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Fluorine in PDB 3t34: Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State

Protein crystallography data

The structure of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State, PDB code: 3t34 was solved by L.M.Yan, Y.Y.Ma, Y.N.Sun, Z.Y.Lou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.31 / 2.41
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.471, 86.407, 88.485, 90.00, 90.55, 90.00
R / Rfree (%) 23.7 / 28.4

Other elements in 3t34:

The structure of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State (pdb code 3t34). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State, PDB code: 3t34:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3t34

Go back to Fluorine Binding Sites List in 3t34
Fluorine binding site 1 out of 8 in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:53.8
occ:1.00
 F1 A:ALF1001 0.0 53.8 1.0
AL A:ALF1001 1.8 41.2 1.0
N A:VAL67 2.2 39.5 1.0
F3 A:ALF1001 2.4 46.9 1.0
F4 A:ALF1001 2.6 35.8 1.0
N A:THR68 2.6 41.4 1.0
O A:HOH1004 2.7 39.4 1.0
CA A:VAL67 2.9 39.4 1.0
NA A:NA1003 2.9 45.0 1.0
C A:VAL67 3.1 39.4 1.0
O3B A:GDP1000 3.2 33.5 1.0
C A:ILE66 3.4 46.3 1.0
CB A:VAL67 3.5 48.6 1.0
F2 A:ALF1001 3.6 32.6 1.0
O A:HOH1007 3.6 36.6 1.0
CG1 A:VAL67 3.6 46.5 1.0
CA A:THR68 3.7 36.8 1.0
CA A:ILE66 3.8 44.1 1.0
CG2 A:VAL67 3.8 44.8 1.0
O A:THR68 3.9 41.8 1.0
O A:GLY65 3.9 44.9 1.0
MG A:MG1002 3.9 40.0 1.0
CB A:THR68 4.0 38.0 1.0
C A:THR68 4.2 36.5 1.0
OG1 A:THR68 4.2 39.8 1.0
O A:VAL67 4.3 33.4 1.0
O A:ILE66 4.4 47.6 1.0
PB A:GDP1000 4.5 34.5 1.0
O1B A:GDP1000 4.6 39.7 1.0
CG1 A:ILE66 4.7 40.7 1.0
C A:GLY65 4.7 48.2 1.0
N A:ILE66 4.8 42.9 1.0
O2A A:GDP1000 4.9 34.9 1.0
CB A:ILE66 4.9 44.7 1.0

Fluorine binding site 2 out of 8 in 3t34

Go back to Fluorine Binding Sites List in 3t34
Fluorine binding site 2 out of 8 in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:32.6
occ:1.00
 F2 A:ALF1001 0.0 32.6 1.0
AL A:ALF1001 1.8 41.2 1.0
O3B A:GDP1000 2.3 33.5 1.0
F4 A:ALF1001 2.5 35.8 1.0
F3 A:ALF1001 2.6 46.9 1.0
NZ A:LYS47 2.7 32.3 1.0
O A:HOH1004 2.8 39.4 1.0
N A:SER44 3.0 39.1 1.0
O2B A:GDP1000 3.3 36.9 1.0
PB A:GDP1000 3.3 34.5 1.0
N A:GLY145 3.3 44.3 1.0
CA A:GLN43 3.4 44.0 1.0
CA A:GLY145 3.5 38.0 1.0
CE A:LYS47 3.5 37.9 1.0
F1 A:ALF1001 3.6 53.8 1.0
C A:GLN43 3.8 41.8 1.0
O A:HOH1005 3.8 35.8 1.0
O1B A:GDP1000 3.9 39.7 1.0
CA A:SER44 4.0 35.6 1.0
NA A:NA1003 4.2 45.0 1.0
CG A:GLN43 4.2 43.0 1.0
MG A:MG1002 4.2 40.0 1.0
O A:GLY42 4.2 33.8 1.0
CB A:GLN43 4.2 35.7 1.0
N A:GLN43 4.3 37.8 1.0
C A:PRO144 4.4 40.9 1.0
O A:HOH1006 4.7 38.2 1.0
C A:GLY42 4.7 39.9 1.0
O3A A:GDP1000 4.7 39.2 1.0
C A:GLY145 4.7 41.5 1.0
O A:LEU143 4.8 32.1 1.0
CA A:PRO144 4.8 40.0 1.0
OG A:SER44 4.9 33.0 1.0
N A:SER45 5.0 33.6 1.0

