Zinc in PDB 7yhc: Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
Protein crystallography data
The structure of Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid, PDB code: 7yhc
was solved by
G.-B.Li,
Y.-H.Yan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.83 /
2.15
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.24,
246.239,
88.285,
90,
93.95,
90
|
R / Rfree (%)
|
17.3 /
21.7
|
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
16;
Binding sites:
The binding sites of Zinc atom in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
(pdb code 7yhc). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the
Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid, PDB code: 7yhc:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 16 in 7yhc
Go back to
Zinc Binding Sites List in 7yhc
Zinc binding site 1 out
of 16 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
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 Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn301
b:32.6
occ:1.00
|
OD2
|
A:ASP118
|
2.0
|
30.8
|
1.0
|
NE2
|
A:HIS240
|
2.1
|
31.5
|
1.0
|
SG
|
A:CYS198
|
2.2
|
26.4
|
1.0
|
O22
|
A:IU3303
|
2.2
|
29.6
|
1.0
|
O19
|
A:IU3303
|
2.5
|
34.1
|
1.0
|
C21
|
A:IU3303
|
3.0
|
32.1
|
1.0
|
CD2
|
A:HIS240
|
3.0
|
27.9
|
1.0
|
CE1
|
A:HIS240
|
3.1
|
30.0
|
1.0
|
CG
|
A:ASP118
|
3.2
|
26.0
|
1.0
|
C20
|
A:IU3303
|
3.3
|
32.7
|
1.0
|
C17
|
A:IU3303
|
3.3
|
33.9
|
1.0
|
CB
|
A:CYS198
|
3.4
|
23.7
|
1.0
|
C16
|
A:IU3303
|
3.5
|
32.5
|
1.0
|
OD1
|
A:ASP118
|
3.6
|
27.4
|
1.0
|
NH2
|
A:ARG119
|
3.6
|
24.6
|
1.0
|
ZN
|
A:ZN302
|
3.7
|
26.9
|
1.0
|
O23
|
A:IU3303
|
4.1
|
34.6
|
1.0
|
NE
|
A:ARG119
|
4.2
|
25.4
|
1.0
|
ND1
|
A:HIS240
|
4.2
|
25.8
|
1.0
|
CG
|
A:HIS240
|
4.2
|
28.5
|
1.0
|
C12
|
A:IU3303
|
4.2
|
32.5
|
1.0
|
CE1
|
A:HIS114
|
4.3
|
25.1
|
1.0
|
CZ
|
A:ARG119
|
4.3
|
30.1
|
1.0
|
NE2
|
A:HIS179
|
4.4
|
25.2
|
1.0
|
CB
|
A:ASP118
|
4.4
|
25.2
|
1.0
|
C15
|
A:IU3303
|
4.5
|
34.8
|
1.0
|
O18
|
A:IU3303
|
4.5
|
36.2
|
1.0
|
O
|
A:HOH439
|
4.6
|
28.9
|
1.0
|
CA
|
A:CYS198
|
4.6
|
27.7
|
1.0
|
NE2
|
A:HIS114
|
4.6
|
29.6
|
1.0
|
CE1
|
A:HIS179
|
4.6
|
29.3
|
1.0
|
N11
|
A:IU3303
|
4.8
|
32.0
|
1.0
|
N09
|
A:IU3303
|
4.8
|
30.2
|
1.0
|
|
Zinc binding site 2 out
