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:

Magnesium (Mg) 1 atom
Aluminium (Al) 1 atom
Potassium (K) 2 atoms
Calcium (Ca) 2 atoms

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: Sun Dec 13 12:54:00 2020

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