Zinc in PDB 5ni0: Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding
Protein crystallography data
The structure of Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding, PDB code: 5ni0
was solved by
S.Skagseth,
S.Akhter,
M.H.Paulsen,
O.Samuelsen,
Z.Muhammad,
H.-K.S.Leiros,
A.Bayer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
24.77 /
1.67
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.716,
91.070,
122.912,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.8 /
21.4
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding
(pdb code 5ni0). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding, PDB code: 5ni0:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 5ni0
Go back to
Zinc Binding Sites List in 5ni0
Zinc binding site 1 out
of 4 in the Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:22.4
occ:1.00
|
O
|
A:HOH527
|
1.8
|
30.1
|
1.0
|
|
ND1
|
A:HIS118
|
2.0
|
19.2
|
1.0
|
|
NE2
|
A:HIS196
|
2.1
|
21.5
|
1.0
|
|
NE2
|
A:HIS116
|
2.1
|
17.0
|
1.0
|
|
HB2
|
A:HIS118
|
2.8
|
22.8
|
1.0
|
|
HAE
|
A:8XW403
|
2.9
|
65.2
|
1.0
|
|
CE1
|
A:HIS118
|
3.0
|
19.8
|
1.0
|
|
CG
|
A:HIS118
|
3.0
|
19.8
|
1.0
|
|
CD2
|
A:HIS196
|
3.0
|
18.5
|
1.0
|
|
CE1
|
A:HIS116
|
3.0
|
20.0
|
1.0
|
|
CD2
|
A:HIS116
|
3.1
|
20.3
|
1.0
|
|
CE1
|
A:HIS196
|
3.1
|
25.3
|
1.0
|
|
HD2
|
A:HIS196
|
3.2
|
22.2
|
1.0
|
|
HE1
|
A:HIS118
|
3.2
|
23.7
|
1.0
|
|
HE1
|
A:HIS116
|
3.2
|
24.0
|
1.0
|
|
SAD
|
A:8XW403
|
3.3
|
52.0
|
1.0
|
|
HAA
|
A:8XW403
|
3.3
|
55.9
|
1.0
|
|
HD2
|
A:HIS116
|
3.3
|
24.4
|
1.0
|
|
HE1
|
A:HIS196
|
3.3
|
30.4
|
1.0
|
|
CB
|
A:HIS118
|
3.3
|
19.0
|
1.0
|
|
CAE
|
A:8XW403
|
3.5
|
54.4
|
1.0
|
|
HB3
|
A:HIS118
|
3.6
|
22.8
|
1.0
|
|
O
|
A:HOH513
|
3.9
|
45.3
|
1.0
|
|
HAF
|
A:8XW403
|
3.9
|
65.2
|
1.0
|
|
NE2
|
A:HIS118
|
4.1
|
25.9
|
1.0
|
|
CD2
|
A:HIS118
|
4.1
|
26.9
|
1.0
|
|
OD1
|
A:ASP120
|
4.1
|
22.6
|
1.0
|
|
ND1
|
A:HIS116
|
4.1
|
16.6
|
1.0
|
|
ND1
