Fluorine in PDB 6ea1: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion
Protein crystallography data
The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion, PDB code: 6ea1
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)
|
54.46 /
1.82
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.491,
108.920,
118.150,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.7 /
20.1
|
Other elements in 6ea1:
The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) 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 (6DA) and Catalytic Zinc Ion
(pdb code 6ea1). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the
X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion, PDB code: 6ea1:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
Fluorine binding site 1 out
of 7 in 6ea1
Go back to
Fluorine Binding Sites List in 6ea1
Fluorine binding site 1 out
of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) 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 (6DA) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:32.1
occ:0.90
|
FBA
|
A:J0Y1102
|
0.0
|
32.1
|
0.9
|
CAZ
|
A:J0Y1102
|
1.4
|
34.2
|
0.9
|
FBB
|
A:J0Y1102
|
2.1
|
32.5
|
0.9
|
FBC
|
A:J0Y1102
|
2.2
|
36.5
|
0.9
|
CAQ
|
A:J0Y1102
|
2.4
|
16.7
|
0.9
|
CAP
|
A:J0Y1102
|
2.8
|
12.2
|
0.9
|
FAY
|
A:J0Y1102
|
2.9
|
20.1
|
0.9
|
N
|
A:J0Y1102
|
3.3
|
10.0
|
0.9
|
OAR
|
A:J0Y1102
|
3.4
|
9.8
|
0.9
|
CE1
|
A:HIS496
|
3.9
|
9.5
|
1.0
|
ND1
|
A:HIS496
|
3.9
|
9.8
|
1.0
|
NE2
|
A:HIS496
|
3.9
|
10.0
|
1.0
|
CG
|
A:HIS496
|
4.0
|
9.7
|
1.0
|
CD2
|
A:HIS496
|
4.0
|
12.3
|
1.0
|
O
|
A:HOH2173
|
4.3
|
24.0
|
1.0
|
C
|
A:J0Y1102
|
4.3
|
7.6
|
0.9
|
CA
|
A:J0Y1102
|
4.3
|
7.3
|
0.9
|
O
|
A:J0Y1102
|
4.5
|
7.6
|
0.9
|
NAS
|
A:J0Y1102
|
4.5
|
7.3
|
0.9
|
CE2
|
A:TYR580
|
4.6
|
11.1
|
1.0
|
OE2
|
A:GLU497
|
4.6
|
9.6
|
1.0
|
O
|
A:HOH1239
|
4.7
|
11.0
|
1.0
|
CB
|
A:HIS496
|
4.7
|
7.2
|
1.0
|
O
|
A:HOH1997
|
4.8
|
27.5
|
1.0
|
CD2
|
A:TYR580
|
4.9
|
10.9
|
1.0
|
CG2
|
A:VAL493
|
4.9
|
10.1
|
1.0
|
|
Fluorine binding site 2 out
of 7 in 6ea1
Go back to
Fluorine Binding Sites List in 6ea1
Fluorine binding site 2 out
of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) 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 (6DA) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:32.5
