Fluorine in PDB 6i4i: Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Mg-K-Adp-Alfn State
Protein crystallography data
The structure of Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Mg-K-Adp-Alfn State, PDB code: 6i4i
was solved by
E.-P.Kumpula,
A.J.Lopez,
L.Tajedin,
H.Han,
I.Kursula,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.05 /
1.90
|
Space group
|
P 21 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
68.610,
71.330,
109.250,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.9 /
21.7
|
Other elements in 6i4i:
The structure of Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Mg-K-Adp-Alfn State also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Mg-K-Adp-Alfn State
(pdb code 6i4i). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Mg-K-Adp-Alfn State, PDB code: 6i4i:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 6i4i
Go back to
Fluorine Binding Sites List in 6i4i
Fluorine binding site 1 out
of 3 in the Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Mg-K-Adp-Alfn State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Mg-K-Adp-Alfn State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:27.9
occ:1.00
|
F1
|
A:AF3402
|
0.0
|
27.9
|
1.0
|
AL
|
A:AF3402
|
1.6
|
28.4
|
1.0
|
MG
|
A:MG403
|
1.9
|
23.9
|
1.0
|
F3
|
A:AF3402
|
2.7
|
32.0
|
1.0
|
O3B
|
A:ADP401
|
2.7
|
24.4
|
1.0
|
F2
|
A:AF3402
|
2.7
|
33.6
|
1.0
|
O2B
|
A:ADP401
|
2.8
|
29.7
|
1.0
|
K
|
A:K404
|
2.8
|
29.0
|
0.7
|
O
|
A:HOH570
|
2.8
|
25.1
|
1.0
|
O
|
A:HOH518
|
2.8
|
24.4
|
1.0
|
O
|
A:HOH643
|
3.1
|
25.2
|
1.0
|
HA3
|
A:GLY157
|
3.1
|
28.1
|
1.0
|
O
|
A:HOH658
|
3.1
|
36.8
|
1.0
|
PB
|
A:ADP401
|
3.2
|
25.2
|
1.0
|
O
|
A:HOH567
|
3.4
|
34.6
|
1.0
|
H
|
A:SER15
|
4.0
|
28.6
|
1.0
|
HG12
|
A:VAL160
|
4.0
|
36.8
|
1.0
|
O3A
|
A:ADP401
|
4.0
|
26.7
|
1.0
|
HA2
|
A:GLY14
|
4.0
|
33.2
|
1.0
|
CA
|
A:GLY157
|
4.0
|
23.4
|
1.0
|
H
|
A:ASP158
|
4.2
|
32.9
|
1.0
|
O
|
A:HOH524
|
4.2
|
24.3
|
1.0
|
OE1
|
A:GLN138
|
4.3
|
28.2
|
1.0
|
HA2
|
A:GLY157
|
4.4
|
28.1
|
1.0
|
OD1
|
A:ASP155
|
4.4
|
38.6
|
1.0
|
HG
|
A:SER15
|
4.5
|
35.2
|
1.0
|
H
|
A:GLY157
|
4.5
|
27.5
|
1.0
|
O1B
|
A:ADP401
|
4.5
|
24.6
|
1.0
|
N
|
A:GLY157
|
4.6
|
22.9
|
1.0
|
H
|
A:GLY159
|
4.7
|
34.6
|
1.0
|
HG13
|
A:VAL160
|
4.7
|
36.8
|
1.0
|
HA3
|
A:GLY14
|
4.7
|
33.2
|
1.0
|
O2A
|
A:ADP401
|
4.7
|
30.6
|
1.0
|
CG1
|
A:VAL160
|
4.7
|
30.7
|
1.0
|
H
|
A:VAL160
|
4.7
|
40.6
|
1.0
|
N
|
A:SER15
|
4.7
|
23.8
|
1.0
|
O
|
A:HOH552
|
4.8
|
30.1
|
1.0
|
CA
|
A:GLY14
|
4.8
|
27.7
|
1.0
|
N
|
A:ASP158
|
4.8
|
27.4
|
1.0
|
O
|
A:VAL160
|
4.8
|
31.9
|
1.0
|
HB2
|
A:SER15
