
|
1.0
|
O
|
B:GLY219
|
5.0
|
26.6
|
1.0
|
|
Reference:
Y.Yamaguchi,
W.Jin,
K.Matsunaga,
S.Ikemizu,
Y.Yamagata,
J.Wachino,
N.Shibata,
Y.Arakawa,
H.Kurosaki.
Crystallographic Investigation of the Inhibition Mode of A Vim-2 Metallo-Beta-Lactamase From Pseudomonas Aeruginosa By A Mercaptocarboxylate Inhibitor. J.Med.Chem. V. 50 6647 2007.
ISSN: ISSN 0022-2623
PubMed: 18052313
DOI: 10.1021/JM701031N
Page generated: Thu Oct 24 10:30:55 2024
|