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Fluorine in PDB 5i0h: Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke State

Protein crystallography data

The structure of Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke State, PDB code: 5i0h was solved by T.Isabet, F.Blanc, H.L.Sweeney, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.35 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 76.480, 78.300, 78.670, 75.69, 86.38, 76.12
R / Rfree (%) 16.5 / 19

Other elements in 5i0h:

The structure of Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke State also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke State (pdb code 5i0h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke State, PDB code: 5i0h:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5i0h

Go back to Fluorine Binding Sites List in 5i0h
Fluorine binding site 1 out of 6 in the Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke 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 Myosin X Motor Domain in Pre-Powerstroke State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:20.7
occ:1.00
 F1 A:BEF803 0.0 20.7 1.0
BE A:BEF803 1.6 21.2 1.0
F2 A:BEF803 2.5 20.2 1.0
F3 A:BEF803 2.6 18.4 1.0
O3B A:ADP801 2.6 17.9 1.0
N A:GLY437 2.8 20.2 1.0
NZ A:LYS163 2.8 19.3 1.0
O A:HOH1006 2.9 24.7 1.0
CA A:GLY437 3.2 19.3 1.0
CA A:SER159 3.3 16.3 1.0
CE A:LYS163 3.4 18.2 1.0
PB A:ADP801 3.6 18.9 1.0
CB A:SER159 3.8 17.6 1.0
C A:PHE436 3.9 21.7 1.0
O1B A:ADP801 3.9 17.7 1.0
O A:HOH909 4.0 16.9 1.0
OG A:SER159 4.0 18.5 1.0
O2B A:ADP801 4.0 17.7 1.0
N A:SER159 4.0 17.2 1.0
N A:GLY160 4.1 19.6 1.0
MG A:MG802 4.1 20.4 1.0
O A:HOH921 4.1 25.4 1.0
O A:GLU158 4.2 17.8 1.0
CA A:PHE436 4.2 18.0 1.0
C A:SER159 4.2 20.3 1.0
C A:GLY437 4.2 21.6 1.0
O A:ILE435 4.4 21.3 1.0
C A:GLU158 4.4 18.2 1.0
O A:GLY437 4.5 20.5 1.0
CD A:LYS163 4.9 19.1 1.0
O A:GLY157 4.9 19.3 1.0
O A:PHE436 4.9 20.7 1.0
OG A:SER218 4.9 20.2 1.0
N A:SER219 5.0 17.2 1.0
O3A A:ADP801 5.0 18.5 1.0

Fluorine binding site 2 out of 6 in 5i0h

Go back to Fluorine Binding Sites List in 5i0h
Fluorine binding site 2 out of 6 in the Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke 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 Myosin X Motor Domain in Pre-Powerstroke State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:20.2
occ:1.00
 F2 A:BEF803 0.0 20.2 1.0
BE A:BEF803 1.6 21.2 1.0
MG A:MG802 2.0 20.4 1.0
F1 A:BEF803 2.5 20.7 1.0
F3 A:BEF803 2.5 18.4 1.0
O3B A:ADP801 2.6 17.9 1.0
OG A:SER219 2.9 18.7 1.0
N A:SER219 2.9 17.2 1.0
O A:HOH909 2.9 16.9 1.0
O A:HOH1073 3.0 16.8 1.0
O2B A:ADP801 3.0 17.7 1.0
O A:HOH1006 3.1 24.7 1.0
CB A:SER219 3.2 18.0 1.0
PB A:ADP801 3.3 18.9 1.0
CA A:SER219 3.6 16.0 1.0
C A:SER218 3.9 20.6 1.0
ND2 A:ASN215 4.0 17.2 1.0
CA A:SER218 4.0 16.3 1.0
OG1 A:THR164 4.1 16.5 1.0
O A:SER219 4.3 19.5 1.0
OG A:SER218 4.3 20.2 1.0
O1B A:ADP801 4.4 17.7 1.0
O3A A:ADP801 4.5 18.5 1.0
C A:SER219 4.5 18.6 1.0
O A:ASN217 4.5 19.2 1.0
NZ A:LYS163 4.6 19.3 1.0
N A:GLY437 4.6 20.2 1.0
O A:ILE435 4.7 21.3 1.0
CE A:LYS163 4.7 18.2 1.0
CA A:PHE436 4.7 18.0 1.0
CB A:SER218 4.8 18.0 1.0
O2A A:ADP801 4.8 17.5 1.0