|
4.8
|
36.7
|
1.0
|
OD2
|
A:ASP155
|
4.9
|
35.2
|
1.0
|
PA
|
A:ADP401
|
5.0
|
25.0
|
1.0
|
C
|
A:GLY157
|
5.0
|
25.5
|
1.0
|
HE22
|
A:GLN138
|
5.0
|
36.4
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 6i4i
Go back to
Fluorine Binding Sites List in 6i4i
Fluorine binding site 2 out
of 3 in the Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Mg-K-Adp-Alfn State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Mg-K-Adp-Alfn State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:33.6
occ:1.00
|
F2
|
A:AF3402
|
0.0
|
33.6
|
1.0
|
AL
|
A:AF3402
|
1.6
|
28.4
|
1.0
|
HG
|
A:SER15
|
1.7
|
35.2
|
1.0
|
H
|
A:SER15
|
1.9
|
28.6
|
1.0
|
OG
|
A:SER15
|
2.4
|
29.3
|
1.0
|
O
|
A:HOH658
|
2.6
|
36.8
|
1.0
|
F3
|
A:AF3402
|
2.6
|
32.0
|
1.0
|
HB2
|
A:SER15
|
2.7
|
36.7
|
1.0
|
O2B
|
A:ADP401
|
2.7
|
29.7
|
1.0
|
N
|
A:SER15
|
2.7
|
23.8
|
1.0
|
F1
|
A:AF3402
|
2.7
|
27.9
|
1.0
|
CB
|
A:SER15
|
2.9
|
30.6
|
1.0
|
HA2
|
A:GLY75
|
3.0
|
30.7
|
1.0
|
HA2
|
A:GLY14
|
3.3
|
33.2
|
1.0
|
CA
|
A:SER15
|
3.4
|
25.5
|
1.0
|
HG12
|
A:VAL160
|
3.4
|
36.8
|
1.0
|
CA
|
A:GLY75
|
3.7
|
25.6
|
1.0
|
O
|
A:HOH567
|
3.7
|
34.6
|
1.0
|
HA3
|
A:GLY75
|
3.7
|
30.7
|
1.0
|
H
|
A:GLY159
|
3.7
|
34.6
|
1.0
|
H
|
A:GLY75
|
3.7
|
34.6
|
1.0
|
C
|
A:GLY14
|
3.8
|
27.2
|
1.0
|
PB
|
A:ADP401
|
3.8
|
25.2
|
1.0
|
HB3
|
A:SER15
|
3.8
|
36.7
|
1.0
|
N
|
A:GLY75
|
3.9
|
28.8
|
1.0
|
HA
|
A:SER15
|
3.9
|
30.6
|
1.0
|
CA
|
A:GLY14
|
3.9
|
27.7
|
1.0
|
O3B
|
A:ADP401
|
4.1
|
24.4
|
1.0
|
H
|
A:GLY16
|
4.2
|
30.9
|
1.0
|
O
|
A:HOH643
|
4.2
|
25.2
|
1.0
|
MG
|
A:MG403
|
4.2
|
23.9
|
1.0
|
CG1
|
A:VAL160
|
4.2
|
30.7
|
1.0
|
H
|
A:VAL160
|
4.3
|
40.6
|
1.0
|
HG11
|
A:VAL160
|
4.3
|
36.8
|
1.0
|
HA3
|
A:GLY14
|
4.3
|
33.2
|
1.0
|
H
|
A:ASP158
|
4.4
|
32.9
|
1.0
|
HA3
|
A:GLY159
|
4.4
|
37.0
|
1.0
|
O1B
|
A:ADP401
|
4.5
|
24.6
|
1.0
|
N
|
A:GLY159
|
4.5
|
28.8
|
1.0
|
HG22
|
A:ILE72
|
4.5
|
54.1
|
1.0
|
HA3
|
A:GLY157
|
4.6
|
28.1
|
1.0
|
C
|
A:SER15
|
4.6
|
24.7
|
1.0
|
HG21
|
A:ILE72
|
4.6
|
54.1
|
1.0
|
K
|
A:K404
|
4.6
|
29.0
|
0.7
|
N
|
A:GLY16
|
4.7
|
25.7
|
1.0
|
N
|
A:VAL160
|
4.7
|
33.8
|
1.0
|
O
|
A:ASN13
|
4.8
|
37.0
|
1.0
|
HG13
|
A:VAL160
|
4.8
|
36.8
|
1.0
|
C
|
A:HIS74
|
4.8
|
28.3
|
1.0
|
CA
|
A:GLY159
|
4.9
|
30.8
|
1.0
|
O
|
A:GLY14
|
4.9
|
27.4
|
1.0
|
HB3
|
A:ASP158
|
5.0
|
38.5
|
1.0
|
O3A
|
A:ADP401
|
5.0
|
26.7
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 6i4i
Go back to
Fluorine Binding Sites List in 6i4i
Fluorine binding site 3 out
