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Fluorine in PDB 5jcz: RAB11 Bound to Myova-Gtd

Protein crystallography data

The structure of RAB11 Bound to Myova-Gtd, PDB code: 5jcz was solved by O.Pylypenko, W.Attanda, C.Gauquelin, G.Malherbes, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.88 / 2.06
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 215.790, 128.420, 89.020, 90.00, 98.27, 90.00
R / Rfree (%) 18 / 20.8

Other elements in 5jcz:

The structure of RAB11 Bound to Myova-Gtd also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the RAB11 Bound to Myova-Gtd (pdb code 5jcz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the RAB11 Bound to Myova-Gtd, PDB code: 5jcz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5jcz

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Fluorine binding site 1 out of 9 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of RAB11 Bound to Myova-Gtd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:38.7
occ:1.00
F1 A:BEF203 0.0 38.7 1.0
BE A:BEF203 1.4 43.3 1.0
F2 A:BEF203 2.2 40.2 1.0
F3 A:BEF203 2.3 40.8 1.0
O3B A:GDP202 2.5 38.0 1.0
NZ A:LYS24 2.8 35.3 1.0
N A:GLY69 3.0 40.9 1.0
CA A:ALA68 3.2 35.1 1.0
CA A:SER20 3.3 42.3 0.6
CA A:SER20 3.3 42.2 0.5
CE A:LYS24 3.5 39.3 1.0
OG A:SER20 3.5 47.8 0.6
PB A:GDP202 3.6 38.0 1.0
C A:ALA68 3.6 43.5 1.0
O2B A:GDP202 3.7 37.0 1.0
O A:HOH326 3.7 40.1 1.0
CB A:SER20 3.8 42.4 0.6
CB A:ALA68 3.8 41.6 1.0
CB A:SER20 3.8 42.6 0.5
OG A:SER20 3.9 44.6 0.5
MG A:MG201 3.9 43.0 1.0
O1B A:GDP202 4.0 35.9 1.0
CA A:GLY69 4.1 45.7 1.0
N A:GLY21 4.1 38.1 1.0
N A:SER20 4.1 40.4 1.0
O A:THR67 4.1 35.9 1.0
O A:ASP19 4.2 36.3 1.0
C A:SER20 4.3 40.7 1.0
N A:ALA68 4.4 34.8 1.0
C A:ASP19 4.5 41.6 1.0
O A:HOH431 4.6 63.5 1.0
C A:THR67 4.7 36.2 1.0
O A:GLY18 4.8 40.9 1.0
O A:ALA68 4.8 40.8 1.0
OG A:SER42 4.8 78.2 1.0
O3A A:GDP202 4.9 41.4 1.0
N A:THR43 5.0 42.8 1.0
CD A:LYS24 5.0 37.0 1.0

Fluorine binding site 2 out of 9 in 5jcz

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Fluorine binding site 2 out of 9 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of RAB11 Bound to Myova-Gtd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:40.2
occ:1.00
F2 A:BEF203 0.0 40.2 1.0
BE A:BEF203 1.4 43.3 1.0
F3 A:BEF203 2.2 40.8 1.0
F1 A:BEF203 2.2 38.7 1.0
O3B A:GDP202 2.5 38.0 1.0
O A:HOH431 2.6 63.5 1.0
OG A:SER20 2.7 44.6 0.5
OG A:SER42 3.1 78.2 1.0
CB A:SER20 3.4 42.4 0.6
CB A:SER20 3.4 42.6 0.5
OG A:SER20 3.5 47.8 0.6
CA A:SER42 3.5 56.1 1.0
CB A:SER42 3.6 59.4 1.0
CA A:SER20 3.6 42.3 0.6
CA A:SER20 3.6 42.2 0.5
N A:GLY21 3.9 38.1 1.0
N A:THR43 3.9 42.8 1.0
PB A:GDP202 4.0 38.0 1.0
CB A:ALA68 4.1 41.6 1.0
MG A:MG201 4.2 43.0 1.0
C A:SER20 4.2 40.7 1.0
C A:SER42 4.2 43.8 1.0
O A:HOH336 4.3 67.3 1.0
CA A:ALA68 4.4 35.1 1.0
O A:HOH316 4.4 38.8 1.0
O1B A:GDP202 4.5 35.9 1.0
N A:GLY69 4.6 40.9 1.0
N A:SER42 4.6 52.1 1.0
O2B A:GDP202 4.8 37.0 1.0
O3A A:GDP202 4.8 41.4 1.0
NZ A:LYS24 4.9 35.3 1.0
N A:SER20 4.9 40.4 1.0
CA A:GLY21 4.9 38.2 1.0
O A:HOH326 5.0 40.1 1.0

