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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

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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

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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

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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

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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

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