occ:0.90
|
FBB
|
A:J0Y1102
|
0.0
|
32.5
|
0.9
|
CAZ
|
A:J0Y1102
|
1.3
|
34.2
|
0.9
|
FBA
|
A:J0Y1102
|
2.1
|
32.1
|
0.9
|
FBC
|
A:J0Y1102
|
2.1
|
36.5
|
0.9
|
CAQ
|
A:J0Y1102
|
2.3
|
16.7
|
0.9
|
OAR
|
A:J0Y1102
|
2.8
|
9.8
|
0.9
|
CAP
|
A:J0Y1102
|
2.9
|
12.2
|
0.9
|
O
|
A:HOH1997
|
3.4
|
27.5
|
1.0
|
NH2
|
A:ARG489
|
3.4
|
15.7
|
1.0
|
FAY
|
A:J0Y1102
|
3.5
|
20.1
|
0.9
|
NH1
|
A:ARG489
|
3.6
|
14.3
|
1.0
|
CZ
|
A:ARG489
|
3.8
|
16.7
|
1.0
|
CG2
|
A:VAL493
|
3.8
|
10.1
|
1.0
|
N
|
A:J0Y1102
|
4.0
|
10.0
|
0.9
|
CA
|
A:GLY460
|
4.1
|
7.7
|
1.0
|
N
|
A:GLY460
|
4.6
|
7.3
|
1.0
|
O
|
A:HOH2101
|
4.6
|
22.4
|
1.0
|
CG1
|
A:VAL493
|
4.7
|
8.2
|
1.0
|
N
|
A:ALA461
|
4.8
|
7.8
|
1.0
|
CB
|
A:VAL493
|
4.8
|
7.9
|
1.0
|
NE
|
A:ARG489
|
4.9
|
16.1
|
1.0
|
C
|
A:GLY460
|
4.9
|
10.6
|
1.0
|
|
Fluorine binding site 3 out
of 7 in 6ea1
Go back to
Fluorine Binding Sites List in 6ea1
Fluorine binding site 3 out
of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) 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 (6DA) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:36.5
occ:0.90
|
FBC
|
A:J0Y1102
|
0.0
|
36.5
|
0.9
|
CAZ
|
A:J0Y1102
|
1.4
|
34.2
|
0.9
|
FBB
|
A:J0Y1102
|
2.1
|
32.5
|
0.9
|
FBA
|
A:J0Y1102
|
2.2
|
32.1
|
0.9
|
CAQ
|
A:J0Y1102
|
2.4
|
16.7
|
0.9
|
FAY
|
A:J0Y1102
|
2.8
|
20.1
|
0.9
|
O
|
A:HOH1997
|
3.1
|
27.5
|
1.0
|
O
|
A:HOH2173
|
3.2
|
24.0
|
1.0
|
O
|
A:HOH2240
|
3.3
|
49.2
|
1.0
|
CAP
|
A:J0Y1102
|
3.7
|
12.2
|
0.9
|
NH1
|
A:ARG489
|
3.8
|
14.3
|
1.0
|
O
|
A:HOH1412
|
3.9
|
18.3
|
1.0
|
OAR
|
A:J0Y1102
|
4.3
|
9.8
|
0.9
|
N
|
A:J0Y1102
|
4.6
|
10.0
|
0.9
|
O
|
A:HOH2377
|
4.6
|
58.2
|
1.0
|
CZ
|
A:ARG489
|
4.6
|
16.7
|
1.0
|
NH2
|
A:ARG489
|
4.6
|
15.7
|
1.0
|
O
|
A:HOH1239
|
5.0
|
11.0
|
1.0
|
|
Fluorine binding site 4 out
of 7 in 6ea1
Go back to
Fluorine Binding Sites List in 6ea1
Fluorine binding site 4 out
of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:20.1
occ:0.90
|
FAY
|
A:J0Y1102
|
0.0
|
20.1
|
0.9
|
CAQ
|
A:J0Y1102
|
1.4
|
16.7
|
0.9
|
CAP
|
A:J0Y1102
|
2.3
|
12.2
|
0.9
|
CAZ
|
A:J0Y1102
|
2.4
|
34.2
|
0.9
|
N
|
A:J0Y1102
|
2.5
|
10.0
|
0.9
|
FBC
|
A:J0Y1102
|
2.8
|
36.5
|
0.9
|
FBA
|
A:J0Y1102
|