|
A:HIS196
|
4.2
|
20.8
|
1.0
|
|
CG
|
A:HIS196
|
4.2
|
18.3
|
1.0
|
|
CG
|
A:HIS116
|
4.2
|
18.0
|
1.0
|
|
CAA
|
A:8XW403
|
4.2
|
46.6
|
1.0
|
|
HB2
|
A:CYS221
|
4.2
|
27.1
|
1.0
|
|
CAB
|
A:8XW403
|
4.2
|
53.5
|
0.8
|
|
HB3
|
A:CYS221
|
4.4
|
27.1
|
1.0
|
|
H
|
A:HIS118
|
4.4
|
21.6
|
1.0
|
|
ZN
|
A:ZN402
|
4.6
|
29.9
|
0.7
|
|
HB3
|
A:SER197
|
4.6
|
18.9
|
1.0
|
|
CB
|
A:CYS221
|
4.6
|
22.6
|
1.0
|
|
SG
|
A:CYS221
|
4.6
|
23.6
|
1.0
|
|
CA
|
A:HIS118
|
4.7
|
21.7
|
1.0
|
|
HD22
|
A:ASN233
|
4.7
|
63.4
|
1.0
|
|
OAT
|
A:8XW403
|
4.8
|
76.6
|
1.0
|
|
HAB
|
A:8XW403
|
4.8
|
55.9
|
1.0
|
|
CAF
|
A:8XW403
|
4.8
|
68.2
|
0.9
|
|
O
|
A:HOH541
|
4.9
|
27.6
|
1.0
|
|
OD2
|
A:ASP120
|
4.9
|
25.6
|
1.0
|
|
HAC
|
A:8XW403
|
4.9
|
55.9
|
1.0
|
|
CG
|
A:ASP120
|
4.9
|
30.6
|
1.0
|
|
HD2
|
A:HIS118
|
5.0
|
32.2
|
1.0
|
|
HAG
|
A:8XW403
|
5.0
|
81.8
|
0.9
|
|
N
|
A:HIS118
|
5.0
|
18.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 5ni0
Go back to
Zinc Binding Sites List in 5ni0
Zinc binding site 2 out
of 4 in the Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:29.9
occ:0.66
|
HAA
|
A:8XW403
|
1.6
|
55.9
|
1.0
|
|
HAC
|
A:8XW403
|
1.7
|
55.9
|
1.0
|
|
CAA
|
A:8XW403
|
1.9
|
46.6
|
1.0
|
|
OD2
|
A:ASP120
|
2.1
|
25.6
|
1.0
|
|
SG
|
A:CYS221
|
2.2
|
23.6
|
1.0
|
|
NE2
|
A:HIS263
|
2.2
|
43.9
|
1.0
|
|
HAB
|
A:8XW403
|
2.2
|
55.9
|
1.0
|
|
HH21
|
A:ARG121
|
2.7
|
32.9
|
1.0
|
|
HAF
|
A:8XW403
|
2.8
|
65.2
|
1.0
|
|
O
|
A:HOH527
|
3.0
|
30.1
|
1.0
|
|
CE1
|
A:HIS263
|
3.0
|
28.6
|
1.0
|
|
HE1
|
A:HIS263
|
3.1
|
34.2
|
1.0
|
|
CG
|
A:ASP120
|
3.2
|
30.6
|
1.0
|
|
CD2
|
A:HIS263
|
3.2
|
30.9
|
1.0
|
|
CAB
|
A:8XW403
|
3.3
|
53.5
|
0.8
|
|
HE
|
A:ARG121
|
3.3
|
27.7
|
1.0
|
|
HB3
|
A:CYS221
|
3.4
|
27.1
|
1.0
|
|
HD2
|
A:HIS263
|
3.5
|
37.0
|
1.0
|
|
CB
|
A:CYS221
|
3.5
|
22.6
|
1.0
|
|
NH2
|
A:ARG121
|
3.6
|
27.4
|
1.0
|
|
HAJ
|
A:8XW403
|
3.6
|
64.7
|
1.0
|
|
HE1
|
A:HIS116
|
3.7
|
24.0
|