of 16 in 7yhc
Go back to
Zinc Binding Sites List in 7yhc
Zinc binding site 2 out
of 16 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
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 Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn302
b:26.9
occ:1.00
|
O22
|
A:IU3303
|
2.0
|
29.6
|
1.0
|
NE2
|
A:HIS179
|
2.0
|
25.2
|
1.0
|
ND1
|
A:HIS116
|
2.0
|
30.6
|
1.0
|
NE2
|
A:HIS114
|
2.1
|
29.6
|
1.0
|
O23
|
A:IU3303
|
2.6
|
34.6
|
1.0
|
C21
|
A:IU3303
|
2.6
|
32.1
|
1.0
|
CE1
|
A:HIS114
|
2.9
|
25.1
|
1.0
|
CE1
|
A:HIS116
|
2.9
|
33.4
|
1.0
|
CD2
|
A:HIS179
|
3.0
|
25.0
|
1.0
|
CG
|
A:HIS116
|
3.1
|
31.4
|
1.0
|
CE1
|
A:HIS179
|
3.1
|
29.3
|
1.0
|
CD2
|
A:HIS114
|
3.1
|
29.6
|
1.0
|
CB
|
A:HIS116
|
3.5
|
28.9
|
1.0
|
ZN
|
A:ZN301
|
3.7
|
32.6
|
1.0
|
OD1
|
A:ASP118
|
3.9
|
27.4
|
1.0
|
ND1
|
A:HIS114
|
4.0
|
24.4
|
1.0
|
NE2
|
A:HIS116
|
4.0
|
32.9
|
1.0
|
CG
|
A:HIS179
|
4.1
|
25.8
|
1.0
|
C20
|
A:IU3303
|
4.1
|
32.7
|
1.0
|
CD2
|
A:HIS116
|
4.1
|
32.0
|
1.0
|
ND1
|
A:HIS179
|
4.1
|
25.3
|
1.0
|
CG
|
A:HIS114
|
4.2
|
23.7
|
1.0
|
CB
|
A:CYS198
|
4.2
|
23.7
|
1.0
|
O19
|
A:IU3303
|
4.2
|
34.1
|
1.0
|
SG
|
A:CYS198
|
4.3
|
26.4
|
1.0
|
OD2
|
A:ASP118
|
4.4
|
30.8
|
1.0
|
CG
|
A:ASP118
|
4.6
|
26.0
|
1.0
|
N11
|
A:IU3303
|
4.7
|
32.0
|
1.0
|
N09
|
A:IU3303
|
4.8
|
30.2
|
1.0
|
C10
|
A:IU3303
|
4.9
|
38.0
|
1.0
|
CA
|
A:HIS116
|
4.9
|
27.3
|
1.0
|
O
|
A:HOH472
|
4.9
|
33.1
|
1.0
|
C17
|
A:IU3303
|
4.9
|
33.9
|
1.0
|
C12
|
A:IU3303
|
4.9
|
32.5
|
1.0
|
C16
|
A:IU3303
|
5.0
|
32.5
|
1.0
|
|
Zinc binding site 3 out
of 16 in 7yhc
Go back to
Zinc Binding Sites List in 7yhc
Zinc binding site 3 out
of 16 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
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 Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn301
b:40.7
occ:1.00
|
OD2
|
B:ASP118
|
2.0
|
36.2
|
1.0
|
NE2
|
B:HIS240
|
2.1
|
35.3
|
1.0
|
SG
|
B:CYS198
|
2.2
|
33.4
|
1.0
|
O19
|
B:IU3303
|
2.4
|
41.8
|
1.0
|
O22
|
B:IU3303
|
2.4
|
41.9
|
1.0
|
C21
|
B:IU3303
|
3.0
|
40.6
|
1.0
|
CE1
|
B:HIS240
|
3.1
|
31.7
|
1.0
|
CD2
|
B:HIS240
|
3.1
|
35.4
|
1.0
|
CG
|
B:ASP118
|
3.2
|
35.1
|
1.0
|
C17
|
B:IU3303
|
3.3
|
40.9
|
1.0
|
C20
|
B:IU3303
|
3.3
|
39.9
|
1.0
|
