Zinc in PDB 5cbm: Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
Protein crystallography data
The structure of Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor, PDB code: 5cbm
was solved by
C.Ruggeri,
N.Drinkwater,
S.Mcgowan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
48.98 /
2.30
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
174.092,
177.728,
230.981,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
18.2 /
23.5
|
Zinc Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
24;
Binding sites:
The binding sites of Zinc atom in the Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
(pdb code 5cbm). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the
Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor, PDB code: 5cbm:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Zinc binding site 1 out
of 24 in 5cbm
Go back to
Zinc Binding Sites List in 5cbm
Zinc binding site 1 out
of 24 in the Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
 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 Pfa-M17 with Virtual Ligand Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn702
b:18.1
occ:1.00
|
OE2
|
A:GLU461
|
2.0
|
14.6
|
1.0
|
|
OD2
|
A:ASP399
|
2.1
|
17.6
|
1.0
|
|
N12
|
A:4ZN704
|
2.1
|
15.1
|
1.0
|
|
NZ
|
A:LYS374
|
2.1
|
16.2
|
1.0
|
|
O10
|
A:4ZN704
|
2.4
|
17.8
|
1.0
|
|
OD2
|
A:ASP379
|
2.8
|
16.9
|
1.0
|
|
C11
|
A:4ZN704
|
2.9
|
20.3
|
1.0
|
|
CG
|
A:ASP399
|
2.9
|
15.6
|
1.0
|
|
CE
|
A:LYS374
|
3.0
|
20.7
|
1.0
|
|
OD1
|
A:ASP399
|
3.1
|
16.7
|
1.0
|
|
CD
|
A:GLU461
|
3.1
|
14.6
|
1.0
|
|
P08
|
A:4ZN704
|
3.2
|
15.2
|
1.0
|
|
ZN
|
A:ZN703
|
3.4
|
14.3
|
1.0
|
|
OE1
|
A:GLU461
|
3.5
|
14.9
|
1.0
|
|
CG
|
A:ASP379
|
3.5
|
14.6
|
1.0
|
|
O09
|
A:4ZN704
|
3.9
|
17.3
|
1.0
|
|
O2
|
A:CO3701
|
3.9
|
15.4
|
1.0
|
|
CB
|
A:ASP379
|
4.1
|
12.6
|
1.0
|
|
O
|
A:THR486
|
4.2
|
16.5
|
1.0
|
|
C13
|
A:4ZN704
|
4.3
|
16.0
|
1.0
|
|
OD1
|
A:ASP379
|
4.4
|
15.6
|
1.0
|
|
CB
|
A:ASP399
|
4.4
|
16.2
|
1.0
|
|
CG
|
A:GLU461
|
4.4
|
13.9
|
1.0
|
|
CD
|
A:LYS374
|
4.4
|
17.9
