Fluorine in PDB 6eaa: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6I) and Catalytic Zinc Ion
Protein crystallography data
The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6I) and Catalytic Zinc Ion, PDB code: 6eaa
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)
|
46.40 /
1.65
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.399,
108.850,
117.720,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.1 /
18.3
|
Other elements in 6eaa:
The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6I) 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 (6I) and Catalytic Zinc Ion
(pdb code 6eaa). 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 (6I) and Catalytic Zinc Ion, PDB code: 6eaa:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 6eaa
Go back to
Fluorine Binding Sites List in 6eaa
Fluorine binding site 1 out
of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6I) 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 (6I) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:15.6
occ:1.00
|
FAD
|
A:J1V1102
|
0.0
|
15.6
|
1.0
|
CAV
|
A:J1V1102
|
1.4
|
15.2
|
1.0
|
CBA
|
A:J1V1102
|
2.3
|
15.1
|
1.0
|
CAK
|
A:J1V1102
|
2.4
|
12.3
|
1.0
|
FAF
|
A:J1V1102
|
2.7
|
16.0
|
1.0
|
CG2
|
A:THR305
|
3.4
|
14.3
|
1.0
|
CG
|
A:GLN317
|
3.4
|
11.8
|
1.0
|
O
|
A:HOH2181
|
3.5
|
13.1
|
1.0
|
ND2
|
A:ASN458
|
3.5
|
13.7
|
1.0
|
CAW
|
A:J1V1102
|
3.6
|
14.4
|
1.0
|
SD
|
A:MET1034
|
3.7
|
16.8
|
1.0
|
CAY
|
A:J1V1102
|
3.7
|
12.8
|
1.0
|
O
|
A:HOH1778
|
3.9
|
14.9
|
1.0
|
O
|
A:GLU319
|
4.0
|
12.2
|
1.0
|
O
|
A:LEU304
|
4.2
|
13.2
|
1.0
|
CAL
|
A:J1V1102
|
4.2
|
14.1
|
1.0
|
NE2
|
A:GLN317
|
4.2
|
9.7
|
1.0
|
CD
|
A:GLN317
|
4.2
|
11.9
|
1.0
|
CB
|
A:ASN458
|
4.2
|
12.4
|
1.0
|
CE
|
A:MET1034
|
4.3
|
17.4
|
1.0
|
CG
|
A:ASN458
|
4.4
|
12.4
|
1.0
|
O
|
A:HOH1741
|
4.5
|
12.0
|
1.0
|
CB
|
A:THR305
|
4.6
|
14.8
|
1.0
|
CB
|
A:GLN317
|
4.6
|
11.8
|
1.0
|
FAE
|
A:J1V1102
|
4.7
|
15.5
|
1.0
|
CAX
|
A:J1V1102
|
4.8
|
13.1
|
1.0
|
CA
|
A:THR305
|
4.9
|
14.0
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 6eaa
Go back to
Fluorine Binding Sites List in 6eaa
Fluorine binding site 2 out
of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6I) 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 (6I) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:16.0
occ:1.00
|
FAF
|
A:J1V1102
|
0.0
|
16.0
|
1.0
|
CBA
|
A:J1V1102
|
1.4
|
15.1
|
1.0
|
CAV
|
A:J1V1102
|
2.4