CB
|
B:CYS198
|
3.3
|
34.6
|
1.0
|
C16
|
B:IU3303
|
3.4
|
42.8
|
1.0
|
NH2
|
B:ARG119
|
3.7
|
32.5
|
1.0
|
ZN
|
B:ZN302
|
3.7
|
35.8
|
1.0
|
OD1
|
B:ASP118
|
3.8
|
38.1
|
1.0
|
O23
|
B:IU3303
|
4.0
|
40.6
|
1.0
|
NE
|
B:ARG119
|
4.2
|
31.7
|
1.0
|
ND1
|
B:HIS240
|
4.2
|
35.0
|
1.0
|
C12
|
B:IU3303
|
4.2
|
42.1
|
1.0
|
CG
|
B:HIS240
|
4.3
|
31.3
|
1.0
|
CE1
|
B:HIS114
|
4.3
|
36.8
|
1.0
|
CB
|
B:ASP118
|
4.4
|
32.6
|
1.0
|
NE2
|
B:HIS179
|
4.4
|
35.8
|
1.0
|
O
|
B:HOH431
|
4.4
|
35.1
|
1.0
|
CZ
|
B:ARG119
|
4.4
|
31.7
|
1.0
|
C15
|
B:IU3303
|
4.4
|
42.7
|
1.0
|
O18
|
B:IU3303
|
4.4
|
45.3
|
1.0
|
CE1
|
B:HIS179
|
4.5
|
37.7
|
1.0
|
NE2
|
B:HIS114
|
4.5
|
33.7
|
1.0
|
CA
|
B:CYS198
|
4.5
|
30.7
|
1.0
|
N09
|
B:IU3303
|
4.8
|
40.2
|
1.0
|
N11
|
B:IU3303
|
4.8
|
42.9
|
1.0
|
|
Zinc binding site 4 out
of 16 in 7yhc
Go back to
Zinc Binding Sites List in 7yhc
Zinc binding site 4 out
of 16 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
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 Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn302
b:35.8
occ:1.00
|
ND1
|
B:HIS116
|
2.0
|
35.7
|
1.0
|
NE2
|
B:HIS179
|
2.0
|
35.8
|
1.0
|
O22
|
B:IU3303
|
2.0
|
41.9
|
1.0
|
NE2
|
B:HIS114
|
2.1
|
33.7
|
1.0
|
O23
|
B:IU3303
|
2.6
|
40.6
|
1.0
|
C21
|
B:IU3303
|
2.6
|
40.6
|
1.0
|
CE1
|
B:HIS116
|
2.9
|
39.9
|
1.0
|
CE1
|
B:HIS179
|
2.9
|
37.7
|
1.0
|
CG
|
B:HIS116
|
3.0
|
35.8
|
1.0
|
CD2
|
B:HIS179
|
3.0
|
36.5
|
1.0
|
CE1
|
B:HIS114
|
3.0
|
36.8
|
1.0
|
CD2
|
B:HIS114
|
3.1
|
36.0
|
1.0
|
CB
|
B:HIS116
|
3.4
|
37.7
|
1.0
|
ZN
|
B:ZN301
|
3.7
|
40.7
|
1.0
|
OD1
|
B:ASP118
|
4.0
|
38.1
|
1.0
|
NE2
|
B:HIS116
|
4.0
|
38.5
|
1.0
|
ND1
|
B:HIS179
|
4.1
|
34.5
|
1.0
|
CD2
|
B:HIS116
|
4.1
|
38.4
|
1.0
|
ND1
|
B:HIS114
|
4.1
|
34.8
|
1.0
|
CG
|
B:HIS179
|
4.1
|
33.8
|
1.0
|
C20
|
B:IU3303
|
4.1
|
39.9
|
1.0
|
CG
|
B:HIS114
|
4.2
|
34.0
|
1.0
|
OD2
|
B:ASP118
|
4.2
|
36.2
|
1.0
|
SG
|
B:CYS198
|
4.3
|
33.4
|
1.0
|
CB
|
B:CYS198
|
4.3
|
34.6
|
1.0
|
O19
|
B:IU3303
|
4.4
|
41.8
|
1.0
|
CG
|
B:ASP118
|
4.5
|
35.1
|
1.0
|
N11
|
B:IU3303
|
4.7
|
42.9
|
1.0
|
C10
|
B:IU3303
|
4.8
|
45.1
|
1.0
|
CA
|
B:HIS116
|
4.8
|
39.0
|
1.0
|
N09
|
B:IU3303
|
4.8
|
40.2
|
1.0
|
C17
|
B:IU3303
|
4.9
|
40.9
|
1.0
|