|
1.0
|
|
CG1
|
A:ILE376
|
4.6
|
17.2
|
1.0
|
|
N
|
A:GLY462
|
4.7
|
16.6
|
1.0
|
|
C07
|
A:4ZN704
|
4.7
|
17.3
|
1.0
|
|
CB
|
A:ILE376
|
4.9
|
15.7
|
1.0
|
|
CA
|
A:GLY462
|
5.0
|
14.6
|
1.0
|
|
Zinc binding site 2 out
of 24 in 5cbm
Go back to
Zinc Binding Sites List in 5cbm
Zinc binding site 2 out
of 24 in the Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
 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 Pfa-M17 with Virtual Ligand Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn703
b:14.3
occ:1.00
|
OE1
|
A:GLU461
|
2.1
|
14.9
|
1.0
|
|
OD1
|
A:ASP459
|
2.1
|
18.0
|
1.0
|
|
O09
|
A:4ZN704
|
2.1
|
17.3
|
1.0
|
|
OD2
|
A:ASP379
|
2.2
|
16.9
|
1.0
|
|
O
|
A:ASP459
|
2.3
|
18.2
|
1.0
|
|
O10
|
A:4ZN704
|
2.5
|
17.8
|
1.0
|
|
P08
|
A:4ZN704
|
2.8
|
15.2
|
1.0
|
|
CG
|
A:ASP379
|
2.9
|
14.6
|
1.0
|
|
OD1
|
A:ASP379
|
3.0
|
15.6
|
1.0
|
|
CD
|
A:GLU461
|
3.0
|
14.6
|
1.0
|
|
CG
|
A:ASP459
|
3.1
|
17.6
|
1.0
|
|
C
|
A:ASP459
|
3.1
|
15.7
|
1.0
|
|
OE2
|
A:GLU461
|
3.3
|
14.6
|
1.0
|
|
ZN
|
A:ZN702
|
3.4
|
18.1
|
1.0
|
|
CA
|
A:ASP459
|
3.5
|
15.1
|
1.0
|
|
NZ
|
A:LYS386
|
3.6
|
14.2
|
1.0
|
|
N12
|
A:4ZN704
|
3.8
|
15.1
|
1.0
|
|
CB
|
A:ASP459
|
3.8
|
17.2
|
1.0
|
|
OD2
|
A:ASP459
|
3.9
|
20.0
|
1.0
|
|
CE
|
A:LYS386
|
4.0
|
15.7
|
1.0
|
|
C11
|
A:4ZN704
|
4.1
|
20.3
|
1.0
|
|
C07
|
A:4ZN704
|
4.2
|
17.3
|
1.0
|
|
N
|
A:ALA460
|
4.2
|
14.2
|
1.0
|
|
CB
|
A:ASP379
|
4.4
|
12.6
|
1.0
|
|
N
|
A:GLU461
|
4.4
|
15.6
|
1.0
|
|
CG
|
A:GLU461
|
4.4
|
13.9
|
1.0
|
|
C06
|
A:4ZN704
|
4.6
|
23.6
|
1.0
|
|
O2
|
A:CO3701
|
4.6
|
15.4
|
1.0
|
|
ND2
|
A:ASN432
|
4.6
|
11.6
|
1.0
|
|
CA
|
A:ALA460
|
4.7
|
16.3
|
1.0
|
|
CA
|
A:GLY381
|
4.8
|
14.7
|
1.0
|
|
N
|
A:ASP459
|
4.9
|
16.8
|
1.0
|
|
CB
|
A:GLU461
|
4.9
|
13.9
|
1.0
|
|
OD2
|
A:ASP399
|
4.9
|
17.6
|
1.0
|
|
Zinc binding site 3 out
of 24 in 5cbm
Go back to
Zinc Binding Sites List in 5cbm
Zinc binding site 3 out
of 24 in the Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