of 3 in the Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Mg-K-Adp-Alfn State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Plasmodium Falciparum Actin I (F54Y Mutant) in the Mg-K-Adp-Alfn State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:32.0
occ:1.00
|
F3
|
A:AF3402
|
0.0
|
32.0
|
1.0
|
AL
|
A:AF3402
|
1.6
|
28.4
|
1.0
|
H
|
A:GLY159
|
2.1
|
34.6
|
1.0
|
H
|
A:VAL160
|
2.3
|
40.6
|
1.0
|
HA3
|
A:GLY157
|
2.4
|
28.1
|
1.0
|
O2B
|
A:ADP401
|
2.5
|
29.7
|
1.0
|
F2
|
A:AF3402
|
2.6
|
33.6
|
1.0
|
H
|
A:ASP158
|
2.6
|
32.9
|
1.0
|
F1
|
A:AF3402
|
2.7
|
27.9
|
1.0
|
HG12
|
A:VAL160
|
2.8
|
36.8
|
1.0
|
N
|
A:GLY159
|
2.9
|
28.8
|
1.0
|
N
|
A:ASP158
|
3.0
|
27.4
|
1.0
|
N
|
A:VAL160
|
3.1
|
33.8
|
1.0
|
CA
|
A:GLY157
|
3.2
|
23.4
|
1.0
|
K
|
A:K404
|
3.3
|
29.0
|
0.7
|
O
|
A:VAL160
|
3.3
|
31.9
|
1.0
|
C
|
A:GLY157
|
3.3
|
25.5
|
1.0
|
H
|
A:GLY157
|
3.4
|
27.5
|
1.0
|
HB2
|
A:SER15
|
3.4
|
36.7
|
1.0
|
HG
|
A:SER15
|
3.7
|
35.2
|
1.0
|
N
|
A:GLY157
|
3.7
|
22.9
|
1.0
|
CA
|
A:GLY159
|
3.7
|
30.8
|
1.0
|
CG1
|
A:VAL160
|
3.8
|
30.7
|
1.0
|
PB
|
A:ADP401
|
3.8
|
25.2
|
1.0
|
C
|
A:GLY159
|
3.8
|
31.2
|
1.0
|
C
|
A:ASP158
|
3.9
|
28.5
|
1.0
|
HA3
|
A:GLY159
|
3.9
|
37.0
|
1.0
|
CA
|
A:ASP158
|
3.9
|
28.9
|
1.0
|
HA2
|
A:GLY157
|
3.9
|
28.1
|
1.0
|
OG
|
A:SER15
|
4.0
|
29.3
|
1.0
|
CA
|
A:VAL160
|
4.0
|
31.1
|
1.0
|
HG13
|
A:VAL160
|
4.1
|
36.8
|
1.0
|
H
|
A:SER15
|
4.1
|
28.6
|
1.0
|
C
|
A:VAL160
|
4.1
|
30.5
|
1.0
|
O3A
|
A:ADP401
|
4.1
|
26.7
|
1.0
|
CB
|
A:SER15
|
4.1
|
30.6
|
1.0
|
HB3
|
A:ASP158
|
4.2
|
38.5
|
1.0
|
O
|
A:GLY157
|
4.3
|
26.1
|
1.0
|
O3B
|
A:ADP401
|
4.4
|
24.4
|
1.0
|
HG11
|
A:VAL160
|
4.4
|
36.8
|
1.0
|
CB
|
A:VAL160
|
4.5
|
32.1
|
1.0
|
HB1
|
A:ALA182
|
4.5
|
37.5
|
0.6
|
HB1
|
A:ALA182
|
4.5
|
37.5
|
0.5
|
MG
|
A:MG403
|
4.5
|
23.9
|
1.0
|
O
|
A:HOH567
|
4.5
|
34.6
|
1.0
|
O
|
A:HOH570
|
4.6
|
25.1
|
1.0
|
CB
|
A:ASP158
|
4.6
|
32.0
|
1.0
|
HA2
|
A:GLY159
|
4.6
|
37.0
|
1.0
|
HB
|
A:VAL160
|
4.7
|
38.6
|
1.0
|
O
|
A:HOH658
|
4.7
|
36.8
|
1.0
|
HB3
|
A:SER15
|
4.7
|
36.7
|
1.0
|
HA
|
A:ASP158
|
4.7
|
34.7
|
1.0
|
N
|
A:SER15
|
4.8
|
23.8
|
1.0
|
HA
|
A:VAL160
|
4.9
|
37.4
|
1.0
|
HB2
|
A:ASP158
|
4.9
|
38.5
|
1.0
|
O1B
|
A:ADP401
|
4.9
|
24.6
|
1.0
|
HB3
|
A:ALA182
|
4.9
|
37.5
|
0.6
|
HB3
|
A:ALA182
|
5.0
|
37.5
|
0.5
|
H
|
A:GLY16
|
5.0
|
30.9
|
1.0
|
HB2
|
A:ALA182
|
5.0
|
37.5
|
0.6
|
O
|
A:ASP158
|
5.0
|
26.7
|
1.0
|
|
Reference:
E.P.Kumpula,
A.J.Lopez,
L.Tajedin,
H.Han,
I.Kursula.
Atomic View Into Plasmodium Actin Polymerization, Atp Hydrolysis, and Fragmentation. Plos Biol. V. 17 00315 2019.
ISSN: ESSN 1545-7885
PubMed: 31199804
DOI: 10.1371/JOURNAL.PBIO.3000315
Page generated: Thu Aug 1 21:22:09 2024
|