C12
|
B:IU3303
|
4.9
|
42.1
|
1.0
|
|
Zinc binding site 5 out
of 16 in 7yhc
Go back to
Zinc Binding Sites List in 7yhc
Zinc binding site 5 out
of 16 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn301
b:30.6
occ:1.00
|
OD2
|
C:ASP118
|
2.0
|
27.0
|
1.0
|
NE2
|
C:HIS240
|
2.1
|
26.3
|
1.0
|
SG
|
C:CYS198
|
2.2
|
23.0
|
1.0
|
O22
|
C:IU3303
|
2.2
|
31.1
|
1.0
|
O18
|
C:IU3303
|
2.5
|
31.7
|
1.0
|
CD2
|
C:HIS240
|
3.0
|
29.0
|
1.0
|
C21
|
C:IU3303
|
3.0
|
26.6
|
1.0
|
CE1
|
C:HIS240
|
3.1
|
23.9
|
1.0
|
CG
|
C:ASP118
|
3.1
|
28.4
|
1.0
|
C17
|
C:IU3303
|
3.3
|
30.9
|
1.0
|
CB
|
C:CYS198
|
3.3
|
22.3
|
1.0
|
C20
|
C:IU3303
|
3.3
|
30.7
|
1.0
|
C16
|
C:IU3303
|
3.5
|
27.9
|
1.0
|
OD1
|
C:ASP118
|
3.6
|
26.1
|
1.0
|
NH2
|
C:ARG119
|
3.8
|
28.4
|
1.0
|
ZN
|
C:ZN302
|
3.8
|
26.1
|
1.0
|
O23
|
C:IU3303
|
4.1
|
27.5
|
1.0
|
CG
|
C:HIS240
|
4.1
|
25.9
|
1.0
|
ND1
|
C:HIS240
|
4.2
|
23.1
|
1.0
|
NE
|
C:ARG119
|
4.2
|
25.1
|
1.0
|
C12
|
C:IU3303
|
4.3
|
29.9
|
1.0
|
CE1
|
C:HIS114
|
4.3
|
21.5
|
1.0
|
CB
|
C:ASP118
|
4.4
|
25.1
|
1.0
|
CZ
|
C:ARG119
|
4.5
|
26.4
|
1.0
|
C15
|
C:IU3303
|
4.5
|
32.2
|
1.0
|
NE2
|
C:HIS179
|
4.5
|
23.5
|
1.0
|
O19
|
C:IU3303
|
4.5
|
32.2
|
1.0
|
O
|
C:HOH448
|
4.5
|
27.0
|
1.0
|
CE1
|
C:HIS179
|
4.5
|
20.7
|
1.0
|
CA
|
C:CYS198
|
4.5
|
23.0
|
1.0
|
NE2
|
C:HIS114
|
4.6
|
24.9
|
1.0
|
N09
|
C:IU3303
|
4.7
|
27.4
|
1.0
|
N11
|
C:IU3303
|
4.8
|
28.4
|
1.0
|
|
Zinc binding site 6 out
of 16 in 7yhc
Go back to
Zinc Binding Sites List in 7yhc
Zinc binding site 6 out
of 16 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn302
b:26.1
occ:1.00
|
ND1
|
C:HIS116
|
2.0
|
24.9
|
1.0
|
NE2
|
C:HIS179
|
2.1
|
23.5
|
1.0
|
O22
|
C:IU3303
|
2.1
|
31.1
|
1.0
|
NE2
|
C:HIS114
|
2.1
|
24.9
|
1.0
|
O23
|
C:IU3303
|
2.5
|
27.5
|
1.0
|
C21
|
C:IU3303
|
2.7
|
26.6
|
1.0
|
CE1
|
C:HIS116
|
3.0
|
26.1
|
1.0
|
CE1
|
C:HIS114
|
3.0
|
21.5
|
1.0
|
CE1
|
C:HIS179
|
3.0
|
20.7
|
1.0
|
CG
|
C:HIS116
|
3.0
|
22.4
|
1.0
|
CD2
|
C:HIS179
|
3.1
|
21.4
|
1.0
|
CD2
|
C:HIS114
|
3.1
|
24.1
|
1.0
|
CB
|
C:HIS116
|
3.4
|
21.7
|
1.0
|
OD1
|
C:ASP118
|
3.8
|
26.1
|
1.0
|
ZN
|
C:ZN301
|
3.8
|
30.6
|
1.0
|
NE2
|
C:HIS116
|
4.1
|
28.2
|
1.0
|
ND1
|
C:HIS114
|
4.1
|
24.8
|
1.0
|
ND1
|
C:HIS179
|
4.1
|
