Atomistry » Fluorine » PDB 5y6d-5zab » 5yew
Atomistry »
  Fluorine »
    PDB 5y6d-5zab »
      5yew »

Fluorine in PDB 5yew: Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion

Protein crystallography data

The structure of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion, PDB code: 5yew was solved by L.Yan, Y.Qi, X.Huang, C.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 207.942, 207.942, 107.893, 90.00, 90.00, 120.00
R / Rfree (%) 22.3 / 25.7

Other elements in 5yew:

The structure of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Potassium (K) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion (pdb code 5yew). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion, PDB code: 5yew:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5yew

Go back to Fluorine Binding Sites List in 5yew
Fluorine binding site 1 out of 9 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:69.9
occ:1.00
 F1 A:BEF802 0.0 69.9 1.0
BE A:BEF802 1.8 59.7 1.0
O1B A:GDP801 2.4 89.9 1.0
OG1 A:THR109 2.5 61.8 1.0
MG A:MG804 2.6 52.4 1.0
O3B A:GDP801 2.7 65.9 1.0
N A:THR109 2.8 57.1 1.0
CB A:THR109 2.9 61.2 1.0
PB A:GDP801 3.0 78.6 1.0
F3 A:BEF802 3.0 64.5 1.0
F2 A:BEF802 3.0 53.5 1.0
CA A:THR109 3.3 57.4 1.0
O3A A:GDP801 3.4 75.3 1.0
C A:ILE108 3.9 61.4 1.0
N A:ILE108 4.0 63.4 1.0
O A:THR109 4.1 56.2 1.0
OG A:SER89 4.1 65.3 1.0
CB A:ILE108 4.1 64.0 1.0
K A:K803 4.1 70.3 1.0
C A:THR109 4.2 53.7 1.0
CA A:ILE108 4.2 63.7 1.0
CG2 A:THR109 4.3 64.9 1.0
O2B A:GDP801 4.4 45.1 1.0
CG2 A:ILE108 4.4 73.9 1.0
O A:SER179 4.4 70.8 1.0
CA A:PRO180 4.9 57.9 1.0
NZ A:LYS88 4.9 73.3 1.0
N A:GLY181 4.9 71.5 1.0
O A:ILE108 5.0 69.0 1.0
PA A:GDP801 5.0 65.0 1.0

Fluorine binding site 2 out of 9 in 5yew

Go back to Fluorine Binding Sites List in 5yew
Fluorine binding site 2 out of 9 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:53.5
occ:1.00
 F2 A:BEF802 0.0 53.5 1.0
BE A:BEF802 1.8 59.7 1.0
N A:GLY181 2.8 71.5 1.0
O3B A:GDP801 2.9 65.9 1.0
F1 A:BEF802 3.0 69.9 1.0
F3 A:BEF802 3.1 64.5 1.0
CA A:GLY181 3.1 70.4 1.0
CG2 A:THR84 3.4 61.6 1.0
CA A:THR84 3.6 57.2 1.0
C A:PRO180 3.8 67.9 1.0
CB A:THR84 3.8 58.0 1.0
OG1 A:THR84 3.8 62.6 1.0
NZ A:LYS88 3.9 73.3 1.0
PB A:GDP801 4.0 78.6 1.0
ND1 A:HIS107 4.0 56.5 1.0
O1B A:GDP801 4.2 89.9 1.0
CA A:PRO180 4.2 57.9 1.0
N A:SER85 4.4 59.9 1.0
CE A:LYS88 4.5 69.8 1.0
N A:THR84 4.5 57.8 1.0
C A:THR84 4.5 55.4 1.0
C A:GLY181 4.6 75.7 1.0
CE1 A:HIS107 4.6 61.0 1.0
O A:PRO180 4.7 83.4 1.0
O A:ARG83 4.7 64.4 1.0
O A:THR109 4.8 56.2 1.0
N A:ILE108 4.9 63.4 1.0
K A:K803 4.9 70.3 1.0
O2B A:GDP801 4.9 45.1 1.0
N A:THR109 4.9 57.1 1.0
C A:ARG83 4.9 61.5 1.0
O A:SER179 5.0 70.8 1.0
CB A:PRO180 5.0 53.6 1.0