Fluorine binding site 3 out of 9 in 5jcz

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Fluorine binding site 3 out of 9 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of RAB11 Bound to Myova-Gtd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:40.8
occ:1.00
F3 A:BEF203 0.0 40.8 1.0
BE A:BEF203 1.4 43.3 1.0
MG A:MG201 2.1 43.0 1.0
F2 A:BEF203 2.2 40.2 1.0
F1 A:BEF203 2.3 38.7 1.0
O3B A:GDP202 2.5 38.0 1.0
O A:HOH326 2.9 40.1 1.0
OG1 A:THR43 3.0 40.4 1.0
N A:THR43 3.0 42.8 1.0
O A:HOH316 3.1 38.8 1.0
O1B A:GDP202 3.1 35.9 1.0
PB A:GDP202 3.4 38.0 1.0
CB A:THR43 3.4 36.9 1.0
CA A:ALA68 3.7 35.1 1.0
CA A:THR43 3.8 40.8 1.0
CB A:ALA68 3.9 41.6 1.0
CA A:SER42 4.0 56.1 1.0
C A:SER42 4.0 43.8 1.0
OG A:SER25 4.2 39.0 1.0
OG A:SER42 4.2 78.2 1.0
O A:HOH431 4.2 63.5 1.0
O2B A:GDP202 4.3 37.0 1.0
N A:ALA68 4.3 34.8 1.0
O A:THR67 4.4 35.9 1.0
NZ A:LYS24 4.4 35.3 1.0
O3A A:GDP202 4.6 41.4 1.0
C A:THR67 4.6 36.2 1.0
CE A:LYS24 4.7 39.3 1.0
CB A:SER42 4.7 59.4 1.0
N A:GLY69 4.7 40.9 1.0
O2A A:GDP202 4.7 41.8 1.0
O A:LYS41 4.7 44.6 1.0
C A:ALA68 4.8 43.5 1.0
CG2 A:THR43 4.8 36.2 1.0
O A:HOH336 4.8 67.3 1.0
OG A:SER20 4.9 44.6 0.5
C A:THR43 4.9 40.4 1.0
O A:THR43 4.9 43.2 1.0

Fluorine binding site 4 out of 9 in 5jcz

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Fluorine binding site 4 out of 9 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of RAB11 Bound to Myova-Gtd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:49.2
occ:1.00
F1 D:BEF203 0.0 49.2 1.0
BE D:BEF203 1.4 46.8 1.0
F2 D:BEF203 2.2 49.3 1.0
F3 D:BEF203 2.2 46.0 1.0
O1B D:GDP202 2.5 45.9 1.0
NZ D:LYS24 2.9 42.7 1.0
N D:GLY69 3.0 48.5 1.0
CA D:ALA68 3.2 50.2 1.0
CA D:SER20 3.3 50.8 1.0
PB D:GDP202 3.6 47.0 1.0
C D:ALA68 3.6 53.0 1.0
CE D:LYS24 3.7 45.8 1.0
O D:HOH326 3.7 42.6 1.0
CB D:SER20 3.7 58.9 1.0
O3B D:GDP202 3.8 48.9 1.0
OG D:SER20 3.8 70.1 1.0
CB D:ALA68 3.8 45.5 1.0
MG D:MG201 3.9 47.5 1.0
O2B D:GDP202 4.0 41.7 1.0
O D:THR67 4.0 45.7 1.0
N D:GLY21 4.1 47.4 1.0
CA D:GLY69 4.1 53.3 1.0
N D:SER20 4.1 51.1 1.0
C D:SER20 4.2 54.6 1.0
N D:ALA68 4.3 45.2 1.0
O D:ASP19 4.3 50.9 1.0
C D:ASP19 4.6 51.8 1.0
C D:THR67 4.6 48.2 1.0
OG D:SER42 4.8 54.1 0.5
O D:ALA68 4.8 48.5 1.0
O D:GLY18 4.8 49.5 1.0
O3A D:GDP202 5.0 49.2 1.0
N D:THR43 5.0 47.3 1.0