21.9
|
1.0
|
CD2
|
C:HIS116
|
4.1
|
26.7
|
1.0
|
O18
|
C:IU3303
|
4.2
|
31.7
|
1.0
|
C20
|
C:IU3303
|
4.2
|
30.7
|
1.0
|
CG
|
C:HIS179
|
4.2
|
20.0
|
1.0
|
CG
|
C:HIS114
|
4.2
|
20.0
|
1.0
|
CB
|
C:CYS198
|
4.3
|
22.3
|
1.0
|
SG
|
C:CYS198
|
4.3
|
23.0
|
1.0
|
OD2
|
C:ASP118
|
4.4
|
27.0
|
1.0
|
CG
|
C:ASP118
|
4.5
|
28.4
|
1.0
|
N09
|
C:IU3303
|
4.7
|
27.4
|
1.0
|
N11
|
C:IU3303
|
4.7
|
28.4
|
1.0
|
CA
|
C:HIS116
|
4.8
|
25.0
|
1.0
|
C17
|
C:IU3303
|
4.9
|
30.9
|
1.0
|
N08
|
C:IU3303
|
4.9
|
30.0
|
1.0
|
O
|
C:HOH454
|
5.0
|
21.5
|
1.0
|
ND2
|
C:ASN210
|
5.0
|
32.2
|
1.0
|
C10
|
C:IU3303
|
5.0
|
30.7
|
1.0
|
C12
|
C:IU3303
|
5.0
|
29.9
|
1.0
|
|
Zinc binding site 7 out
of 16 in 7yhc
Go back to
Zinc Binding Sites List in 7yhc
Zinc binding site 7 out
of 16 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn301
b:30.8
occ:1.00
|
O22
|
D:IU3303
|
2.0
|
33.1
|
1.0
|
ND1
|
D:HIS116
|
2.0
|
31.6
|
1.0
|
NE2
|
D:HIS179
|
2.1
|
26.5
|
1.0
|
NE2
|
D:HIS114
|
2.1
|
25.9
|
1.0
|
O23
|
D:IU3303
|
2.6
|
35.1
|
1.0
|
C21
|
D:IU3303
|
2.6
|
33.2
|
1.0
|
CE1
|
D:HIS116
|
2.9
|
31.5
|
1.0
|
CE1
|
D:HIS179
|
3.0
|
25.8
|
1.0
|
CE1
|
D:HIS114
|
3.0
|
24.8
|
1.0
|
CG
|
D:HIS116
|
3.0
|
35.9
|
1.0
|
CD2
|
D:HIS114
|
3.1
|
29.1
|
1.0
|
CD2
|
D:HIS179
|
3.2
|
26.1
|
1.0
|
CB
|
D:HIS116
|
3.4
|
31.6
|
1.0
|
ZN
|
D:ZN302
|
3.7
|
34.1
|
1.0
|
OD1
|
D:ASP118
|
3.9
|
29.9
|
1.0
|
NE2
|
D:HIS116
|
4.1
|
31.7
|
1.0
|
C20
|
D:IU3303
|
4.1
|
33.2
|
1.0
|
O18
|
D:IU3303
|
4.1
|
33.7
|
1.0
|
CD2
|
D:HIS116
|
4.1
|
38.6
|
1.0
|
ND1
|
D:HIS179
|
4.1
|
22.0
|
1.0
|
ND1
|
D:HIS114
|
4.1
|
27.7
|
1.0
|
CG
|
D:HIS114
|
4.2
|
24.8
|
1.0
|
CG
|
D:HIS179
|
4.3
|
24.4
|
1.0
|
CB
|
D:CYS198
|
4.3
|
26.8
|
1.0
|
SG
|
D:CYS198
|
4.3
|
29.2
|
1.0
|
OD2
|
D:ASP118
|
4.4
|
30.9
|
1.0
|
CG
|
D:ASP118
|
4.6
|
27.7
|
1.0
|
N11
|
D:IU3303
|
4.7
|
40.2
|
1.0
|
C10
|
D:IU3303
|
4.7
|
39.5
|
1.0
|
CA
|
D:HIS116
|
4.8
|
29.4
|
1.0
|
C17
|
D:IU3303
|
4.8
|
33.1
|
1.0
|
C12
|
D:IU3303
|
4.9
|
33.6
|
1.0
|
N09
|
D:IU3303
|
4.9
|
36.5
|
1.0
|
C16
|
D:IU3303
|
5.0
|
36.4
|
1.0
|
|
Zinc binding site 8 out
of 16 in 7yhc
Go back to
Zinc Binding Sites List in 7yhc
Zinc binding site 8 out
of 16 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn302