Fluorine binding site 3 out of 9 in 5yew

Go back to Fluorine Binding Sites List in 5yew
Fluorine binding site 3 out of 9 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:64.5
occ:1.00
 F3 A:BEF802 0.0 64.5 1.0
BE A:BEF802 1.8 59.7 1.0
K A:K803 2.2 70.3 1.0
O3B A:GDP801 2.5 65.9 1.0
O A:GLY106 2.7 48.5 1.0
N A:ILE108 2.9 63.4 1.0
F1 A:BEF802 3.0 69.9 1.0
F2 A:BEF802 3.1 53.5 1.0
CG2 A:THR84 3.3 61.6 1.0
CA A:HIS107 3.3 50.8 1.0
C A:HIS107 3.6 58.4 1.0
C A:GLY106 3.7 49.1 1.0
PB A:GDP801 3.8 78.6 1.0
OG A:SER85 3.9 68.9 1.0
O3A A:GDP801 3.9 75.3 1.0
CA A:ILE108 3.9 63.7 1.0
CB A:ILE108 3.9 64.0 1.0
N A:HIS107 4.0 48.8 1.0
N A:SER85 4.2 59.9 1.0
N A:THR109 4.3 57.1 1.0
O A:GLY104 4.5 60.5 1.0
O1B A:GDP801 4.5 89.9 1.0
CB A:HIS107 4.5 48.5 1.0
CB A:THR84 4.6 58.0 1.0
ND1 A:HIS107 4.6 56.5 1.0
C A:ILE108 4.6 61.4 1.0
CA A:THR84 4.7 57.2 1.0
C A:THR84 4.7 55.4 1.0
CG1 A:ILE108 4.7 63.1 1.0
O A:HIS107 4.8 63.6 1.0
CA A:SER85 4.8 60.4 1.0
CG A:HIS107 4.8 54.1 1.0
CD1 A:ILE108 4.9 60.5 1.0
CB A:SER85 5.0 65.2 1.0
O2B A:GDP801 5.0 45.1 1.0

Fluorine binding site 4 out of 9 in 5yew

Go back to Fluorine Binding Sites List in 5yew
Fluorine binding site 4 out of 9 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:99.4
occ:1.00
 F1 B:BEF802 0.0 99.4 1.0
BE B:BEF802 1.7 76.0 1.0
K B:K803 2.2 78.7 1.0
O3B B:GDP801 2.5 73.5 1.0
F3 B:BEF802 3.0 1.0 1.0
F2 B:BEF802 3.0 76.3 1.0
CG2 B:THR84 3.1 62.3 1.0
O B:GLY106 3.3 62.1 1.0
N B:ILE108 3.5 68.5 1.0
PB B:GDP801 3.7 66.2 1.0
N B:SER85 3.7 63.8 1.0
OG B:SER85 3.9 70.2 1.0
CA B:HIS107 3.9 65.0 1.0
O2B B:GDP801 4.0 57.1 1.0
CA B:THR84 4.1 62.4 1.0
CB B:THR84 4.2 62.7 1.0
C B:HIS107 4.2 67.5 1.0
C B:THR84 4.2 58.0 1.0
MG B:MG804 4.3 46.2 1.0
C B:GLY106 4.3 63.3 1.0
O3A B:GDP801 4.3 61.7 1.0
OG1 B:THR109 4.4 88.1 1.0
CA B:SER85 4.4 68.4 1.0
CB B:ILE108 4.5 79.4 1.0
CA B:ILE108 4.5 77.5 1.0
N B:THR109 4.5 76.0 1.0
N B:HIS107 4.5 67.6 1.0
O1A B:GDP801 4.8 63.5 1.0
CB B:SER85 4.8 70.9 1.0
ND1 B:HIS107 4.8 78.1 1.0
O B:GLY104 4.8 60.9 1.0
O1B B:GDP801 4.9 87.4 1.0
OG1 B:THR84 4.9 58.3 1.0
CB B:HIS107 5.0 61.6 1.0