Fluorine binding site 3 out of 6 in 5i0h

Go back to Fluorine Binding Sites List in 5i0h
Fluorine binding site 3 out of 6 in the Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke 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 Myosin X Motor Domain in Pre-Powerstroke State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:18.4
occ:1.00
 F3 A:BEF803 0.0 18.4 1.0
BE A:BEF803 1.6 21.2 1.0
F2 A:BEF803 2.5 20.2 1.0
F1 A:BEF803 2.6 20.7 1.0
O3B A:ADP801 2.6 17.9 1.0
OG A:SER159 2.6 18.5 1.0
O A:HOH1006 2.8 24.7 1.0
OG A:SER218 3.0 20.2 1.0
ND2 A:ASN215 3.2 17.2 1.0
CA A:SER218 3.4 16.3 1.0
CB A:SER218 3.4 18.0 1.0
CB A:SER159 3.4 17.6 1.0
CA A:SER159 3.6 16.3 1.0
N A:GLY160 3.7 19.6 1.0
CB A:ASN215 3.7 17.2 1.0
N A:SER219 3.8 17.2 1.0
CG A:ASN215 3.9 22.3 1.0
C A:SER159 4.0 20.3 1.0
PB A:ADP801 4.0 18.9 1.0
C A:SER218 4.1 20.6 1.0
O A:HOH921 4.3 25.4 1.0
MG A:MG802 4.4 20.4 1.0
N A:SER218 4.5 17.5 1.0
O A:HOH1073 4.5 16.8 1.0
O2B A:ADP801 4.6 17.7 1.0
O A:HOH1004 4.6 24.7 1.0
CA A:GLY160 4.7 19.8 1.0
O3A A:ADP801 4.8 18.5 1.0
N A:GLY437 4.8 20.2 1.0
N A:SER159 4.9 17.2 1.0
O A:ASN217 4.9 19.2 1.0
O A:SER219 5.0 19.5 1.0
CA A:SER219 5.0 16.0 1.0
O1B A:ADP801 5.0 17.7 1.0

Fluorine binding site 4 out of 6 in 5i0h

Go back to Fluorine Binding Sites List in 5i0h
Fluorine binding site 4 out of 6 in the Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:22.0
occ:1.00
 F1 B:BEF803 0.0 22.0 1.0
BE B:BEF803 1.5 22.3 1.0
F2 B:BEF803 2.5 19.9 1.0
F3 B:BEF803 2.6 22.3 1.0
O1B B:ADP801 2.6 22.7 1.0
N B:GLY437 2.7 20.4 1.0
NZ B:LYS163 2.8 23.0 1.0
O B:HOH1002 2.9 24.6 1.0
CA B:GLY437 3.2 20.9 1.0
CA B:SER159 3.3 19.0 1.0
CE B:LYS163 3.4 19.2 1.0
PB B:ADP801 3.6 20.6 1.0
C B:PHE436 3.9 23.7 1.0
CB B:SER159 3.9 22.7 1.0
O2B B:ADP801 3.9 20.0 1.0
O B:HOH910 3.9 19.2 1.0
O3B B:ADP801 4.0 19.1 1.0
OG B:SER159 4.0 21.6 1.0
N B:SER159 4.0 20.1 1.0
MG B:MG802 4.0 22.0 1.0
N B:GLY160 4.1 21.3 1.0
O B:HOH914 4.2 30.4 1.0
CA B:PHE436 4.2 19.4 1.0
O B:GLU158 4.2 22.6 1.0
C B:GLY437 4.3 23.5 1.0
C B:SER159 4.3 23.3 1.0
O B:ILE435 4.3 20.3 0.5
O B:ILE435 4.4 23.4 0.5
C B:GLU158 4.4 23.7 1.0
O B:GLY437 4.5 23.3 1.0
CD B:LYS163 4.9 19.0 1.0
OG B:SER218 4.9 23.4 1.0
O B:PHE436 4.9 22.0 1.0
N B:SER219 5.0 19.0 1.0
O B:GLY157 5.0 22.6 1.0
O3A B:ADP801 5.0 20.0 1.0