b:34.1
occ:1.00
|
OD2
|
D:ASP118
|
2.1
|
30.9
|
1.0
|
NE2
|
D:HIS240
|
2.1
|
28.0
|
1.0
|
SG
|
D:CYS198
|
2.2
|
29.2
|
1.0
|
O22
|
D:IU3303
|
2.2
|
33.1
|
1.0
|
O18
|
D:IU3303
|
2.5
|
33.7
|
1.0
|
CD2
|
D:HIS240
|
3.0
|
30.1
|
1.0
|
C21
|
D:IU3303
|
3.0
|
33.2
|
1.0
|
CG
|
D:ASP118
|
3.2
|
27.7
|
1.0
|
CE1
|
D:HIS240
|
3.2
|
28.9
|
1.0
|
C17
|
D:IU3303
|
3.3
|
33.1
|
1.0
|
C20
|
D:IU3303
|
3.3
|
33.2
|
1.0
|
CB
|
D:CYS198
|
3.4
|
26.8
|
1.0
|
C16
|
D:IU3303
|
3.4
|
36.4
|
1.0
|
OD1
|
D:ASP118
|
3.6
|
29.9
|
1.0
|
ZN
|
D:ZN301
|
3.7
|
30.8
|
1.0
|
NH2
|
D:ARG119
|
3.8
|
28.8
|
1.0
|
O23
|
D:IU3303
|
4.2
|
35.1
|
1.0
|
CG
|
D:HIS240
|
4.2
|
25.9
|
1.0
|
NE
|
D:ARG119
|
4.2
|
29.2
|
1.0
|
O
|
D:HOH426
|
4.2
|
32.7
|
1.0
|
ND1
|
D:HIS240
|
4.3
|
26.3
|
1.0
|
C12
|
D:IU3303
|
4.3
|
33.6
|
1.0
|
CE1
|
D:HIS114
|
4.4
|
24.8
|
1.0
|
C15
|
D:IU3303
|
4.4
|
34.2
|
1.0
|
O19
|
D:IU3303
|
4.4
|
39.3
|
1.0
|
CB
|
D:ASP118
|
4.5
|
28.8
|
1.0
|
NE2
|
D:HIS179
|
4.5
|
26.5
|
1.0
|
CZ
|
D:ARG119
|
4.5
|
31.3
|
1.0
|
CE1
|
D:HIS179
|
4.5
|
25.8
|
1.0
|
NE2
|
D:HIS114
|
4.6
|
25.9
|
1.0
|
CA
|
D:CYS198
|
4.6
|
29.3
|
1.0
|
N11
|
D:IU3303
|
4.8
|
40.2
|
1.0
|
N09
|
D:IU3303
|
5.0
|
36.5
|
1.0
|
|
Zinc binding site 9 out
of 16 in 7yhc
Go back to
Zinc Binding Sites List in 7yhc
Zinc binding site 9 out
of 16 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn301
b:35.9
occ:1.00
|
OD2
|
E:ASP118
|
2.0
|
29.5
|
1.0
|
NE2
|
E:HIS240
|
2.1
|
29.4
|
1.0
|
O18
|
E:IU3303
|
2.3
|
35.5
|
1.0
|
O22
|
E:IU3303
|
2.3
|
32.1
|
1.0
|
SG
|
E:CYS198
|
2.3
|
27.0
|
1.0
|
C21
|
E:IU3303
|
3.0
|
33.6
|
1.0
|
CE1
|
E:HIS240
|
3.1
|
26.8
|
1.0
|
CD2
|
E:HIS240
|
3.1
|
27.6
|
1.0
|
C17
|
E:IU3303
|
3.1
|
34.3
|
1.0
|
CG
|
E:ASP118
|
3.2
|
28.1
|
1.0
|
CB
|
E:CYS198
|
3.3
|
27.0
|
1.0
|
C20
|
E:IU3303
|
3.3
|
34.4
|
1.0
|
C16
|
E:IU3303
|
3.4
|
34.5
|
1.0
|
OD1
|
E:ASP118
|
3.6
|
29.1
|
1.0
|
NH2
|
E:ARG119
|
3.7
|
30.8
|
1.0
|
ZN
|
E:ZN302
|
3.7
|
30.4
|
1.0
|
O23
|
E:IU3303
|
4.0
|
34.1
|
1.0
|
ND1
|
E:HIS240
|
4.2
|
28.6
|
1.0
|
NE
|
E:ARG119
|
4.2
|
28.3
|
1.0
|
CG
|
E:HIS240
|
4.3
|
29.0
|
1.0
|
CE1
|
E:HIS114
|
4.3
|
27.9
|
1.0
|
NE2
|
E:HIS179
|
4.3
|
26.1
|
1.0
|
O19
|
E:IU3303
|
4.3
|
36.4
|
1.0
|
O
|
E:HOH447