Fluorine binding site 3 out of 8 in 3t34

Go back to Fluorine Binding Sites List in 3t34
Fluorine binding site 3 out of 8 in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:46.9
occ:1.00
 F3 A:ALF1001 0.0 46.9 1.0
AL A:ALF1001 1.8 41.2 1.0
F1 A:ALF1001 2.4 53.8 1.0
NA A:NA1003 2.4 45.0 1.0
F2 A:ALF1001 2.6 32.6 1.0
O A:GLY65 2.8 44.9 1.0
O3B A:GDP1000 2.9 33.5 1.0
O A:HOH1004 2.9 39.4 1.0
CG A:GLN43 3.3 43.0 1.0
N A:SER44 3.5 39.1 1.0
CA A:ILE66 3.5 44.1 1.0
N A:VAL67 3.5 39.5 1.0
F4 A:ALF1001 3.6 35.8 1.0
OG A:SER44 3.6 33.0 1.0
CD A:GLN43 3.7 45.5 1.0
C A:GLY65 3.8 48.2 1.0
O A:HOH1005 3.9 35.8 1.0
C A:ILE66 4.0 46.3 1.0
CA A:SER44 4.1 35.6 1.0
N A:ILE66 4.1 42.9 1.0
NE2 A:GLN43 4.1 49.5 1.0
CA A:GLN43 4.2 44.0 1.0
C A:GLN43 4.2 41.8 1.0
CB A:GLN43 4.2 35.7 1.0
OE1 A:GLN43 4.3 41.9 1.0
CB A:SER44 4.3 36.4 1.0
PB A:GDP1000 4.4 34.5 1.0
CB A:ILE66 4.6 44.7 1.0
CG1 A:ILE66 4.6 40.7 1.0
CA A:VAL67 4.8 39.4 1.0
CG1 A:VAL67 4.8 46.5 1.0
N A:THR68 4.9 41.4 1.0
O A:GLY63 5.0 39.2 1.0

Fluorine binding site 4 out of 8 in 3t34

Go back to Fluorine Binding Sites List in 3t34
Fluorine binding site 4 out of 8 in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:35.8
occ:1.00
 F4 A:ALF1001 0.0 35.8 1.0
AL A:ALF1001 1.8 41.2 1.0
MG A:MG1002 2.2 40.0 1.0
O A:HOH1004 2.5 39.4 1.0
F2 A:ALF1001 2.5 32.6 1.0
F1 A:ALF1001 2.6 53.8 1.0
O3B A:GDP1000 2.7 33.5 1.0
CB A:THR68 2.9 38.0 1.0
O A:HOH1006 3.0 38.2 1.0
O1B A:GDP1000 3.1 39.7 1.0
OG1 A:THR68 3.2 39.8 1.0
N A:THR68 3.4 41.4 1.0
PB A:GDP1000 3.4 34.5 1.0
O A:HOH1007 3.5 36.6 1.0
F3 A:ALF1001 3.6 46.9 1.0
CA A:THR68 3.6 36.8 1.0
O A:THR68 3.7 41.8 1.0
O A:LEU143 4.0 32.1 1.0
CG2 A:THR68 4.0 37.4 1.0
NZ A:LYS47 4.1 32.3 1.0
N A:GLY145 4.1 44.3 1.0
C A:THR68 4.1 36.5 1.0
O2B A:GDP1000 4.1 36.9 1.0
CA A:PRO144 4.3 40.0 1.0
CE A:LYS47 4.3 37.9 1.0
OG A:SER48 4.5 33.5 1.0
NA A:NA1003 4.5 45.0 1.0
C A:PRO144 4.6 40.9 1.0
C A:VAL67 4.6 39.4 1.0
N A:VAL67 4.6 39.5 1.0
C A:LEU143 4.8 42.0 1.0
O3A A:GDP1000 4.9 39.2 1.0
N A:PRO144 4.9 42.8 1.0
O A:HOH1005 5.0 35.8 1.0