2.9
|
32.1
|
0.9
|
O
|
A:HOH2377
|
3.2
|
58.2
|
1.0
|
O
|
A:HOH2156
|
3.3
|
28.8
|
1.0
|
CE2
|
A:TYR580
|
3.3
|
11.1
|
1.0
|
OAR
|
A:J0Y1102
|
3.5
|
9.8
|
0.9
|
FBB
|
A:J0Y1102
|
3.5
|
32.5
|
0.9
|
O
|
A:HOH2240
|
3.5
|
49.2
|
1.0
|
CD2
|
A:TYR580
|
3.6
|
10.9
|
1.0
|
CA
|
A:J0Y1102
|
4.0
|
7.3
|
0.9
|
CZ
|
A:TYR580
|
4.0
|
9.5
|
1.0
|
O
|
A:HOH1997
|
4.0
|
27.5
|
1.0
|
O
|
A:HOH2101
|
4.1
|
22.4
|
1.0
|
O
|
A:HOH2162
|
4.2
|
29.2
|
1.0
|
CG
|
A:TYR580
|
4.4
|
10.5
|
1.0
|
O
|
A:HOH1412
|
4.4
|
18.3
|
1.0
|
O
|
A:J0Y1102
|
4.5
|
7.6
|
0.9
|
OH
|
A:TYR580
|
4.5
|
7.3
|
1.0
|
C
|
A:J0Y1102
|
4.6
|
7.6
|
0.9
|
CAK
|
A:J0Y1102
|
4.7
|
7.3
|
0.9
|
CE1
|
A:TYR580
|
4.8
|
8.7
|
1.0
|
CAJ
|
A:J0Y1102
|
4.8
|
6.9
|
0.9
|
CD1
|
A:TYR580
|
5.0
|
11.1
|
1.0
|
|
Fluorine binding site 5 out
of 7 in 6ea1
Go back to
Fluorine Binding Sites List in 6ea1
Fluorine binding site 5 out
of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:10.8
occ:0.90
|
FAV
|
A:J0Y1102
|
0.0
|
10.8
|
0.9
|
CAA
|
A:J0Y1102
|
1.3
|
9.6
|
0.9
|
CAF
|
A:J0Y1102
|
2.3
|
10.2
|
0.9
|
CAB
|
A:J0Y1102
|
2.3
|
7.5
|
0.9
|
FAW
|
A:J0Y1102
|
2.8
|
10.8
|
0.9
|
O
|
A:HOH1751
|
3.2
|
8.9
|
1.0
|
N
|
A:ALA320
|
3.4
|
8.9
|
1.0
|
CA
|
A:GLU572
|
3.5
|
17.9
|
1.0
|
CAE
|
A:J0Y1102
|
3.6
|
7.9
|
0.9
|
CAC
|
A:J0Y1102
|
3.6
|
7.9
|
0.9
|
CG
|
A:GLU572
|
3.6
|
18.3
|
1.0
|
CE1
|
A:TYR575
|
3.7
|
9.4
|
1.0
|
O
|
A:GLU319
|
3.7
|
10.0
|
1.0
|
O
|
A:MET571
|
3.8
|
19.5
|
1.0
|
C
|
A:GLU319
|
4.0
|
8.4
|
1.0
|
N
|
A:GLU572
|
4.0
|
16.9
|
1.0
|
CB
|
A:GLU572
|
4.0
|
18.2
|
1.0
|
CD1
|
A:TYR575
|
4.1
|
7.6
|
1.0
|
C
|
A:MET571
|
4.1
|
16.6
|
1.0
|
CAD
|
A:J0Y1102
|
4.1
|
7.5
|
0.9
|
CB
|
A:ALA320
|
4.2
|
8.3
|
1.0
|
CZ
|
A:TYR575
|
4.4
|
7.4
|
1.0
|
CA
|
A:ALA320
|
4.4
|
8.4
|
1.0
|
C
|
A:GLU572
|
4.5
|
20.8
|
1.0
|
CE
|
A:MET1034
|
4.5
|
12.2
|
1.0
|
O
|
A:GLU572
|
4.7
|
22.0
|
1.0
|
FAX
|
A:J0Y1102
|
4.7
|
7.9
|
0.9
|
OH
|
A:TYR575
|
4.7
|
9.0
|
1.0
|
CB
|
A:MET571
|
4.8
|
18.6
|
1.0
|
SD
|
A:MET1034
|
4.8
|
11.5
|
1.0
|
O
|
A:HOH1512
|
4.8
|
12.7
|
1.0
|
CAG
|
A:J0Y1102
|
4.8
|
7.2
|
0.9
|
CD
|
A:GLU572
|
4.9
|
21.1
|
1.0
|
CG
|
A:TYR575
|
5.0
|
8.0
|
1.0
|
|
Fluorine binding site 6 out
of 7 in 6ea1
Go back to
Fluorine Binding Sites List in 6ea1