 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 Pfa-M17 with Virtual Ligand Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn702
b:17.7
occ:1.00
|
OE2
|
B:GLU461
|
2.0
|
11.6
|
1.0
|
|
OD2
|
B:ASP399
|
2.1
|
16.4
|
1.0
|
|
N12
|
B:4ZN704
|
2.1
|
14.2
|
1.0
|
|
NZ
|
B:LYS374
|
2.2
|
15.8
|
1.0
|
|
O09
|
B:4ZN704
|
2.3
|
15.8
|
1.0
|
|
OD2
|
B:ASP379
|
2.6
|
12.9
|
1.0
|
|
CG
|
B:ASP399
|
2.9
|
16.7
|
1.0
|
|
C11
|
B:4ZN704
|
3.0
|
18.2
|
1.0
|
|
CD
|
B:GLU461
|
3.0
|
14.3
|
1.0
|
|
OD1
|
B:ASP399
|
3.0
|
12.2
|
1.0
|
|
CE
|
B:LYS374
|
3.1
|
13.1
|
1.0
|
|
P08
|
B:4ZN704
|
3.2
|
16.9
|
1.0
|
|
ZN
|
B:ZN703
|
3.4
|
15.7
|
1.0
|
|
OE1
|
B:GLU461
|
3.4
|
13.3
|
1.0
|
|
CG
|
B:ASP379
|
3.5
|
16.2
|
1.0
|
|
O1
|
B:CO3701
|
3.8
|
16.7
|
1.0
|
|
CB
|
B:ASP379
|
4.1
|
11.8
|
1.0
|
|
O
|
B:THR486
|
4.1
|
16.8
|
1.0
|
|
O10
|
B:4ZN704
|
4.2
|
21.5
|
1.0
|
|
CG
|
B:GLU461
|
4.3
|
11.6
|
1.0
|
|
CB
|
B:ASP399
|
4.3
|
14.1
|
1.0
|
|
C13
|
B:4ZN704
|
4.4
|
19.8
|
1.0
|
|
OD1
|
B:ASP379
|
4.4
|
16.1
|
1.0
|
|
CD
|
B:LYS374
|
4.4
|
13.5
|
1.0
|
|
C07
|
B:4ZN704
|
4.6
|
24.8
|
1.0
|
|
CG1
|
B:ILE376
|
4.7
|
13.9
|
1.0
|
|
N
|
B:GLY462
|
4.7
|
15.5
|
1.0
|
|
O
|
B:ASP459
|
4.9
|
14.4
|
1.0
|
|
CB
|
B:ILE376
|
5.0
|
15.8
|
1.0
|
|
Zinc binding site 4 out
of 24 in 5cbm
Go back to
Zinc Binding Sites List in 5cbm
Zinc binding site 4 out
of 24 in the Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
 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 Pfa-M17 with Virtual Ligand Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn703
b:15.7
occ:1.00
|
OD1
|
B:ASP459
|
2.0
|
20.3
|
1.0
|
|
OD2
|
B:ASP379
|
2.1
|
12.9
|
1.0
|
|
OE1
|
B:GLU461
|
2.1
|
13.3
|
1.0
|
|
O
|
B:ASP459
|
2.2
|
14.4
|
1.0
|
|
O09
|
B:4ZN704
|
2.2
|
15.8
|
1.0
|
|
C07
|
B:4ZN704
|
2.8
|
24.8
|
1.0
|
|
P08
|
B:4ZN704
|
2.8
|
16.9
|
1.0
|
|
CG
|
B:ASP379
|
2.9
|
16.2
|
1.0
|
|
CG
|
B:ASP459
|
3.0
|
17.1
|
1.0
|
|
C
|
B:ASP459
|
3.1
|
14.6
|
1.0
|
|
OD1
|
B:ASP379
|
3.1
|
16.1
|
1.0
|
|
CD
|
B:GLU461
|
3.1
|
14.3
|
1.0
|
|
ZN
|
B:ZN702
|
3.4
|
17.7
|
1.0
|
|
OE2
|
B:GLU461
|
3.4
|
11.6
|
1.0
|
|
CA
|