Fluorine binding site 5 out of 8 in 3t34

Go back to Fluorine Binding Sites List in 3t34
Fluorine binding site 5 out of 8 in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:47.1
occ:1.00
 F1 B:ALF1001 0.0 47.1 1.0
AL B:ALF1001 1.8 46.4 1.0
O B:HOH1004 2.4 40.3 1.0
F4 B:ALF1001 2.5 46.9 1.0
O3B B:GDP1000 2.5 37.6 1.0
F3 B:ALF1001 2.6 60.0 1.0
NA B:NA1003 2.6 42.5 1.0
N B:VAL67 2.9 42.9 1.0
CG2 B:VAL67 2.9 56.7 1.0
N B:THR68 3.3 41.0 1.0
O B:HOH1007 3.5 45.9 1.0
F2 B:ALF1001 3.5 49.8 1.0
O B:GLY65 3.6 44.0 1.0
CA B:VAL67 3.7 46.7 1.0
CB B:VAL67 3.8 53.6 1.0
PB B:GDP1000 3.9 38.6 1.0
C B:ILE66 3.9 49.6 1.0
C B:VAL67 3.9 48.1 1.0
CA B:ILE66 4.1 50.3 1.0
O2A B:GDP1000 4.2 43.4 1.0
O B:THR68 4.2 42.2 1.0
O1B B:GDP1000 4.3 46.3 1.0
CA B:THR68 4.3 47.7 1.0
O B:GLY63 4.3 50.4 1.0
MG B:MG1002 4.4 50.6 1.0
CB B:THR68 4.5 45.4 1.0
CG1 B:VAL67 4.5 46.3 1.0
O B:HOH1005 4.5 38.1 1.0
C B:GLY65 4.6 47.9 1.0
O2B B:GDP1000 4.6 39.7 1.0
N B:SER44 4.7 33.7 1.0
OG1 B:THR68 4.7 49.6 1.0
C B:THR68 4.7 49.4 1.0
CG B:GLN43 4.8 44.9 1.0
OG B:SER44 4.8 38.9 1.0
N B:ILE66 4.8 41.3 1.0
CA B:SER44 5.0 37.9 1.0

Fluorine binding site 6 out of 8 in 3t34

Go back to Fluorine Binding Sites List in 3t34
Fluorine binding site 6 out of 8 in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:49.8
occ:1.00
 F2 B:ALF1001 0.0 49.8 1.0
AL B:ALF1001 1.8 46.4 1.0
NZ B:LYS47 2.3 37.6 1.0
F3 B:ALF1001 2.4 60.0 1.0
F4 B:ALF1001 2.6 46.9 1.0
O2B B:GDP1000 2.7 39.7 1.0
N B:GLY145 2.8 41.7 1.0
CA B:GLY145 2.9 40.5 1.0
O3B B:GDP1000 3.1 37.6 1.0
N B:SER44 3.1 33.7 1.0
O B:HOH1004 3.2 40.3 1.0
CE B:LYS47 3.3 48.4 1.0
PB B:GDP1000 3.3 38.6 1.0
F1 B:ALF1001 3.5 47.1 1.0
CA B:GLN43 3.6 42.3 1.0
C B:GLN43 3.8 37.7 1.0
O B:GLY42 3.8 37.2 1.0
O1B B:GDP1000 3.9 46.3 1.0
C B:PRO144 4.0 44.6 1.0
MG B:MG1002 4.1 50.6 1.0
CA B:SER44 4.2 37.9 1.0
C B:GLY145 4.2 42.4 1.0
N B:GLN43 4.3 40.4 1.0
O B:HOH1005 4.4 38.1 1.0
C B:GLY42 4.4 40.9 1.0
O B:LEU143 4.4 52.2 1.0
CG B:GLN43 4.5 44.9 1.0
CB B:GLN43 4.6 37.0 1.0
CD B:LYS47 4.6 43.0 1.0
CA B:PRO144 4.7 46.6 1.0
O B:GLY145 4.7 39.5 1.0
O3A B:GDP1000 4.7 37.1 1.0
O B:HOH1007 4.8 45.9 1.0
N B:SER45 4.8 38.2 1.0
CG B:LYS47 4.9 36.4 1.0
CB B:LYS47 4.9 32.1 1.0
O B:PRO144 4.9 38.0 1.0
NA B:NA1003 4.9 42.5 1.0