Fluorine binding site 5 out of 9 in 5jcz

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Fluorine binding site 5 out of 9 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of RAB11 Bound to Myova-Gtd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:49.3
occ:1.00
F2 D:BEF203 0.0 49.3 1.0
BE D:BEF203 1.4 46.8 1.0
F3 D:BEF203 2.2 46.0 1.0
F1 D:BEF203 2.2 49.2 1.0
O1B D:GDP202 2.5 45.9 1.0
OG D:SER20 2.6 70.1 1.0
OG D:SER42 3.1 54.1 0.5
CB D:SER20 3.4 58.9 1.0
CA D:SER42 3.5 54.2 0.5
CA D:SER42 3.5 54.3 0.5
CB D:SER42 3.5 56.9 0.5
CB D:SER42 3.6 56.9 0.5
CA D:SER20 3.6 50.8 1.0
N D:GLY21 3.8 47.4 1.0
O D:HOH333 3.9 63.2 1.0
PB D:GDP202 3.9 47.0 1.0
N D:THR43 4.0 47.3 1.0
CB D:ALA68 4.1 45.5 1.0
C D:SER20 4.1 54.6 1.0
MG D:MG201 4.2 47.5 1.0
C D:SER42 4.3 48.0 1.0
CA D:ALA68 4.4 50.2 1.0
O2B D:GDP202 4.4 41.7 1.0
O D:HOH309 4.5 40.6 1.0
N D:SER42 4.6 54.5 1.0
N D:GLY69 4.6 48.5 1.0
O D:HOH404 4.7 77.5 1.0
O3B D:GDP202 4.8 48.9 1.0
O3A D:GDP202 4.8 49.2 1.0
CA D:GLY21 4.9 43.8 1.0
NZ D:LYS24 4.9 42.7 1.0
OG D:SER42 4.9 59.3 0.5
N D:SER20 4.9 51.1 1.0
O D:HOH326 5.0 42.6 1.0

Fluorine binding site 6 out of 9 in 5jcz

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Fluorine binding site 6 out of 9 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of RAB11 Bound to Myova-Gtd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:46.0
occ:1.00
F3 D:BEF203 0.0 46.0 1.0
BE D:BEF203 1.4 46.8 1.0
MG D:MG201 2.1 47.5 1.0
F2 D:BEF203 2.2 49.3 1.0
F1 D:BEF203 2.2 49.2 1.0
O1B D:GDP202 2.5 45.9 1.0
O D:HOH326 2.9 42.6 1.0
O2B D:GDP202 3.0 41.7 1.0
O D:HOH309 3.1 40.6 1.0
N D:THR43 3.1 47.3 1.0
OG1 D:THR43 3.1 51.0 1.0
PB D:GDP202 3.3 47.0 1.0
CB D:THR43 3.5 51.6 1.0
CA D:ALA68 3.7 50.2 1.0
CA D:THR43 3.9 47.3 1.0
CA D:SER42 3.9 54.2 0.5
CA D:SER42 3.9 54.3 0.5
CB D:ALA68 4.0 45.5 1.0
C D:SER42 4.0 48.0 1.0
OG D:SER25 4.1 44.7 1.0
OG D:SER42 4.2 54.1 0.5
O3B D:GDP202 4.2 48.9 1.0
N D:ALA68 4.4 45.2 1.0
O D:THR67 4.4 45.7 1.0
NZ D:LYS24 4.4 42.7 1.0
O D:HOH333 4.5 63.2 1.0
O1A D:GDP202 4.5 49.1 1.0
O3A D:GDP202 4.5 49.2 1.0
CB D:SER42 4.6 56.9 0.5
CB D:SER42 4.6 56.9 0.5
C D:THR67 4.6 48.2 1.0
O D:LYS41 4.6 52.5 1.0
OG D:SER20 4.8 70.1 1.0
N D:GLY69 4.8 48.5 1.0
CE D:LYS24 4.8 45.8 1.0
C D:ALA68 4.8 53.0 1.0
CG2 D:THR43 5.0 45.9 1.0

Fluorine binding site 7 out of 9 in 5jcz

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Fluorine binding site 7 out of 9 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of RAB11 Bound to Myova-Gtd within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F203

b:40.1
occ:0.30
F1 I:BEF203 0.0 40.1 0.3
BE I:BEF203 1.4 41.9 0.3
F3 I:BEF203 2.2 40.8 0.3
F2 I:BEF203 2.2 40.2 0.3
O3B I:GDP202 2.4 45.8 0.3
NZ I:LYS24 2.8 41.4 0.3
N I:GLY69 3.0 48.4 0.3
CA I:ALA68 3.3 48.6 0.3
CA I:SER20 3.4 50.5 0.3
PB I:GDP202 3.5 45.6 0.3
CE I:LYS24 3.5 37.8 0.3
O2B I:GDP202 3.6 44.0 0.3
C I:ALA68 3.6 50.1 0.3
OG I:SER20 3.7 50.0 0.3
O I:HOH303 3.8 88.1 1.0
CB I:SER20 3.8 48.9 0.3
CB I:ALA68 3.8 50.1 0.3
O1B I:GDP202 3.9 48.1 0.3
MG I:MG201 4.0 42.1 0.3
N I:GLY21 4.0 49.4 0.3
CA I:GLY69 4.1 48.7 0.3
O I:THR67 4.2 55.1 0.3
O I:ASP19 4.2 51.3 0.3
N I:SER20 4.3 49.7 0.3
C I:SER20 4.3 51.0 0.3
N I:ALA68 4.4 42.7 0.3
C I:ASP19 4.5 49.0 0.3
C I:THR67 4.7 46.0 0.3
OG I:SER42 4.8 59.0 0.3
O I:ALA68 4.8 35.4 0.3
O3A I:GDP202 4.9 54.1 0.3
N I:THR43 5.0 47.9 0.3
CD I:LYS24 5.0 41.4 0.3

