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Fluorine in PDB 4hlq: Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens

Protein crystallography data

The structure of Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens, PDB code: 4hlq was solved by E.M.Gazdag, K.Gavriljuk, A.Itzen, C.Koetting, K.Gerwert, R.S.Goody, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.22 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.170, 118.640, 290.110, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 27.4

Other elements in 4hlq:

The structure of Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens (pdb code 4hlq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 15 binding sites of Fluorine where determined in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens, PDB code: 4hlq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 15 in 4hlq

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Fluorine binding site 1 out of 15 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


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 Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:64.5
occ:1.00
F1 B:BEF203 0.0 64.5 1.0
BE B:BEF203 1.5 64.5 1.0
F3 B:BEF203 2.5 64.8 1.0
F2 B:BEF203 2.6 64.2 1.0
N B:GLY66 2.6 54.1 1.0
O1B B:GDP202 2.8 53.8 1.0
NZ B:LYS21 3.0 54.2 1.0
CA B:GLY66 3.0 54.1 1.0
OG B:SER17 3.2 59.4 1.0
CA B:SER17 3.4 58.5 1.0
CB B:SER17 3.5 59.3 1.0
C B:ALA65 3.7 54.4 1.0
O B:ASP16 3.9 57.1 1.0
PB B:GDP202 4.0 52.9 1.0
N B:GLY18 4.0 58.4 1.0
CA B:ALA65 4.0 54.8 1.0
CE B:LYS21 4.0 54.4 1.0
OE1 A:GLN144 4.0 52.9 1.0
O B:THR64 4.2 54.1 1.0
O2B B:GDP202 4.2 53.3 1.0
MG B:MG201 4.2 65.6 1.0
C B:SER17 4.2 58.6 1.0
C B:GLY66 4.3 55.2 1.0
N B:SER17 4.4 48.2 1.0
N B:GLN67 4.4 55.9 1.0
NE2 A:GLN144 4.5 53.2 1.0
C B:ASP16 4.5 57.7 1.0
CD A:GLN144 4.7 52.1 1.0
O B:ALA65 4.7 54.6 1.0
O3B B:GDP202 4.8 51.8 1.0
C B:THR64 4.9 54.5 1.0
N B:ALA65 5.0 55.0 1.0

Fluorine binding site 2 out of 15 in 4hlq

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Fluorine binding site 2 out of 15 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


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 Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:64.2
occ:1.00
F2 B:BEF203 0.0 64.2 1.0
BE B:BEF203 1.6 64.5 1.0
F3 B:BEF203 2.5 64.8 1.0
F1 B:BEF203 2.6 64.5 1.0
NH1 A:ARG105 2.7 56.9 1.0
NH2 A:ARG105 2.8 55.1 1.0
O1B B:GDP202 2.9 53.8 1.0
NE2 A:GLN144 3.0 53.2 1.0
CZ A:ARG105 3.2 56.4 1.0
OG B:SER17 3.3 59.4 1.0
O2B B:GDP202 3.6 53.3 1.0
PB B:GDP202 3.8 52.9 1.0
N B:GLY18 3.9 58.4 1.0
CD A:GLN144 3.9 52.1 1.0
OE1 A:GLN144 3.9 52.9 1.0
MG B:MG201 4.2 65.6 1.0
N B:THR40 4.2 57.5 1.0
O3A B:GDP202 4.3 53.9 1.0
CB B:SER17 4.4 59.3 1.0
NE A:ARG105 4.5 57.0 1.0
CA B:SER17 4.5 58.5 1.0
C B:SER17 4.6 58.6 1.0
OG1 B:THR40 4.6 54.8 1.0
CA B:GLY18 4.6 58.9 1.0
CA B:SER39 4.6 59.8 1.0
O2A B:GDP202 4.7 54.8 1.0
N B:GLY66 4.8 54.1 1.0
O B:THR40 4.8 56.3 1.0
NZ B:LYS21 4.9 54.2 1.0
C B:SER39 4.9 59.2 1.0
CB B:THR40 5.0 55.7 1.0