Fluorine binding site 6 out
of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:10.8
occ:0.90
|
FAW
|
A:J0Y1102
|
0.0
|
10.8
|
0.9
|
CAF
|
A:J0Y1102
|
1.4
|
10.2
|
0.9
|
CAE
|
A:J0Y1102
|
2.4
|
7.9
|
0.9
|
CAA
|
A:J0Y1102
|
2.4
|
9.6
|
0.9
|
FAX
|
A:J0Y1102
|
2.7
|
7.9
|
0.9
|
FAV
|
A:J0Y1102
|
2.8
|
10.8
|
0.9
|
CG
|
A:GLU572
|
3.2
|
18.3
|
1.0
|
O
|
A:HOH1512
|
3.2
|
12.7
|
1.0
|
O
|
A:HOH1754
|
3.3
|
12.5
|
1.0
|
OE2
|
A:GLU572
|
3.4
|
19.6
|
1.0
|
CG2
|
A:THR305
|
3.5
|
9.5
|
1.0
|
O
|
A:GLU319
|
3.5
|
10.0
|
1.0
|
O
|
A:HOH1751
|
3.6
|
8.9
|
1.0
|
CD
|
A:GLU572
|
3.6
|
21.1
|
1.0
|
SD
|
A:MET1034
|
3.7
|
11.5
|
1.0
|
CAD
|
A:J0Y1102
|
3.7
|
7.5
|
0.9
|
CAB
|
A:J0Y1102
|
3.7
|
7.5
|
0.9
|
CAC
|
A:J0Y1102
|
4.2
|
7.9
|
0.9
|
CB
|
A:GLU572
|
4.2
|
18.2
|
1.0
|
C
|
A:GLU319
|
4.4
|
8.4
|
1.0
|
CE
|
A:MET1034
|
4.4
|
12.2
|
1.0
|
N
|
A:ALA320
|
4.4
|
8.9
|
1.0
|
CB
|
A:THR305
|
4.6
|
10.9
|
1.0
|
OE1
|
A:GLU572
|
4.6
|
21.5
|
1.0
|
CA
|
A:GLU572
|
4.7
|
17.9
|
1.0
|
|
Fluorine binding site 7 out
of 7 in 6ea1
Go back to
Fluorine Binding Sites List in 6ea1
Fluorine binding site 7 out
of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:7.9
occ:0.90
|
FAX
|
A:J0Y1102
|
0.0
|
7.9
|
0.9
|
CAE
|
A:J0Y1102
|
1.4
|
7.9
|
0.9
|
CAF
|
A:J0Y1102
|
2.4
|
10.2
|
0.9
|
CAD
|
A:J0Y1102
|
2.4
|
7.5
|
0.9
|
FAW
|
A:J0Y1102
|
2.7
|
10.8
|
0.9
|
CG
|
A:GLN317
|
3.3
|
8.2
|
1.0
|
O
|
A:HOH2102
|
3.5
|
10.6
|
1.0
|
CG2
|
A:THR305
|
3.5
|
9.5
|
1.0
|
ND2
|
A:ASN458
|
3.5
|
8.1
|
1.0
|
CAA
|
A:J0Y1102
|
3.7
|
9.6
|
0.9
|
SD
|
A:MET1034
|
3.7
|
11.5
|
1.0
|
CAC
|
A:J0Y1102
|
3.7
|
7.9
|
0.9
|
O
|
A:GLU319
|
3.9
|
10.0
|
1.0
|
O
|
A:HOH1754
|
3.9
|
12.5
|
1.0
|
CD
|
A:GLN317
|
4.1
|
9.9
|
1.0
|
NE2
|
A:GLN317
|
4.1
|
8.0
|
1.0
|
CB
|
A:ASN458
|
4.2
|
9.3
|
1.0
|
CE
|
A:MET1034
|
4.2
|
12.2
|
1.0
|
CAB
|
A:J0Y1102
|
4.2
|
7.5
|
0.9
|
O
|
A:LEU304
|
4.2
|
10.7
|
1.0
|
CG
|
A:ASN458
|
4.3
|
10.1
|
1.0
|
O
|
A:HOH1702
|
4.4
|
9.9
|
1.0
|
CB
|
A:GLN317
|
4.5
|
8.6
|
1.0
|
CB
|
A:THR305
|
4.7
|
10.9
|
1.0
|
FAV
|
A:J0Y1102
|
4.7
|
10.8
|
0.9
|
CAG
|
A:J0Y1102
|
4.8
|
7.2
|
0.9
|
|
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: Thu Aug 1 19:26:14 2024
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