Fluorine binding site 8 out of 9 in 5jcz

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Fluorine binding site 8 out of 9 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of RAB11 Bound to Myova-Gtd within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F203

b:40.2
occ:0.30
F2 I:BEF203 0.0 40.2 0.3
BE I:BEF203 1.4 41.9 0.3
F3 I:BEF203 2.2 40.8 0.3
F1 I:BEF203 2.2 40.1 0.3
O3B I:GDP202 2.5 45.8 0.3
OG I:SER42 3.0 59.0 0.3
CA I:SER42 3.4 52.5 0.3
CB I:SER42 3.5 55.2 0.3
CB I:SER20 3.6 48.9 0.3
O I:HOH307 3.7 91.8 1.0
N I:THR43 3.8 47.9 0.3
CA I:SER20 3.8 50.5 0.3
OG I:SER20 3.9 50.0 0.3
PB I:GDP202 3.9 45.6 0.3
CB I:ALA68 4.0 50.1 0.3
N I:GLY21 4.0 49.4 0.3
MG I:MG201 4.0 42.1 0.3
C I:SER42 4.1 47.9 0.3
CA I:ALA68 4.3 48.6 0.3
C I:SER20 4.3 51.0 0.3
O1B I:GDP202 4.4 48.1 0.3
O I:HOH301 4.5 56.8 1.0
N I:SER42 4.6 50.7 0.3
N I:GLY69 4.6 48.4 0.3
O2B I:GDP202 4.8 44.0 0.3
O3A I:GDP202 4.8 54.1 0.3
O I:HOH303 4.8 88.1 1.0
NZ I:LYS24 4.9 41.4 0.3
CA I:THR43 5.0 47.3 0.3
CA I:GLY21 5.0 45.8 0.3
C I:ALA68 5.0 50.1 0.3

Fluorine binding site 9 out of 9 in 5jcz

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Fluorine binding site 9 out of 9 in the RAB11 Bound to Myova-Gtd


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of RAB11 Bound to Myova-Gtd within 5.0Å range:
probe atom residue distance (Å) B Occ
I:F203

b:40.8
occ:0.30
F3 I:BEF203 0.0 40.8 0.3
BE I:BEF203 1.4 41.9 0.3
MG I:MG201 2.1 42.1 0.3
F1 I:BEF203 2.2 40.1 0.3
F2 I:BEF203 2.2 40.2 0.3
O3B I:GDP202 2.6 45.8 0.3
O I:HOH303 2.7 88.1 1.0
OG1 I:THR43 3.0 43.1 0.3
N I:THR43 3.0 47.9 0.3
O1B I:GDP202 3.1 48.1 0.3
CB I:THR43 3.3 44.3 0.3
O I:HOH301 3.3 56.8 1.0
PB I:GDP202 3.4 45.6 0.3
CA I:ALA68 3.5 48.6 0.3
CB I:ALA68 3.7 50.1 0.3
CA I:THR43 3.7 47.3 0.3
C I:SER42 4.0 47.9 0.3
CA I:SER42 4.1 52.5 0.3
N I:ALA68 4.1 42.7 0.3
OG I:SER42 4.1 59.0 0.3
OG I:SER25 4.1 40.0 0.3
O2B I:GDP202 4.3 44.0 0.3
O I:THR67 4.3 55.1 0.3
NZ I:LYS24 4.4 41.4 0.3
C I:THR67 4.5 46.0 0.3
C I:ALA68 4.6 50.1 0.3
N I:GLY69 4.6 48.4 0.3
O I:HOH307 4.6 91.8 1.0
CE I:LYS24 4.6 37.8 0.3
CB I:SER42 4.7 55.2 0.3
CG2 I:THR43 4.7 45.4 0.3
O2A I:GDP202 4.7 53.8 0.3
O3A I:GDP202 4.7 54.1 0.3
O I:THR43 4.8 35.9 0.3
C I:THR43 4.8 42.4 0.3
O I:LYS41 4.8 50.0 0.3

Reference:

O.Pylypenko, T.Welz, J.Tittel, M.Kollmar, F.Chardon, G.Malherbe, S.Weiss, C.I.Michel, A.Samol-Wolf, A.T.Grasskamp, A.Hume, B.Goud, B.Baron, P.England, M.A.Titus, P.Schwille, T.Weidemann, A.Houdusse, E.Kerkhoff. Coordinated Recruitment of Spir Actin Nucleators and Myosin V Motors to RAB11 Vesicle Membranes. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27623148
DOI: 10.7554/ELIFE.17523
Page generated: Tue Jul 15 04:21:34 2025

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