Fluorine binding site 3 out of 15 in 4hlq

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Fluorine binding site 3 out of 15 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


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 Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:64.8
occ:1.00
F3 B:BEF203 0.0 64.8 1.0
BE B:BEF203 1.5 64.5 1.0
MG B:MG201 2.1 65.6 1.0
F2 B:BEF203 2.5 64.2 1.0
F1 B:BEF203 2.5 64.5 1.0
O2B B:GDP202 2.6 53.3 1.0
OG1 B:THR40 2.7 54.8 1.0
O1B B:GDP202 3.0 53.8 1.0
CB B:THR40 3.1 55.7 1.0
PB B:GDP202 3.3 52.9 1.0
O B:THR64 3.5 54.1 1.0
N B:THR40 3.7 57.5 1.0
NZ B:LYS21 3.7 54.2 1.0
OG B:SER22 3.8 55.7 1.0
CA B:THR40 3.9 56.8 1.0
O B:THR40 3.9 56.3 1.0
O3B B:GDP202 4.3 51.8 1.0
N B:GLY66 4.3 54.1 1.0
NH1 A:ARG105 4.3 56.9 1.0
CA B:ALA65 4.3 54.8 1.0
CG2 B:THR40 4.3 55.8 1.0
CE B:LYS21 4.4 54.4 1.0
C B:THR40 4.4 57.1 1.0
O3A B:GDP202 4.5 53.9 1.0
C B:THR64 4.5 54.5 1.0
OE1 A:GLN144 4.7 52.9 1.0
O2A B:GDP202 4.8 54.8 1.0
C B:ALA65 4.8 54.4 1.0
NE2 A:GLN144 4.9 53.2 1.0
C B:SER39 4.9 59.2 1.0
N B:ALA65 4.9 55.0 1.0
NH2 A:ARG105 4.9 55.1 1.0

Fluorine binding site 4 out of 15 in 4hlq

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Fluorine binding site 4 out of 15 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


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 Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:76.1
occ:1.00
F1 D:BEF203 0.0 76.1 1.0
BE D:BEF203 1.5 76.1 1.0
MG D:MG201 2.2 55.6 1.0
O3B D:GDP202 2.5 68.0 1.0
OG1 D:THR40 2.5 62.5 1.0
F3 D:BEF203 2.6 75.8 1.0
F2 D:BEF203 2.6 75.8 1.0
OG D:SER22 2.6 63.0 1.0
NZ D:LYS21 3.0 64.5 1.0
O1B D:GDP202 3.2 67.8 1.0
O D:THR64 3.2 64.4 1.0
CB D:THR40 3.2 63.3 1.0
PB D:GDP202 3.3 67.5 1.0
O3A D:GDP202 3.8 66.3 1.0
CB D:SER22 4.0 63.5 1.0
CE D:LYS21 4.1 63.6 1.0
N D:THR40 4.2 64.6 1.0
OD1 D:ASP63 4.2 64.7 1.0
CG2 D:THR40 4.3 63.5 1.0
CD D:LYS21 4.3 63.0 1.0
CA D:THR40 4.3 64.2 1.0
C D:THR64 4.4 64.5 1.0
OD2 D:ASP63 4.5 65.9 1.0
NH1 C:ARG105 4.5 69.1 1.0
N D:SER22 4.6 63.1 1.0
CA D:ALA65 4.6 65.0 1.0
O2B D:GDP202 4.7 67.7 1.0
CG D:ASP63 4.8 65.1 1.0
N D:GLY66 4.8 65.2 1.0
CB D:LYS21 4.8 62.4 1.0
CA D:SER22 4.9 63.5 1.0
O D:THR40 4.9 64.7 1.0
N D:ALA65 5.0 64.9 1.0