Fluorine binding site 5 out of 9 in 5yew

Go back to Fluorine Binding Sites List in 5yew
Fluorine binding site 5 out of 9 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:76.3
occ:1.00
 F2 B:BEF802 0.0 76.3 1.0
BE B:BEF802 1.7 76.0 1.0
NZ B:LYS88 2.6 79.5 1.0
F1 B:BEF802 3.0 99.4 1.0
F3 B:BEF802 3.0 1.0 1.0
N B:GLY181 3.1 70.1 1.0
O3B B:GDP801 3.1 73.5 1.0
O2B B:GDP801 3.1 57.1 1.0
CE B:LYS88 3.2 79.2 1.0
CA B:GLY181 3.3 71.0 1.0
PB B:GDP801 3.5 66.2 1.0
CA B:THR84 3.7 62.4 1.0
C B:PRO180 3.7 69.3 1.0
OG1 B:THR109 3.9 88.1 1.0
O B:ARG83 3.9 74.1 1.0
MG B:MG804 3.9 46.2 1.0
N B:SER85 4.0 63.8 1.0
CG2 B:THR84 4.2 62.3 1.0
O1B B:GDP801 4.2 87.4 1.0
O B:SER179 4.3 58.0 1.0
CA B:PRO180 4.3 68.5 1.0
O B:PRO180 4.4 70.4 1.0
N B:THR84 4.4 67.7 1.0
CB B:THR84 4.4 62.7 1.0
C B:THR84 4.4 58.0 1.0
C B:ARG83 4.4 70.2 1.0
OG1 B:THR84 4.6 58.3 1.0
CD B:LYS88 4.7 73.8 1.0
C B:GLY181 4.8 72.4 1.0
K B:K803 4.8 78.7 1.0
O3A B:GDP801 4.9 61.7 1.0

Fluorine binding site 6 out of 9 in 5yew

Go back to Fluorine Binding Sites List in 5yew
Fluorine binding site 6 out of 9 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:1.0
occ:1.00
 F3 B:BEF802 0.0 1.0 1.0
BE B:BEF802 1.8 76.0 1.0
ND1 B:HIS107 2.8 78.1 1.0
F1 B:BEF802 3.0 99.4 1.0
F2 B:BEF802 3.0 76.3 1.0
CE1 B:HIS107 3.1 79.8 1.0
O B:THR109 3.2 74.5 1.0
N B:GLY181 3.4 70.1 1.0
N B:THR109 3.5 76.0 1.0
OG1 B:THR109 3.5 88.1 1.0
N B:ILE108 3.6 68.5 1.0
CG B:HIS107 3.8 67.3 1.0
CA B:PRO180 3.9 68.5 1.0
C B:THR109 3.9 77.4 1.0
CA B:THR109 4.0 75.6 1.0
C B:PRO180 4.1 69.3 1.0
C B:ILE108 4.1 80.8 1.0
NE2 B:HIS107 4.2 77.9 1.0
CA B:HIS107 4.2 65.0 1.0
CG2 B:THR84 4.2 62.3 1.0
CB B:THR109 4.2 78.8 1.0
CB B:PRO180 4.3 66.9 1.0
CA B:GLY181 4.3 71.0 1.0
C B:HIS107 4.3 67.5 1.0
O3B B:GDP801 4.3 73.5 1.0
CA B:ILE108 4.5 77.5 1.0
CB B:HIS107 4.5 61.6 1.0
CD2 B:HIS107 4.5 69.9 1.0
MG B:MG804 4.7 46.2 1.0
O B:ILE108 4.9 0.3 1.0
OG1 B:THR84 5.0 58.3 1.0

Fluorine binding site 7 out of 9 in 5yew

Go back to Fluorine Binding Sites List in 5yew
Fluorine binding site 7 out of 9 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F802

b:48.9
occ:1.00
 F1 C:BEF802 0.0 48.9 1.0
BE C:BEF802 1.8 57.3 1.0
O3B C:GDP801 2.4 60.1 1.0
K C:K803 2.6 65.5 1.0
F2 C:BEF802 3.0 70.1 1.0
F3 C:BEF802 3.1 68.2 1.0
N C:ILE108 3.2 51.9 1.0
MG C:MG804 3.2 37.4 1.0
N C:THR109 3.5 51.5 1.0
PB C:GDP801 3.7 60.2 1.0
CA C:ILE108 3.9 53.4 1.0
CB C:ILE108 3.9 53.2 1.0
O C:GLY106 4.0 45.0 1.0
OG1 C:THR109 4.0 47.4 1.0
CG2 C:THR84 4.0 44.9 1.0
O1B C:GDP801 4.1 77.8 1.0
C C:ILE108 4.2 54.2 1.0
C C:HIS107 4.2 48.8 1.0
CA C:HIS107 4.2 44.4 1.0
O3A C:GDP801 4.2 57.8 1.0
CB C:THR109 4.4 49.8 1.0
O1A C:GDP801 4.5 68.0 1.0
CA C:THR109 4.5 48.2 1.0
N C:SER85 4.6 47.8 1.0
ND1 C:HIS107 4.7 45.6 1.0
CG2 C:ILE108 4.8 60.2 1.0
O C:THR109 4.9 49.0 1.0
C C:GLY106 4.9 46.2 1.0
OG C:SER85 4.9 58.5 1.0
CA C:THR84 5.0 47.3 1.0
O2B C:GDP801 5.0 56.4 1.0