Fluorine binding site 5 out of 6 in 5i0h

Go back to Fluorine Binding Sites List in 5i0h
Fluorine binding site 5 out of 6 in the Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:19.9
occ:1.00
 F2 B:BEF803 0.0 19.9 1.0
BE B:BEF803 1.5 22.3 1.0
MG B:MG802 2.0 22.0 1.0
F1 B:BEF803 2.5 22.0 1.0
F3 B:BEF803 2.5 22.3 1.0
O1B B:ADP801 2.6 22.7 1.0
OG B:SER219 2.9 21.2 1.0
N B:SER219 2.9 19.0 1.0
O B:HOH910 2.9 19.2 1.0
O3B B:ADP801 3.0 19.1 1.0
O B:HOH963 3.0 19.5 1.0
O B:HOH1002 3.1 24.6 1.0
CB B:SER219 3.2 20.1 1.0
PB B:ADP801 3.4 20.6 1.0
CA B:SER219 3.6 18.1 1.0
C B:SER218 3.9 21.8 1.0
ND2 B:ASN215 4.0 18.8 1.0
CA B:SER218 4.0 18.6 1.0
OG1 B:THR164 4.1 19.5 1.0
OG B:SER218 4.3 23.4 1.0
O B:SER219 4.3 20.7 1.0
O2B B:ADP801 4.4 20.0 1.0
C B:SER219 4.5 21.2 1.0
O3A B:ADP801 4.5 20.0 1.0
N B:GLY437 4.5 20.4 1.0
O B:ASN217 4.6 22.3 1.0
NZ B:LYS163 4.6 23.0 1.0
O B:ILE435 4.7 23.4 0.5
CB B:SER218 4.7 21.7 1.0
CE B:LYS163 4.7 19.2 1.0
O B:ILE435 4.7 20.3 0.5
CA B:PHE436 4.7 19.4 1.0
O1A B:ADP801 4.8 19.7 1.0

Fluorine binding site 6 out of 6 in 5i0h

Go back to Fluorine Binding Sites List in 5i0h
Fluorine binding site 6 out of 6 in the Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Myosin X Motor Domain in Pre-Powerstroke State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:22.3
occ:1.00
 F3 B:BEF803 0.0 22.3 1.0
BE B:BEF803 1.6 22.3 1.0
F2 B:BEF803 2.5 19.9 1.0
F1 B:BEF803 2.6 22.0 1.0
O1B B:ADP801 2.6 22.7 1.0
OG B:SER159 2.6 21.6 1.0
O B:HOH1002 3.0 24.6 1.0
OG B:SER218 3.0 23.4 1.0
ND2 B:ASN215 3.2 18.8 1.0
CA B:SER218 3.4 18.6 1.0
CB B:SER218 3.4 21.7 1.0
CB B:SER159 3.4 22.7 1.0
CA B:SER159 3.5 19.0 1.0
N B:GLY160 3.6 21.3 1.0
CB B:ASN215 3.7 22.7 1.0
N B:SER219 3.8 19.0 1.0
CG B:ASN215 3.9 25.3 1.0
C B:SER159 4.0 23.3 1.0
PB B:ADP801 4.0 20.6 1.0
C B:SER218 4.1 21.8 1.0
MG B:MG802 4.4 22.0 1.0
O B:HOH914 4.4 30.4 1.0
N B:SER218 4.5 20.4 1.0
O B:HOH963 4.5 19.5 1.0
O3B B:ADP801 4.6 19.1 1.0
O B:HOH925 4.6 23.4 1.0
CA B:GLY160 4.7 21.4 1.0
O3A B:ADP801 4.8 20.0 1.0
N B:GLY437 4.8 20.4 1.0
N B:SER159 4.9 20.1 1.0
O B:ASN217 4.9 22.3 1.0
O2B B:ADP801 5.0 20.0 1.0

Reference:

V.Ropars, Z.Yang, T.Isabet, F.Blanc, K.Zhou, T.Lin, X.Liu, P.Hissier, F.Samazan, B.Amigues, E.D.Yang, H.Park, O.Pylypenko, M.Cecchini, C.V.Sindelar, H.L.Sweeney, A.Houdusse. The Myosin X Motor Is Optimized For Movement on Actin Bundles. Nat Commun V. 7 12456 2016.
ISSN: ESSN 2041-1723
PubMed: 27580874
DOI: 10.1038/NCOMMS12456
Page generated: Thu Aug 1 10:03:53 2024

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