B:ASP459
|
3.5
|
13.7
|
1.0
|
|
NZ
|
B:LYS386
|
3.7
|
16.7
|
1.0
|
|
OD2
|
B:ASP459
|
3.7
|
19.9
|
1.0
|
|
CB
|
B:ASP459
|
3.8
|
14.2
|
1.0
|
|
N12
|
B:4ZN704
|
3.8
|
14.2
|
1.0
|
|
O10
|
B:4ZN704
|
3.9
|
21.5
|
1.0
|
|
C06
|
B:4ZN704
|
4.0
|
31.5
|
1.0
|
|
C11
|
B:4ZN704
|
4.1
|
18.2
|
1.0
|
|
CE
|
B:LYS386
|
4.2
|
14.3
|
1.0
|
|
N
|
B:ALA460
|
4.2
|
12.8
|
1.0
|
|
N
|
B:GLU461
|
4.3
|
12.5
|
1.0
|
|
O1
|
B:CO3701
|
4.4
|
16.7
|
1.0
|
|
CB
|
B:ASP379
|
4.4
|
11.8
|
1.0
|
|
CG
|
B:GLU461
|
4.5
|
11.6
|
1.0
|
|
CA
|
B:ALA460
|
4.7
|
12.6
|
1.0
|
|
ND2
|
B:ASN432
|
4.7
|
14.6
|
1.0
|
|
C19
|
B:4ZN704
|
4.7
|
19.3
|
0.5
|
|
OD2
|
B:ASP399
|
4.8
|
16.4
|
1.0
|
|
N
|
B:ASP459
|
4.9
|
13.5
|
1.0
|
|
CB
|
B:GLU461
|
4.9
|
13.7
|
1.0
|
|
CA
|
B:GLY381
|
4.9
|
17.2
|
1.0
|
|
Zinc binding site 5 out
of 24 in 5cbm
Go back to
Zinc Binding Sites List in 5cbm
Zinc binding site 5 out
of 24 in the Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
 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 Pfa-M17 with Virtual Ligand Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn702
b:19.3
occ:1.00
|
OE2
|
C:GLU461
|
2.1
|
12.6
|
1.0
|
|
OD2
|
C:ASP399
|
2.1
|
17.8
|
1.0
|
|
NZ
|
C:LYS374
|
2.2
|
14.7
|
1.0
|
|
N12
|
C:4ZN704
|
2.2
|
15.2
|
1.0
|
|
O09
|
C:4ZN704
|
2.5
|
15.9
|
1.0
|
|
OD2
|
C:ASP379
|
2.6
|
14.8
|
1.0
|
|
CG
|
C:ASP399
|
3.0
|
16.8
|
1.0
|
|
C11
|
C:4ZN704
|
3.0
|
15.2
|
1.0
|
|
OD1
|
C:ASP399
|
3.1
|
16.9
|
1.0
|
|
P08
|
C:4ZN704
|
3.2
|
15.1
|
1.0
|
|
CD
|
C:GLU461
|
3.2
|
14.2
|
1.0
|
|
CE
|
C:LYS374
|
3.2
|
14.0
|
1.0
|
|
ZN
|
C:ZN703
|
3.3
|
15.8
|
1.0
|
|
OE1
|
C:GLU461
|
3.5
|
15.5
|
1.0
|
|
CG
|
C:ASP379
|
3.5
|
11.7
|
1.0
|
|
O10
|
C:4ZN704
|
3.8
|
18.1
|
1.0
|
|
O2
|
C:CO3701
|
3.8
|
15.1
|
1.0
|
|
CB
|
C:ASP379
|
4.0
|
13.7
|
1.0
|
|
O
|
C:THR486
|
4.1
|
16.9
|
1.0
|
|
CB
|
C:ASP399
|
4.4
|
12.0
|
1.0
|
|
C13
|
C:4ZN704
|
4.4
|
18.9
|
1.0
|
|
OD1
|
C:ASP379
|
4.4
|
13.9
|
1.0
|
|
CG
|
C:GLU461
|
4.5
|
13.7
|
1.0
|
|
CD
|
C:LYS374
|
4.6
|
16.1
|
1.0
|
|
CG1
|
C:ILE376
|
4.8
|
16.4
|
1.0
|
|
C07
|
C:4ZN704
|
4.8
|
20.6
|
1.0
|
|
N
|
C:GLY462
|
4.8
|
14.1
|
1.0
|
|
O
|
C:ASP459
|
4.9
|
12.2
|
1.0
|
|
CB
|
C:ILE376
|
5.0
|
15.4
|
1.0
|
|
Zinc binding site 6 out
of 24 in 5cbm
Go back to
Zinc Binding Sites List in 5cbm
Zinc binding site 6 out
of 24 in the Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
 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 Pfa-M17 with Virtual Ligand Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn703
b:15.8
occ:1.00
|
OD1
|
C:ASP459
|
2.0
|
17.7
|
1.0
|
|
OD2
|
C:ASP379
|
2.1
|
14.8
|
1.0
|
|
OE1
|
C:GLU461
|
2.2
|
15.5
|
1.0
|
|
O10
|
C:4ZN704
|
2.2
|
18.1
|
1.0
|
|
O
|
C:ASP459
|
2.2
|
12.2
|
1.0
|
|
O09
|
C:4ZN704
|
2.6
|
15.9
|
1.0
|
|
P08
|
C:4ZN704
|
2.9
|
15.1
|
1.0
|
|
CG
|
C:ASP379
|
2.9
|
11.7
|
1.0
|
|
CG
|
C:ASP459
|
3.0
|
19.2
|
1.0
|
|
CD
|
C:GLU461
|
3.1
|
14.2
|
1.0
|
|
OD1
|
C:ASP379
|
3.1
|
13.9
|
1.0
|
|
C
|
C:ASP459
|
3.1
|
14.3
|
1.0
|
|
ZN
|
C:ZN702
|
3.3
|
19.3
|
1.0
|
|
OE2
|
C:GLU461
|
3.3
|
12.6
|
1.0
|
|
CA
|
C:ASP459
|
3.6
|
14.1
|
1.0
|
|
OD2
|
C:ASP459
|
3.7
|
17.8
|
1.0
|
|
NZ
|
C:LYS386
|
3.8
|
18.2
|
1.0
|
|
CB
|
C:ASP459
|
3.8
|
17.2
|
1.0
|
|
CE
|
C:LYS386
|
4.0
|
17.2
|
1.0
|
|
N12
|
C:4ZN704
|
4.0
|
15.2
|
1.0
|
|
C11
|
C:4ZN704
|
4.2
|
15.2
|
1.0
|
|
N
|
C:ALA460
|
4.3
|
15.8
|
1.0
|
|
C07
|
C:4ZN704
|
4.3
|
20.6
|
1.0
|
|
C06
|
C:4ZN704
|
4.3
|
22.5
|
0.5
|
|
CB
|
C:ASP379
|
4.4
|
13.7
|
1.0
|
|
N
|
C:GLU461
|
4.4
|
13.1
|
1.0
|
|
O2
|
C:CO3701
|
4.4
|
15.1
|
1.0
|
|
CG
|
C:GLU461
|
4.5
|
13.7
|
1.0
|
|
CA
|
C:ALA460
|
4.7
|
14.7
|
1.0
|
|
ND2
|
C:ASN432
|
4.7
|
17.2
|
1.0
|
|
CA
|
C:GLY381
|
4.8
|
15.0
|
1.0
|
|
OD2
|
C:ASP399
|
4.8
|
17.8
|
1.0
|
|
N
|
C:ASP459
|
4.9
|
13.2
|
1.0
|
|
CB
|
C:GLU461
|
5.0
|
15.0
|
1.0
|
|
Zinc binding site 7 out
of 24 in 5cbm
Go back to
Zinc Binding Sites List in 5cbm
Zinc binding site 7 out
of 24 in the Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
 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 Pfa-M17 with Virtual Ligand Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn702
b:17.3
occ:1.00
|
OE2
|
D:GLU461
|
1.9
|
15.2
|
1.0
|
|
OD2
|
D:ASP399
|
2.2
|
18.4
|
1.0
|
|
NZ
|
D:LYS374
|
2.2
|
19.9
|
1.0
|
|
O09
|
D:4ZN704
|
2.4
|
19.5
|
1.0
|
|
N12
|
D:4ZN704
|
2.5
|
15.5
|
1.0
|
|
OD2
|
D:ASP379
|
2.8
|
18.4
|
1.0
|
|
CG
|
D:ASP399
|
2.9
|
19.1
|
1.0
|
|
OD1
|
D:ASP399
|
3.0
|
16.7
|
1.0
|
|
CD
|
D:GLU461
|
3.1
|
18.7
|
1.0
|
|
CE
|
D:LYS374
|
3.1
|
15.0
|
1.0
|
|
C11
|
D:4ZN704
|
3.3
|
16.9
|
1.0
|
|
ZN
|
D:ZN703
|
3.3
|
17.8
|
1.0
|
|
P08
|
D:4ZN704
|
3.4
|
16.2
|
1.0
|
|
OE1
|
D:GLU461
|
3.5
|
17.3
|
1.0
|
|
CG
|
D:ASP379
|
3.6
|
17.6
|
1.0
|
|
O10
|
D:4ZN704
|
3.8
|
13.7
|
1.0
|
|
O1
|
D:CO3701
|
3.9
|
16.4
|
1.0
|
|
CB
|
D:ASP379
|
4.1
|
14.5
|
1.0
|
|
O
|
D:THR486
|
4.1
|
22.3
|
1.0
|
|
CG
|
D:GLU461
|
4.3
|
15.2
|
1.0
|
|
CB
|
D:ASP399
|
4.4
|
15.4
|
1.0
|
|
CD
|
D:LYS374
|
4.5
|
14.5
|
1.0
|
|
OD1
|
D:ASP379
|
4.6
|
17.7
|
1.0
|
|
C13
|
D:4ZN704
|
4.6
|
22.5
|
1.0
|
|
CG1
|
D:ILE376
|
4.7
|
13.2
|
1.0
|
|
O
|
D:ASP459
|
4.8
|
15.2
|
1.0
|
|
N
|
D:GLY462
|
4.8
|
17.6
|
1.0
|
|
C07
|
D:4ZN704
|
4.9
|
18.1
|
1.0
|
|
CB
|
D:ILE376
|
5.0
|
12.3
|
1.0
|
|
Zinc binding site 8 out
of 24 in 5cbm
Go back to
Zinc Binding Sites List in 5cbm
Zinc binding site 8 out
of 24 in the Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
 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 Pfa-M17 with Virtual Ligand Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn703
b:17.8
occ:1.00
|
OD2
|
D:ASP379
|
2.1
|
18.4
|
1.0
|
|
OE1
|
D:GLU461
|
2.1
|
17.3
|
1.0
|
|
O
|
D:ASP459
|
2.1
|
15.2
|
1.0
|
|
OD1
|
D:ASP459
|
2.2
|
20.8
|
1.0
|
|
O10
|
D:4ZN704
|
2.2
|
13.7
|
1.0
|
|
O09
|
D:4ZN704
|
2.6
|
19.5
|
1.0
|
|
CG
|
D:ASP379
|
2.9
|
17.6
|
1.0
|
|
CD
|
D:GLU461
|
3.0
|
18.7
|
1.0
|
|
P08
|
D:4ZN704
|
3.0
|
16.2
|
1.0
|
|
CG
|
D:ASP459
|
3.1
|
20.5
|
1.0
|
|
C
|
D:ASP459
|
3.1
|
16.2
|
1.0
|
|
OD1
|
D:ASP379
|
3.2
|
17.7
|
1.0
|
|
OE2
|
D:GLU461
|
3.2
|
15.2
|
1.0
|
|
ZN
|
D:ZN702
|
3.3
|
17.3
|
1.0
|
|
CA
|
D:ASP459
|
3.5
|
15.3
|
1.0
|
|
NZ
|
D:LYS386
|