Fluorine binding site 7 out of 8 in 3t34

Go back to Fluorine Binding Sites List in 3t34
Fluorine binding site 7 out of 8 in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:60.0
occ:1.00
 F3 B:ALF1001 0.0 60.0 1.0
AL B:ALF1001 1.8 46.4 1.0
N B:SER44 2.2 33.7 1.0
F2 B:ALF1001 2.4 49.8 1.0
F1 B:ALF1001 2.6 47.1 1.0
O3B B:GDP1000 2.6 37.6 1.0
NA B:NA1003 2.8 42.5 1.0
CA B:SER44 2.8 37.9 1.0
CG B:GLN43 3.0 44.9 1.0
C B:GLN43 3.0 37.7 1.0
O B:HOH1004 3.2 40.3 1.0
CA B:GLN43 3.2 42.3 1.0
OG B:SER44 3.4 38.9 1.0
CB B:SER44 3.4 46.2 1.0
F4 B:ALF1001 3.6 46.9 1.0
O2B B:GDP1000 3.6 39.7 1.0
PB B:GDP1000 3.6 38.6 1.0
CB B:GLN43 3.7 37.0 1.0
O B:GLN43 4.1 45.0 1.0
CD B:GLN43 4.2 47.4 1.0
C B:SER44 4.2 39.6 1.0
O B:HOH1005 4.3 38.1 1.0
O B:GLY65 4.3 44.0 1.0
NZ B:LYS47 4.5 37.6 1.0
N B:GLN43 4.6 40.4 1.0
O3A B:GDP1000 4.6 37.1 1.0
N B:GLY145 4.6 41.7 1.0
O B:GLY42 4.6 37.2 1.0
N B:SER45 4.7 38.2 1.0
CA B:GLY145 4.7 40.5 1.0
O1B B:GDP1000 4.7 46.3 1.0
NE2 B:GLN43 4.8 41.5 1.0
OE1 B:GLN43 4.8 47.4 1.0

Fluorine binding site 8 out of 8 in 3t34

Go back to Fluorine Binding Sites List in 3t34
Fluorine binding site 8 out of 8 in the Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Arabidopsis Thaliana Dynamin-Related Protein 1A (ATDRP1A) in Prefission State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:46.9
occ:1.00
 F4 B:ALF1001 0.0 46.9 1.0
AL B:ALF1001 1.8 46.4 1.0
MG B:MG1002 2.4 50.6 1.0
F1 B:ALF1001 2.5 47.1 1.0
O B:HOH1004 2.6 40.3 1.0
F2 B:ALF1001 2.6 49.8 1.0
O B:HOH1007 2.8 45.9 1.0
O3B B:GDP1000 3.0 37.6 1.0
CB B:THR68 3.0 45.4 1.0
O1B B:GDP1000 3.2 46.3 1.0
OG1 B:THR68 3.5 49.6 1.0
PB B:GDP1000 3.5 38.6 1.0
N B:THR68 3.5 41.0 1.0
F3 B:ALF1001 3.6 60.0 1.0
N B:GLY145 3.7 41.7 1.0
CA B:THR68 3.7 47.7 1.0
O B:HOH1006 3.8 58.1 1.0
O B:THR68 3.8 42.2 1.0
O B:LEU143 3.8 52.2 1.0
O2B B:GDP1000 3.9 39.7 1.0
CA B:PRO144 4.0 46.6 1.0
CG2 B:THR68 4.2 43.6 1.0
C B:THR68 4.2 49.4 1.0
NZ B:LYS47 4.2 37.6 1.0
C B:PRO144 4.3 44.6 1.0
CG2 B:VAL67 4.3 56.7 1.0
CE B:LYS47 4.4 48.4 1.0
OG B:SER48 4.5 47.1 1.0
C B:LEU143 4.6 51.3 1.0
CA B:GLY145 4.6 40.5 1.0
N B:PRO144 4.7 51.7 1.0
O B:HOH1005 4.7 38.1 1.0
C B:VAL67 4.7 48.1 1.0
NA B:NA1003 4.8 42.5 1.0
N B:VAL67 4.8 42.9 1.0
O2A B:GDP1000 4.9 43.4 1.0

Reference:

L.M.Yan, Y.Y.Ma, Y.N.Sun, J.Gao, X.Chen, J.Liu, C.Wang, Z.Rao, Z.Y.Lou. Structural Basis For Mechanochemical Role of Arabidopsis Thaliana Dynamin-Related Protein in Membrane Fission J Mol Cell Biol V. 3 378 2011.
ISSN: ISSN 1674-2788
PubMed: 22107825
DOI: 10.1093/JMCB/MJR032
Page generated: Sun Dec 13 11:55:39 2020

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