|
4.3
|
29.5
|
1.0
|
C12
|
E:IU3303
|
4.3
|
33.8
|
1.0
|
CB
|
E:ASP118
|
4.4
|
28.0
|
1.0
|
C15
|
E:IU3303
|
4.4
|
34.3
|
1.0
|
CZ
|
E:ARG119
|
4.4
|
28.9
|
1.0
|
NE2
|
E:HIS114
|
4.5
|
31.3
|
1.0
|
CE1
|
E:HIS179
|
4.5
|
29.2
|
1.0
|
CA
|
E:CYS198
|
4.6
|
28.2
|
1.0
|
N09
|
E:IU3303
|
4.8
|
34.4
|
1.0
|
N11
|
E:IU3303
|
4.9
|
37.4
|
1.0
|
|
Zinc binding site 10 out
of 16 in 7yhc
Go back to
Zinc Binding Sites List in 7yhc
Zinc binding site 10 out
of 16 in the Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 10 of Crystal Structure of Vim-2 Mbl in Complex with 3-(4-(3-Aminophenyl)- 1H-1,2,3-Triazol-1-Yl)Phthalic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn302
b:30.4
occ:1.00
|
ND1
|
E:HIS116
|
2.0
|
31.5
|
1.0
|
NE2
|
E:HIS179
|
2.0
|
26.1
|
1.0
|
O22
|
E:IU3303
|
2.1
|
32.1
|
1.0
|
NE2
|
E:HIS114
|
2.1
|
31.3
|
1.0
|
O23
|
E:IU3303
|
2.7
|
34.1
|
1.0
|
C21
|
E:IU3303
|
2.7
|
33.6
|
1.0
|
CE1
|
E:HIS116
|
3.0
|
29.9
|
1.0
|
CE1
|
E:HIS114
|
3.0
|
27.9
|
1.0
|
CD2
|
E:HIS179
|
3.0
|
28.2
|
1.0
|
CG
|
E:HIS116
|
3.1
|
31.9
|
1.0
|
CE1
|
E:HIS179
|
3.1
|
29.2
|
1.0
|
CD2
|
E:HIS114
|
3.1
|
28.8
|
1.0
|
CB
|
E:HIS116
|
3.4
|
31.8
|
1.0
|
ZN
|
E:ZN301
|
3.7
|
35.9
|
1.0
|
OD1
|
E:ASP118
|
3.9
|
29.1
|
1.0
|
ND1
|
E:HIS114
|
4.0
|
31.7
|
1.0
|
NE2
|
E:HIS116
|
4.1
|
30.6
|
1.0
|
O18
|
E:IU3303
|
4.1
|
35.5
|
1.0
|
CG
|
E:HIS179
|
4.1
|
27.9
|
1.0
|
ND1
|
E:HIS179
|
4.1
|
27.6
|
1.0
|
CG
|
E:HIS114
|
4.1
|
31.6
|
1.0
|
CD2
|
E:HIS116
|
4.2
|
30.1
|
1.0
|
C20
|
E:IU3303
|
4.2
|
34.4
|
1.0
|
CB
|
E:CYS198
|
4.4
|
27.0
|
1.0
|
SG
|
E:CYS198
|
4.4
|
27.0
|
1.0
|
OD2
|
E:ASP118
|
4.4
|
29.5
|
1.0
|
CG
|
E:ASP118
|
4.5
|
28.1
|
1.0
|
N09
|
E:IU3303
|
4.7
|
34.4
|
1.0
|
N11
|
E:IU3303
|
4.8
|
37.4
|
1.0
|
CA
|
E:HIS116
|
4.8
|
29.9
|
1.0
|
C17
|
E:IU3303
|
4.9
|
34.3
|
1.0
|
|
Reference:
Y.H.Yan,
H.S.Ding,
K.R.Zhu,
B.S.Mu,
Y.Zheng,
M.Y.Huang,
C.Zhou,
W.F.Li,
Z.Wang,
Y.Wu,
G.B.Li.
Metal Binding Pharmacophore Click-Derived Discovery of New Broad-Spectrum Metallo-Beta-Lactamase Inhibitors. Eur.J.Med.Chem. V. 257 15473 2023.
ISSN: ISSN 0223-5234
PubMed: 37209449
DOI: 10.1016/J.EJMECH.2023.115473
Page generated: Wed Oct 30 15:50:42 2024
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