Fluorine binding site 5 out of 15 in 4hlq

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Fluorine binding site 5 out of 15 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


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 Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:75.8
occ:1.00
F2 D:BEF203 0.0 75.8 1.0
BE D:BEF203 1.6 76.1 1.0
F3 D:BEF203 2.5 75.8 1.0
O3B D:GDP202 2.6 68.0 1.0
F1 D:BEF203 2.6 76.1 1.0
N D:GLY66 2.9 65.2 1.0
OG D:SER17 3.1 63.2 1.0
CA D:SER17 3.3 62.5 1.0
CA D:GLY66 3.4 65.6 1.0
CB D:SER17 3.7 63.1 1.0
NZ D:LYS21 3.8 64.5 1.0
C D:ALA65 3.8 65.2 1.0
CD D:LYS21 3.9 63.0 1.0
O D:ASP16 3.9 62.0 1.0
PB D:GDP202 3.9 67.5 1.0
CE D:LYS21 3.9 63.6 1.0
CA D:ALA65 4.0 65.0 1.0
N D:SER17 4.0 43.4 1.0
O D:THR64 4.1 64.4 1.0
N D:GLY18 4.2 62.3 1.0
C D:ASP16 4.3 62.4 1.0
O1B D:GDP202 4.3 67.8 1.0
C D:SER17 4.3 62.7 1.0
MG D:MG201 4.4 55.6 1.0
OE1 C:GLN144 4.5 57.1 1.0
NH1 C:ARG105 4.6 69.1 1.0
O D:GLY15 4.7 62.4 1.0
O2B D:GDP202 4.7 67.7 1.0
C D:GLY66 4.8 66.6 1.0
C D:THR64 4.8 64.5 1.0
N D:ALA65 4.8 64.9 1.0
OG1 D:THR40 4.9 62.5 1.0
O3A D:GDP202 4.9 66.3 1.0
O D:ALA65 5.0 65.8 1.0
NE2 C:GLN144 5.0 57.4 1.0

Fluorine binding site 6 out of 15 in 4hlq

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Fluorine binding site 6 out of 15 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


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 Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F203

b:75.8
occ:1.00
F3 D:BEF203 0.0 75.8 1.0
BE D:BEF203 1.5 76.1 1.0
F2 D:BEF203 2.5 75.8 1.0
O3B D:GDP202 2.5 68.0 1.0
F1 D:BEF203 2.6 76.1 1.0
NH1 C:ARG105 2.7 69.1 1.0
MG D:MG201 3.0 55.6 1.0
OG D:SER17 3.2 63.2 1.0
NH2 C:ARG105 3.2 66.7 1.0
OE1 C:GLN144 3.3 57.1 1.0
CZ C:ARG105 3.3 67.9 1.0
N D:THR40 3.6 64.6 1.0
OG1 D:THR40 3.8 62.5 1.0
PB D:GDP202 3.9 67.5 1.0
CD C:GLN144 4.0 56.7 1.0
O3A D:GDP202 4.1 66.3 1.0
CB D:THR40 4.1 63.3 1.0
NE2 C:GLN144 4.2 57.4 1.0
O D:THR40 4.2 64.7 1.0
CA D:SER39 4.2 66.2 1.0
CA D:THR40 4.3 64.2 1.0
C D:SER39 4.3 65.6 1.0
CB D:SER17 4.4 63.1 1.0
CB D:SER39 4.4 66.7 1.0
CA D:SER17 4.5 62.5 1.0
NE C:ARG105 4.5 67.8 1.0
OG D:SER22 4.6 63.0 1.0
N D:GLY18 4.6 62.3 1.0
N D:GLY66 4.6 65.2 1.0
O1B D:GDP202 4.6 67.8 1.0
C D:THR40 4.7 64.8 1.0
O2B D:GDP202 4.9 67.7 1.0
O D:THR64 5.0 64.4 1.0
CA D:ALA65 5.0 65.0 1.0

Fluorine binding site 7 out of 15 in 4hlq

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Fluorine binding site 7 out of 15 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F203

b:70.4
occ:1.00
F1 F:BEF203 0.0 70.4 1.0
BE F:BEF203 1.5 70.9 1.0
F3 F:BEF203 2.5 71.4 1.0
F2 F:BEF203 2.6 71.0 1.0
O2B F:GDP202 2.7 64.3 1.0
OG F:SER17 2.8 60.5 1.0
OE1 E:GLN144 3.1 58.4 1.0
NH2 E:ARG105 3.2 59.9 1.0
NH1 E:ARG105 3.2 61.5 1.0
CA F:SER17 3.5 59.1 1.0
CB F:SER17 3.5 60.1 1.0
N F:GLY18 3.6 58.3 1.0
CZ E:ARG105 3.6 60.7 1.0
N F:GLY66 3.6 62.3 1.0
NE2 E:GLN144 3.8 56.6 1.0
CD E:GLN144 3.8 56.6 1.0
C F:SER17 4.0 58.7 1.0
CA F:GLY66 4.0 62.2 1.0
PB F:GDP202 4.0 64.1 1.0
MG F:MG201 4.4 61.8 1.0
NZ F:LYS21 4.5 59.1 1.0
O3A F:GDP202 4.5 63.7 1.0
O3B F:GDP202 4.5 64.2 1.0
CA F:GLY18 4.7 58.3 1.0
N F:SER17 4.7 43.3 1.0
C F:ALA65 4.8 62.9 1.0
C F:GLY66 4.8 63.1 1.0
O F:THR40 4.8 64.0 1.0
N F:THR40 4.9 63.0 1.0
N F:GLN67 4.9 64.0 1.0
NE E:ARG105 5.0 60.7 1.0
CD2 E:LEU101 5.0 58.7 1.0
OE1 E:GLN98 5.0 53.7 1.0

Fluorine binding site 8 out of 15 in 4hlq

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Fluorine binding site 8 out of 15 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F203

b:71.0
occ:1.00
F2 F:BEF203 0.0 71.0 1.0
BE F:BEF203 1.6 70.9 1.0
MG F:MG201 2.3 61.8 1.0
F3 F:BEF203 2.5 71.4 1.0
F1 F:BEF203 2.6 70.4 1.0
OG1 F:THR40 2.9 62.0 1.0
NH1 E:ARG105 2.9 61.5 1.0
O2B F:GDP202 2.9 64.3 1.0
N F:THR40 3.0 63.0 1.0
O3B F:GDP202 3.1 64.2 1.0
CB F:THR40 3.3 62.6 1.0
PB F:GDP202 3.5 64.1 1.0
CA F:THR40 3.7 63.5 1.0
CZ E:ARG105 3.8 60.7 1.0
O3A F:GDP202 3.9 63.7 1.0
C F:SER39 4.0 63.7 1.0
NH2 E:ARG105 4.0 59.9 1.0
OG F:SER22 4.1 59.6 1.0
CA F:SER39 4.1 63.6 1.0
O F:THR40 4.1 64.0 1.0
C F:THR40 4.4 64.3 1.0
NE2 E:GLN144 4.4 56.6 1.0
O2A F:GDP202 4.6 63.6 1.0
O F:THR64 4.7 62.0 1.0
CG2 F:THR40 4.7 63.3 1.0
O F:ILE38 4.7 63.6 1.0
CB F:SER39 4.8 64.1 1.0
NE E:ARG105 4.8 60.7 1.0
O1B F:GDP202 4.9 64.2 1.0
N F:GLY66 4.9 62.3 1.0
PA F:GDP202 4.9 63.3 1.0
OE1 E:GLN144 4.9 58.4 1.0

Fluorine binding site 9 out of 15 in 4hlq

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Fluorine binding site 9 out of 15 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F203

b:71.4
occ:1.00
F3 F:BEF203 0.0 71.4 1.0
BE F:BEF203 1.5 70.9 1.0
O2B F:GDP202 2.5 64.3 1.0
F2 F:BEF203 2.5 71.0 1.0
F1 F:BEF203 2.5 70.4 1.0
NZ F:LYS21 2.6 59.1 1.0
N F:GLY66 3.0 62.3 1.0
MG F:MG201 3.0 61.8 1.0
O F:THR64 3.2 62.0 1.0
O3B F:GDP202 3.3 64.2 1.0
PB F:GDP202 3.3 64.1 1.0
CE F:LYS21 3.6 58.6 1.0
CA F:GLY66 3.6 62.2 1.0
C F:ALA65 3.8 62.9 1.0
CA F:ALA65 3.8 63.1 1.0
OG1 F:THR40 4.1 62.0 1.0
CB F:THR40 4.2 62.6 1.0
C F:THR64 4.2 62.7 1.0
O1B F:GDP202 4.2 64.2 1.0
N F:ALA65 4.5 63.3 1.0
CD F:LYS21 4.5 58.1 1.0
CA F:SER17 4.5 59.1 1.0
O3A F:GDP202 4.6 63.7 1.0
O F:ASP16 4.6 57.8 1.0
N F:GLY18 4.6 58.3 1.0
NH1 E:ARG105 4.6 61.5 1.0
OG F:SER22 4.8 59.6 1.0
O F:ALA65 4.9 63.4 1.0
O F:THR40 4.9 64.0 1.0
OD1 F:ASP63 5.0 62.8 1.0
OE1 E:GLN144 5.0 58.4 1.0
OG F:SER17 5.0 60.5 1.0

Fluorine binding site 10 out of 15 in 4hlq

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Fluorine binding site 10 out of 15 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F203

b:0.7
occ:1.00
F1 H:BEF203 0.0 0.7 1.0
BE H:BEF203 1.5 0.4 1.0
F3 H:BEF203 2.5 0.9 1.0
F2 H:BEF203 2.6 0.6 1.0
MG H:MG201 2.7 61.3 1.0
O2B H:GDP202 2.8 80.3 1.0
N H:THR40 3.1 94.9 1.0
OE1 G:GLN144 3.1 81.8 1.0
NH1 G:ARG105 3.2 90.6 1.0
OG1 H:THR40 3.5 94.7 1.0
O H:THR40 3.6 93.2 1.0
CB H:THR40 3.6 94.6 1.0
O3B H:GDP202 3.8 80.8 1.0
CA H:THR40 3.8 95.4 1.0
PB H:GDP202 3.8 80.5 1.0
C H:SER39 4.0 96.5 1.0
CZ G:ARG105 4.1 89.5 1.0
CA H:SER39 4.1 96.2 1.0
C H:THR40 4.1 94.8 1.0
NH2 G:ARG105 4.2 88.3 1.0
CD G:GLN144 4.2 81.1 1.0
N H:GLY66 4.4 90.3 1.0
CB H:SER39 4.5 95.7 1.0
O H:THR64 4.7 94.6 1.0
NE2 G:GLN144 4.7 81.0 1.0
CB H:SER17 4.7 89.5 1.0
CA H:ALA65 4.7 93.0 1.0
O1A H:GDP202 4.7 77.8 1.0
OG H:SER22 4.8 97.7 1.0
O3A H:GDP202 4.8 79.1 1.0
O1B H:GDP202 4.9 80.2 1.0

Reference:

K.Gavriljuk, E.M.Gazdag, A.Itzen, C.Kotting, R.S.Goody, K.Gerwert. Catalytic Mechanism of A Mammalian Rab-Rabgap Complex in Atomic Detail. Proc.Natl.Acad.Sci.Usa V. 109 21348 2012.
ISSN: ISSN 0027-8424
PubMed: 23236136
DOI: 10.1073/PNAS.1214431110
Page generated: Thu Aug 1 02:06:03 2024

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Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
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