3.7
|
18.7
|
1.0
|
|
CB
|
D:ASP459
|
3.8
|
15.0
|
1.0
|
|
OD2
|
D:ASP459
|
3.8
|
18.8
|
1.0
|
|
N12
|
D:4ZN704
|
3.9
|
15.5
|
1.0
|
|
CE
|
D:LYS386
|
4.1
|
17.9
|
1.0
|
|
C07
|
D:4ZN704
|
4.2
|
18.1
|
1.0
|
|
N
|
D:ALA460
|
4.2
|
16.4
|
1.0
|
|
C11
|
D:4ZN704
|
4.3
|
16.9
|
1.0
|
|
N
|
D:GLU461
|
4.3
|
18.8
|
1.0
|
|
CB
|
D:ASP379
|
4.3
|
14.5
|
1.0
|
|
CG
|
D:GLU461
|
4.4
|
15.2
|
1.0
|
|
O1
|
D:CO3701
|
4.4
|
16.4
|
1.0
|
|
ND2
|
D:ASN432
|
4.6
|
14.3
|
1.0
|
|
CA
|
D:ALA460
|
4.7
|
16.8
|
1.0
|
|
OD2
|
D:ASP399
|
4.8
|
18.4
|
1.0
|
|
CB
|
D:GLU461
|
4.9
|
17.7
|
1.0
|
|
N
|
D:ASP459
|
4.9
|
16.2
|
1.0
|
|
CA
|
D:GLY381
|
4.9
|
14.9
|
1.0
|
|
Zinc binding site 9 out
of 24 in 5cbm
Go back to
Zinc Binding Sites List in 5cbm
Zinc binding site 9 out
of 24 in the Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
 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 Pfa-M17 with Virtual Ligand Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn702
b:17.9
occ:1.00
|
OE2
|
E:GLU461
|
1.9
|
16.7
|
1.0
|
|
OD2
|
E:ASP399
|
1.9
|
16.4
|
1.0
|
|
NZ
|
E:LYS374
|
2.2
|
17.3
|
1.0
|
|
N12
|
E:4ZN704
|
2.4
|
18.1
|
1.0
|
|
O10
|
E:4ZN704
|
2.5
|
17.8
|
1.0
|
|
CG
|
E:ASP399
|
2.7
|
13.7
|
1.0
|
|
OD2
|
E:ASP379
|
2.8
|
16.5
|
1.0
|
|
OD1
|
E:ASP399
|
2.9
|
14.5
|
1.0
|
|
CE
|
E:LYS374
|
3.0
|
20.2
|
1.0
|
|
CD
|
E:GLU461
|
3.1
|
16.0
|
1.0
|
|
C11
|
E:4ZN704
|
3.2
|
19.3
|
1.0
|
|
P08
|
E:4ZN704
|
3.3
|
16.4
|
1.0
|
|
ZN
|
E:ZN703
|
3.4
|
17.7
|
1.0
|
|
CG
|
E:ASP379
|
3.6
|
16.0
|
1.0
|
|
OE1
|
E:GLU461
|
3.6
|
18.5
|
1.0
|
|
O09
|
E:4ZN704
|
3.7
|
19.5
|
1.0
|
|
O2
|
E:CO3701
|
3.8
|
18.7
|
1.0
|
|
CB
|
E:ASP379
|
4.0
|
13.7
|
1.0
|
|
O
|
E:THR486
|
4.1
|
16.3
|
1.0
|
|
CB
|
E:ASP399
|
4.2
|
8.8
|
1.0
|
|
CG
|
E:GLU461
|
4.3
|
15.8
|
1.0
|
|
CD
|
E:LYS374
|
4.4
|
19.0
|
1.0
|
|
OD1
|
E:ASP379
|
4.5
|
19.3
|
1.0
|
|
C13
|
E:4ZN704
|
4.6
|
21.1
|
1.0
|
|
N
|
E:GLY462
|
4.8
|
17.3
|
1.0
|
|
CG1
|
E:ILE376
|
4.8
|
17.4
|
1.0
|
|
O
|
E:ASP459
|
4.9
|
17.2
|
1.0
|
|
OG1
|
E:THR486
|
4.9
|
17.4
|
1.0
|
|
CB
|