Fluorine binding site 8 out of 9 in 5yew

Go back to Fluorine Binding Sites List in 5yew
Fluorine binding site 8 out of 9 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F802

b:70.1
occ:1.00
 F2 C:BEF802 0.0 70.1 1.0
BE C:BEF802 1.7 57.3 1.0
O3B C:GDP801 2.5 60.1 1.0
NZ C:LYS88 2.5 77.6 1.0
N C:GLY181 2.9 53.7 1.0
F1 C:BEF802 3.0 48.9 1.0
F3 C:BEF802 3.0 68.2 1.0
CE C:LYS88 3.1 66.1 1.0
CA C:GLY181 3.1 54.9 1.0
C C:PRO180 3.5 52.3 1.0
PB C:GDP801 3.6 60.2 1.0
CA C:THR84 3.7 47.3 1.0
MG C:MG804 3.8 37.4 1.0
O C:ARG83 3.9 49.2 1.0
O2B C:GDP801 4.1 56.4 1.0
CA C:PRO180 4.1 48.5 1.0
O1B C:GDP801 4.1 77.8 1.0
O C:PRO180 4.2 59.6 1.0
N C:SER85 4.2 47.8 1.0
O C:SER179 4.2 44.5 1.0
CG2 C:THR84 4.3 44.9 1.0
N C:THR84 4.4 49.8 1.0
CB C:THR84 4.4 45.4 1.0
C C:ARG83 4.5 53.5 1.0
C C:THR84 4.5 46.4 1.0
CD C:LYS88 4.6 61.4 1.0
OG1 C:THR84 4.6 43.0 1.0
C C:GLY181 4.7 59.0 1.0
K C:K803 4.8 65.5 1.0
O C:GLY82 4.9 59.5 1.0
O3A C:GDP801 4.9 57.8 1.0

Fluorine binding site 9 out of 9 in 5yew

Go back to Fluorine Binding Sites List in 5yew
Fluorine binding site 9 out of 9 in the Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structural Basis For Gtp Hydrolysis and Conformational Change of Mitofusin 1 in Mediating Mitochondrial Fusion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F802

b:68.2
occ:1.00
 F3 C:BEF802 0.0 68.2 1.0
BE C:BEF802 1.8 57.3 1.0
ND1 C:HIS107 2.6 45.6 1.0
F2 C:BEF802 3.0 70.1 1.0
CG2 C:THR84 3.1 44.9 1.0
F1 C:BEF802 3.1 48.9 1.0
N C:GLY181 3.1 53.7 1.0
CE1 C:HIS107 3.3 51.6 1.0
OG1 C:THR84 3.5 43.0 1.0
CA C:GLY181 3.5 54.9 1.0
CG C:HIS107 3.7 41.7 1.0
CB C:THR84 3.8 45.4 1.0
CA C:HIS107 4.0 44.4 1.0
CB C:HIS107 4.0 41.5 1.0
C C:PRO180 4.2 52.3 1.0
CA C:THR84 4.2 47.3 1.0
N C:ILE108 4.3 51.9 1.0
CA C:PRO180 4.4 48.5 1.0
O C:THR109 4.4 49.0 1.0
O3B C:GDP801 4.5 60.1 1.0
NE2 C:HIS107 4.5 49.8 1.0
C C:HIS107 4.6 48.8 1.0
CD2 C:HIS107 4.7 45.2 1.0
C C:GLY181 4.7 59.0 1.0
CG1 C:VAL184 4.7 63.1 1.0
CB C:PRO180 4.7 48.3 1.0
O C:GLY181 4.8 59.1 1.0
N C:THR109 4.9 51.5 1.0

Reference:

L.Yan, Y.Qi, X.Huang, C.Yu, L.Lan, X.Guo, Z.Rao, J.Hu, Z.Lou. Structural Basis For Gtp Hydrolysis and Conformational Change of MFN1 in Mediating Membrane Fusion Nat. Struct. Mol. Biol. V. 25 233 2018.
ISSN: ESSN 1545-9985
PubMed: 29483649
DOI: 10.1038/S41594-018-0034-8
Page generated: Thu Aug 1 17:13:19 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy