Fluorine in PDB 6ee4: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion
Protein crystallography data
The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion, PDB code: 6ee4
was solved by
N.Drinkwater,
S.Mcgowan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.29 /
1.58
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.110,
108.860,
118.080,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.8 /
18.9
|
Other elements in 6ee4:
The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion
(pdb code 6ee4). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion, PDB code: 6ee4:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 6ee4
Go back to
Fluorine Binding Sites List in 6ee4
Fluorine binding site 1 out
of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:11.8
occ:1.00
|
FAM
|
A:J4S1102
|
0.0
|
11.8
|
1.0
|
CAK
|
A:J4S1102
|
1.3
|
10.6
|
1.0
|
CAJ
|
A:J4S1102
|
2.3
|
9.6
|
1.0
|
CAL
|
A:J4S1102
|
2.4
|
9.2
|
1.0
|
FAN
|
A:J4S1102
|
2.7
|
13.3
|
1.0
|
O
|
A:HOH1823
|
3.1
|
12.2
|
1.0
|
N
|
A:ALA320
|
3.4
|
7.7
|
1.0
|
CA
|
A:GLU572
|
3.5
|
14.1
|
1.0
|
CAI
|
A:J4S1102
|
3.6
|
9.4
|
1.0
|
CAG
|
A:J4S1102
|
3.6
|
8.5
|
1.0
|
CG
|
A:GLU572
|
3.6
|
13.1
|
1.0
|
O
|
A:GLU319
|
3.7
|
10.6
|
1.0
|
O
|
A:MET571
|
3.8
|
13.3
|
1.0
|
CE1
|
A:TYR575
|
3.9
|
8.6
|
1.0
|
C
|
A:GLU319
|
3.9
|
7.5
|
1.0
|
N
|
A:GLU572
|
3.9
|
11.7
|
1.0
|
C
|
A:MET571
|
4.0
|
9.3
|
1.0
|
CAH
|
A:J4S1102
|
4.1
|
8.6
|
1.0
|
CB
|
A:GLU572
|
4.1
|
14.1
|
1.0
|
CB
|
A:ALA320
|
4.2
|
9.6
|
1.0
|
CD1
|
A:TYR575
|
4.3
|
11.1
|
1.0
|
CA
|
A:ALA320
|
4.4
|
7.7
|
1.0
|
CE
|
A:MET1034
|
4.5
|
12.8
|
1.0
|
CZ
|
A:TYR575
|
4.5
|
10.1
|
1.0
|
O
|
A:HOH1434
|
4.6
|
13.1
|
1.0
|
C
|
A:GLU572
|
4.6
|
15.4
|
1.0
|
FAO
|
A:J4S1102
|
4.7
|
10.9
|
1.0
|
SD
|
A:MET1034
|
4.7
|
12.4
|
1.0
|
CB
|
A:MET571
|
4.7
|
15.9
|
1.0
|
O
|
A:GLU572
|
4.8
|
16.8
|
1.0
|
OH
|
A:TYR575
|
4.8
|
11.8
|
1.0
|
CD
|
A:GLU572
|
4.8
|
16.9
|
1.0
|
CAF
|
A:J4S1102
|
4.8
|
9.8
|
1.0
|
O
|
A:HOH1700
|
5.0
|
12.0
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 6ee4
Go back to
Fluorine Binding Sites List in 6ee4
Fluorine binding site 2 out
of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:13.3
occ:1.00
|
FAN
|
A:J4S1102
|
0.0
|
13.3
|
1.0
|
CAJ
|
A:J4S1102
|
1.4
|
9.6
|
1.0
|
CAK
|
A:J4S1102
|
2.4
|
10.6
|
1.0
|
CAI
|
A:J4S1102
|
2.4
|
9.4
|
1.0
|
FAM
|
A:J4S1102
|
2.7
|
11.8
|
1.0
|
FAO
|
A:J4S1102
|
2.7
|
10.9
|
1.0
|
O
|
A:HOH1434
|
3.2
|
13.1
|
1.0
|
CG
|
A:GLU572
|
3.3
|
13.1
|
1.0
|
O
|
A:HOH1700
|
3.3
|
12.0
|
1.0
|
OE2
|
A:GLU572
|
3.4
|
16.1
|
1.0
|
CG2
|
A:THR305
|
3.5
|
15.2
|
1.0
|
O
|
A:GLU319
|
3.5
|
10.6
|
1.0
|
CD
|
A:GLU572
|
3.6
|
16.9
|
1.0
|
SD
|
A:MET1034
|
3.6
|
12.4
|
1.0
|
CAH
|
A:J4S1102
|
3.6
|
8.6
|
1.0
|
O
|
A:HOH1823
|
3.7
|
12.2
|
1.0
|
CAL
|
A:J4S1102
|
3.7
|
9.2
|
1.0
|
CAG
|
A:J4S1102
|
4.2
|
8.5
|
1.0
|
CB
|
A:GLU572
|
4.3
|
14.1
|
1.0
|
CE
|
A:MET1034
|
4.3
|
12.8
|
1.0
|
C
|
A:GLU319
|
4.4
|
7.5
|
1.0
|
N
|
A:ALA320
|
4.5
|
7.7
|
1.0
|
CB
|
A:THR305
|
4.5
|
13.5
|
1.0
|
OE1
|
A:GLU572
|
4.6
|
16.7
|
1.0
|
CA
|
A:GLU572
|
4.6
|
14.1
|
1.0
|
ND2
|
A:ASN458
|
5.0
|
11.0
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 6ee4
Go back to
Fluorine Binding Sites List in 6ee4
Fluorine binding site 3 out
of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:10.9
occ:1.00
|
FAO
|
A:J4S1102
|
0.0
|
10.9
|
1.0
|
CAI
|
A:J4S1102
|
1.4
|
9.4
|
1.0
|
CAJ
|
A:J4S1102
|
2.4
|
9.6
|
1.0
|
CAH
|
A:J4S1102
|
2.4
|
8.6
|
1.0
|
FAN
|
A:J4S1102
|
2.7
|
13.3
|
1.0
|
CG
|
A:GLN317
|
3.3
|
9.1
|
1.0
|
ND2
|
A:ASN458
|
3.4
|
11.0
|
1.0
|
O
|
A:HOH2234
|
3.5
|
8.8
|
1.0
|
CG2
|
A:THR305
|
3.5
|
15.2
|
1.0
|
CAK
|
A:J4S1102
|
3.6
|
10.6
|
1.0
|
SD
|
A:MET1034
|
3.7
|
12.4
|
1.0
|
CAG
|
A:J4S1102
|
3.7
|
8.5
|
1.0
|
O
|
A:HOH1700
|
4.0
|
12.0
|
1.0
|
O
|
A:GLU319
|
4.0
|
10.6
|
1.0
|
O
|
A:LEU304
|
4.1
|
9.2
|
1.0
|
CB
|
A:ASN458
|
4.1
|
7.5
|
1.0
|
CD
|
A:GLN317
|
4.2
|
10.1
|
1.0
|
CAL
|
A:J4S1102
|
4.2
|
9.2
|
1.0
|
NE2
|
A:GLN317
|
4.2
|
8.5
|
1.0
|
CG
|
A:ASN458
|
4.2
|
9.2
|
1.0
|
CE
|
A:MET1034
|
4.3
|
12.8
|
1.0
|
O
|
A:HOH1812
|
4.4
|
9.3
|
1.0
|
CB
|
A:GLN317
|
4.5
|
9.6
|
1.0
|
CB
|
A:THR305
|
4.7
|
13.5
|
1.0
|
FAM
|
A:J4S1102
|
4.7
|
11.8
|
1.0
|
CAF
|
A:J4S1102
|
4.8
|
9.8
|
1.0
|
CA
|
A:THR305
|
5.0
|
9.9
|
1.0
|
|
Reference:
N.B.Vinh,
N.Drinkwater,
T.R.Malcolm,
M.Kassiou,
L.Lucantoni,
P.M.Grin,
G.S.Butler,
S.Duffy,
C.M.Overall,
V.M.Avery,
P.J.Scammells,
S.Mcgowan.
Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. V. 62 622 2019.
ISSN: ISSN 1520-4804
PubMed: 30537832
DOI: 10.1021/ACS.JMEDCHEM.8B01310
Page generated: Sun Dec 13 12:49:16 2020
|