1.0
|
|
CAE
|
A:8XW403
|
3.7
|
54.4
|
1.0
|
|
OD1
|
A:ASP120
|
3.7
|
22.6
|
1.0
|
|
HAE
|
A:8XW403
|
4.0
|
65.2
|
1.0
|
|
SAD
|
A:8XW403
|
4.0
|
52.0
|
1.0
|
|
NE
|
A:ARG121
|
4.0
|
23.1
|
1.0
|
|
HB2
|
A:CYS221
|
4.1
|
27.1
|
1.0
|
|
HH22
|
A:ARG121
|
4.1
|
32.9
|
1.0
|
|
ND1
|
A:HIS263
|
4.2
|
20.4
|
1.0
|
|
OAC
|
A:8XW403
|
4.2
|
53.9
|
1.0
|
|
CZ
|
A:ARG121
|
4.3
|
29.6
|
1.0
|
|
HA
|
A:CYS221
|
4.3
|
16.5
|
1.0
|
|
CG
|
A:HIS263
|
4.3
|
26.0
|
1.0
|
|
O
|
A:HOH644
|
4.3
|
26.1
|
1.0
|
|
HB2
|
A:ASP120
|
4.4
|
27.4
|
1.0
|
|
CB
|
A:ASP120
|
4.4
|
22.8
|
1.0
|
|
HAI
|
A:8XW403
|
4.4
|
75.3
|
0.8
|
|
HA3
|
A:GLY262
|
4.4
|
20.8
|
1.0
|
|
CE1
|
A:HIS116
|
4.5
|
20.0
|
1.0
|
|
CA
|
A:CYS221
|
4.5
|
13.8
|
1.0
|
|
ZN
|
A:ZN401
|
4.6
|
22.4
|
1.0
|
|
HB3
|
A:ASP120
|
4.6
|
27.4
|
1.0
|
|
CAH
|
A:8XW403
|
4.6
|
54.0
|
1.0
|
|
HAM
|
A:8XW403
|
4.8
|
62.9
|
1.0
|
|
HG2
|
A:ARG121
|
4.8
|
20.1
|
1.0
|
|
CAG
|
A:8XW403
|
4.9
|
62.7
|
0.8
|
|
CAF
|
A:8XW403
|
4.9
|
68.2
|
0.9
|
|
HG
|
A:SER69
|
4.9
|
19.9
|
1.0
|
|
NE2
|
A:HIS196
|
4.9
|
21.5
|
1.0
|
|
NE2
|
A:HIS116
|
5.0
|
17.0
|
1.0
|
|
Zinc binding site 3 out
of 4 in 5ni0
Go back to
Zinc Binding Sites List in 5ni0
Zinc binding site 3 out
of 4 in the Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn401
b:25.3
occ:1.00
|
ND1
|
E:HIS118
|
2.0
|
26.2
|
1.0
|
|
NE2
|
E:HIS196
|
2.0
|
25.3
|
1.0
|
|
NE2
|
E:HIS116
|
2.1
|
20.0
|
1.0
|
|
O
|
E:HOH507
|
2.7
|
45.1
|
1.0
|
|
HB2
|
E:HIS118
|
2.9
|
23.6
|
1.0
|
|
SAD
|
E:8XW403
|
2.9
|
40.0
|
0.9
|
|
HAF
|
E:8XW403
|
2.9
|
60.4
|
1.0
|
|
CD2
|
E:HIS196
|
3.0
|
26.1
|
1.0
|
|
CE1
|
E:HIS196
|
3.0
|
30.3
|
1.0
|
|
CE1
|
E:HIS116
|
3.0
|
19.6
|
1.0
|
|
CE1
|
E:HIS118
|
3.0
|
25.8
|
1.0
|
|
CG
|
E:HIS118
|
3.0
|
25.8
|
1.0
|
|
CD2
|
E:HIS116
|
3.1
|
18.8
|
1.0
|
|
HD2
|
E:HIS196
|
3.2
|
31.3
|
1.0
|
|
HE1
|
E:HIS116
|
3.2
|
23.6
|
1.0
|
|
HE1
|
E:HIS118
|
3.2
|
30.9
|
1.0
|
|
HE1
|
E:HIS196
|
3.2
|
36.4
|
1.0
|
|
HD2
|
E:HIS116
|
3.3
|
22.6
|
1.0
|
|
CB
|
E:HIS118
|
3.3
|
19.7
|
1.0
|
|
CAE
|
E:8XW403
|
3.4
|
50.3
|
1.0
|
|
HB3
|
E:HIS118
|
3.6
|
23.6
|
1.0
|
|
HAE
|
E:8XW403
|
4.0
|
60.4
|
1.0
|
|
CAB
|
E:8XW403
|
4.1
|
49.0
|
0.7
|
|
OD1
|
E:ASP120
|
4.1
|
19.7
|
1.0
|
|
ND1
|
E:HIS196
|
4.1
|
21.2
|
1.0
|
|
ND1
|
E:HIS116
|
4.1
|
15.8
|
1.0
|
|
NE2
|
E:HIS118
|
4.1
|
27.1
|
1.0
|
|
CG
|
E:HIS196
|
4.1
|
25.8
|
1.0
|
|
CD2
|
E:HIS118
|
4.2
|
27.8
|
1.0
|
|
HB2
|
E:CYS221
|
4.2
|
31.0
|
1.0
|
|
CG
|
E:HIS116
|
4.2
|
15.8
|
1.0
|
|
HD22
|
E:ASN233
|
4.3
|
62.4
|
1.0
|
|
HAA
|
E:8XW403
|
4.3
|
53.9
|
1.0
|
|
ZN
|
E:ZN402
|
4.4
|
27.2
|
0.5
|
|
HB3
|
E:CYS221
|
4.4
|
31.0
|
1.0
|
|
H
|
E:HIS118
|
4.4
|
25.1
|
1.0
|
|
OAT
|
E:8XW403
|
4.5
|
74.8
|
1.0
|
|
OAR
|
E:8XW403
|
4.5
|
79.6
|
0.8
|
|
CB
|
E:CYS221
|
4.6
|
25.9
|
1.0
|
|
SG
|
E:CYS221
|
4.6
|
27.6
|
1.0
|
|
HB3
|
E:SER197
|
4.6
|
28.3
|
1.0
|
|
CAF
|
E:8XW403
|
4.6
|
58.2
|
0.6
|
|
OAC
|
E:8XW403
|
4.7
|
36.9
|
1.0
|
|
CA
|
E:HIS118
|
4.7
|
19.2
|
1.0
|
|
PAQ
|
E:8XW403
|
4.8
|
74.1
|
1.0
|
|
CAA
|
E:8XW403
|
4.8
|
44.9
|
1.0
|
|
OD2
|
E:ASP120
|
4.8
|
26.6
|
1.0
|
|
CG
|
E:ASP120
|
4.9
|
24.0
|
1.0
|
|
HB3
|
E:ASN233
|
4.9
|
56.5
|
1.0
|
|
HAI
|
E:8XW403
|
5.0
|
66.9
|
1.0
|
|
ND2
|
E:ASN233
|
5.0
|
52.0
|
1.0
|
|
N
|
E:HIS118
|
5.0
|
20.9
|
1.0
|
|
Zinc binding site 4 out
of 4 in 5ni0
Go back to
Zinc Binding Sites List in 5ni0
Zinc binding site 4 out
of 4 in the Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Vim-2_10C. Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn402
b:27.2
occ:0.51
|
O
|
E:HOH507
|
1.8
|
45.1
|
1.0
|
|
OD2
|
E:ASP120
|
2.1
|
26.6
|
1.0
|
|
SG
|
E:CYS221
|
2.1
|
27.6
|
1.0
|
|
NE2
|
E:HIS263
|
2.2
|
30.5
|
1.0
|
|
OAC
|
E:8XW403
|
2.2
|
36.9
|
1.0
|
|
HH21
|
E:ARG121
|
2.5
|
39.2
|
1.0
|
|
SAD
|
E:8XW403
|
2.8
|
40.0
|
0.9
|
|
CAB
|
E:8XW403
|
2.8
|
49.0
|
0.7
|
|
CE1
|
E:HIS263
|
3.0
|
25.1
|
1.0
|
|
HE1
|
E:HIS263
|
3.0
|
30.1
|
1.0
|
|
HE
|
E:ARG121
|
3.2
|
26.0
|
1.0
|
|
CG
|
E:ASP120
|
3.2
|
24.0
|
1.0
|
|
NH2
|
E:ARG121
|
3.3
|
32.7
|
1.0
|
|
CD2
|
E:HIS263
|
3.4
|
27.0
|
1.0
|
|
HB3
|
E:CYS221
|
3.5
|
31.0
|
1.0
|
|
CB
|
E:CYS221
|
3.5
|
25.9
|
1.0
|
|
HE1
|
E:HIS116
|
3.5
|
23.6
|
1.0
|
|
HD2
|
E:HIS263
|
3.6
|
32.4
|
1.0
|
|
HAK
|
E:8XW403
|
3.7
|
68.3
|
0.7
|
|
OD1
|
E:ASP120
|
3.7
|
19.7
|
1.0
|
|
HAI
|
E:8XW403
|
3.7
|
66.9
|
1.0
|
|
NE
|
E:ARG121
|
3.9
|
21.7
|
1.0
|
|
HH22
|
E:ARG121
|
3.9
|
39.2
|
1.0
|
|
HB2
|
E:CYS221
|
4.0
|
31.0
|
1.0
|
|
CZ
|
E:ARG121
|
4.1
|
26.9
|
1.0
|
|
ND1
|
E:HIS263
|
4.2
|
25.6
|
1.0
|
|
CAA
|
E:8XW403
|
4.3
|
44.9
|
1.0
|
|
ZN
|
E:ZN401
|
4.4
|
25.3
|
1.0
|
|
CE1
|
E:HIS116
|
4.4
|
19.6
|
1.0
|
|
HB2
|
E:ASP120
|
4.4
|
21.1
|
1.0
|
|
O
|
E:HOH527
|
4.4
|
30.6
|
1.0
|
|
HA
|
E:CYS221
|
4.4
|
21.4
|
1.0
|
|
CB
|
E:ASP120
|
4.4
|
17.6
|
1.0
|
|
CG
|
E:HIS263
|
4.4
|
21.6
|
1.0
|
|
CAE
|
E:8XW403
|
4.5
|
50.3
|
1.0
|
|
CAH
|
E:8XW403
|
4.5
|
56.9
|
0.7
|
|
CAG
|
E:8XW403
|
4.5
|
55.8
|
1.0
|
|
CA
|
E:CYS221
|
4.6
|
17.8
|
1.0
|
|
HA3
|
E:GLY262
|
4.6
|
26.0
|
1.0
|
|
HB3
|
E:ASP120
|
4.6
|
21.1
|
1.0
|
|
HAJ
|
E:8XW403
|
4.8
|
68.3
|
0.7
|
|
HAC
|
E:8XW403
|
4.8
|
53.9
|
1.0
|
|
NE2
|
E:HIS116
|
4.8
|
20.0
|
1.0
|
|
HAB
|
E:8XW403
|
4.8
|
53.9
|
1.0
|
|
HG2
|
E:ARG121
|
4.9
|
20.8
|
1.0
|
|
HAA
|
E:8XW403
|
4.9
|
53.9
|
1.0
|
|
HG
|
E:SER69
|
4.9
|
23.4
|
1.0
|
|
NE2
|
E:HIS196
|
5.0
|
25.3
|
1.0
|
|
HE1
|
E:HIS196
|
5.0
|
36.4
|
1.0
|
|
Reference:
S.Skagseth,
S.Akhter,
M.H.Paulsen,
Z.Muhammad,
S.Lauksund,
H.S.Leiros,
A.Bayer.
Metallo-Beta-Lactamase Inhibitors By Bioisosteric Replacement: Preparation, Activity and Binding. Eur J Med Chem V. 135 159 2017.
ISSN: ISSN 1768-3254
PubMed: 28445786
DOI: 10.1016/J.EJMECH.2017.04.035
Page generated: Sun Oct 27 22:48:41 2024
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