|
15.2
|
1.0
|
CAW
|
A:J1V1102
|
2.4
|
14.4
|
1.0
|
FAE
|
A:J1V1102
|
2.7
|
15.5
|
1.0
|
FAD
|
A:J1V1102
|
2.7
|
15.6
|
1.0
|
O
|
A:HOH1387
|
3.2
|
17.1
|
1.0
|
CG
|
A:GLU572
|
3.2
|
23.0
|
1.0
|
OE2
|
A:GLU572
|
3.3
|
22.0
|
1.0
|
O
|
A:HOH1778
|
3.4
|
14.9
|
1.0
|
CG2
|
A:THR305
|
3.5
|
14.3
|
1.0
|
CD
|
A:GLU572
|
3.5
|
24.5
|
1.0
|
O
|
A:HOH1707
|
3.5
|
14.7
|
1.0
|
O
|
A:GLU319
|
3.6
|
12.2
|
1.0
|
CAK
|
A:J1V1102
|
3.7
|
12.3
|
1.0
|
CAL
|
A:J1V1102
|
3.7
|
14.1
|
1.0
|
SD
|
A:MET1034
|
3.8
|
16.8
|
1.0
|
CAY
|
A:J1V1102
|
4.2
|
12.8
|
1.0
|
CB
|
A:GLU572
|
4.2
|
21.5
|
1.0
|
N
|
A:ALA320
|
4.4
|
11.3
|
1.0
|
C
|
A:GLU319
|
4.4
|
11.6
|
1.0
|
CE
|
A:MET1034
|
4.5
|
17.4
|
1.0
|
OE1
|
A:GLU572
|
4.5
|
26.1
|
1.0
|
CB
|
A:THR305
|
4.6
|
14.8
|
1.0
|
CA
|
A:GLU572
|
4.7
|
20.9
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 6eaa
Go back to
Fluorine Binding Sites List in 6eaa
Fluorine binding site 3 out
of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6I) 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 (6I) and Catalytic Zinc Ion within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1102
b:15.5
occ:1.00
|
FAE
|
A:J1V1102
|
0.0
|
15.5
|
1.0
|
CAW
|
A:J1V1102
|
1.3
|
14.4
|
1.0
|
CBA
|
A:J1V1102
|
2.3
|
15.1
|
1.0
|
CAL
|
A:J1V1102
|
2.4
|
14.1
|
1.0
|
FAF
|
A:J1V1102
|
2.7
|
16.0
|
1.0
|
O
|
A:HOH1707
|
3.2
|
14.7
|
1.0
|
N
|
A:ALA320
|
3.4
|
11.3
|
1.0
|
CA
|
A:GLU572
|
3.5
|
20.9
|
1.0
|
CAV
|
A:J1V1102
|
3.6
|
15.2
|
1.0
|
CG
|
A:GLU572
|
3.6
|
23.0
|
1.0
|
CAY
|
A:J1V1102
|
3.6
|
12.8
|
1.0
|
CE2
|
A:TYR575
|
3.7
|
11.7
|
1.0
|
O
|
A:GLU319
|
3.8
|
12.2
|
1.0
|
O
|
A:MET571
|
3.9
|
23.4
|
1.0
|
N
|
A:GLU572
|
4.0
|
21.5
|
1.0
|
C
|
A:GLU319
|
4.0
|
11.6
|
1.0
|
CB
|
A:GLU572
|
4.0
|
21.5
|
1.0
|
CD2
|
A:TYR575
|
4.1
|
13.3
|
1.0
|
CAK
|
A:J1V1102
|
4.1
|
12.3
|
1.0
|
C
|
A:MET571
|
4.1
|
20.2
|
1.0
|
CB
|
A:ALA320
|
4.1
|
12.2
|
1.0
|
CA
|
A:ALA320
|
4.4
|
11.6
|
1.0
|
CZ
|
A:TYR575
|
4.4
|
10.8
|
1.0
|
CE
|
A:MET1034
|
4.5
|
17.4
|
1.0
|
C
|
A:GLU572
|
4.6
|
26.0
|
1.0
|
FAD
|
A:J1V1102
|
4.7
|
15.6
|
1.0
|
O
|
A:GLU572
|
4.7
|
30.2
|
1.0
|
CD
|
A:GLU572
|
4.8
|
24.5
|
1.0
|
SD
|
A:MET1034
|
4.8
|
16.8
|
1.0
|
O
|
A:HOH1387
|
4.8
|
17.1
|
1.0
|
CAX
|
A:J1V1102
|
4.8
|
13.1
|
1.0
|
CB
|
A:MET571
|
4.8
|
22.4
|
1.0
|
OH
|
A:TYR575
|
4.8
|
13.0
|
1.0
|
CG
|
A:TYR575
|
4.9
|
12.6
|
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 12:49:02 2020
|