E:ILE376
|
5.0
|
15.2
|
1.0
|
|
Zinc binding site 10 out
of 24 in 5cbm
Go back to
Zinc Binding Sites List in 5cbm
Zinc binding site 10 out
of 24 in the Crystal Structure of Pfa-M17 with Virtual Ligand Inhibitor
 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 Pfa-M17 with Virtual Ligand Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn703
b:17.7
occ:1.00
|
OD1
|
E:ASP459
|
2.0
|
20.7
|
1.0
|
|
OD2
|
E:ASP379
|
2.0
|
16.5
|
1.0
|
|
OE1
|
E:GLU461
|
2.1
|
18.5
|
1.0
|
|
O09
|
E:4ZN704
|
2.1
|
19.5
|
1.0
|
|
O
|
E:ASP459
|
2.2
|
17.2
|
1.0
|
|
O10
|
E:4ZN704
|
2.7
|
17.8
|
1.0
|
|
CG
|
E:ASP379
|
2.9
|
16.0
|
1.0
|
|
CD
|
E:GLU461
|
2.9
|
16.0
|
1.0
|
|
P08
|
E:4ZN704
|
2.9
|
16.4
|
1.0
|
|
CG
|
E:ASP459
|
3.0
|
19.3
|
1.0
|
|
OE2
|
E:GLU461
|
3.0
|
16.7
|
1.0
|
|
C
|
E:ASP459
|
3.1
|
16.6
|
1.0
|
|
OD1
|
E:ASP379
|
3.1
|
19.3
|
1.0
|
|
ZN
|
E:ZN702
|
3.4
|
17.9
|
1.0
|
|
CA
|
E:ASP459
|
3.5
|
15.3
|
1.0
|
|
OD2
|
E:ASP459
|
3.7
|
16.4
|
1.0
|
|
NZ
|
E:LYS386
|
3.8
|
17.3
|
1.0
|
|
CB
|
E:ASP459
|
3.8
|
17.4
|
1.0
|
|
N12
|
E:4ZN704
|
4.0
|
18.1
|
1.0
|
|
CE
|
E:LYS386
|
4.1
|
16.5
|
1.0
|
|
C07
|
E:4ZN704
|
4.2
|
18.5
|
1.0
|
|
C11
|
E:4ZN704
|
4.2
|
19.3
|
1.0
|
|
N
|
E:ALA460
|
4.3
|
17.9
|
1.0
|
|
CB
|
E:ASP379
|
4.3
|
13.7
|
1.0
|
|
N
|
E:GLU461
|
4.4
|
13.6
|
1.0
|
|
CG
|
E:GLU461
|
4.4
|
15.8
|
1.0
|
|
O2
|
E:CO3701
|
4.5
|
18.7
|
1.0
|
|
ND2
|
E:ASN432
|
4.6
|
15.2
|
1.0
|
|
C06
|
E:4ZN704
|
4.7
|
28.0
|
1.0
|
|
CA
|
E:ALA460
|
4.7
|
19.2
|
1.0
|
|
C05
|
E:4ZN704
|
4.7
|
19.8
|
0.5
|
|
OD2
|
E:ASP399
|
4.7
|
16.4
|
1.0
|
|
CA
|
E:GLY381
|
4.8
|
13.2
|
1.0
|
|
CB
|
E:GLU461
|
4.9
|
15.2
|
1.0
|
|
N
|
E:ASP459
|
4.9
|
16.2
|
1.0
|
|
Reference:
C.Ruggeri,
N.Drinkwater,
K.K.Sivaraman,
R.S.Bamert,
S.Mcgowan,
A.Paiardini.
Identification and Validation of A Potent Dual Inhibitor of the P. Falciparum M1 and M17 Aminopeptidases Using Virtual Screening. Plos One V. 10 38957 2015.
ISSN: ESSN 1932-6203
PubMed: 26406322
DOI: 10.1371/JOURNAL.PONE.0138957
Page generated: Thu Aug 21 01:17:10 2025
|
