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Fluorine in PDB 1zdm: Crystal Structure of Activated Chey Bound to Xe

Protein crystallography data

The structure of Crystal Structure of Activated Chey Bound to Xe, PDB code: 1zdm was solved by T.J.Lowery, M.Doucleff, E.J.Ruiz, S.M.Rubin, A.Pines, D.E.Wemmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.730, 53.820, 161.170, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.7

Other elements in 1zdm:

The structure of Crystal Structure of Activated Chey Bound to Xe also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Xenon (Xe) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Activated Chey Bound to Xe (pdb code 1zdm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Activated Chey Bound to Xe, PDB code: 1zdm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 1zdm

Go back to Fluorine Binding Sites List in 1zdm
Fluorine binding site 1 out of 6 in the Crystal Structure of Activated Chey Bound to Xe


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 Activated Chey Bound to Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F57

b:52.3
occ:1.00
 F1 A:BFD57 0.0 52.3 1.0
BE A:BFD57 1.5 40.3 1.0
MN A:MN192 2.1 39.9 1.0
F2 A:BFD57 2.5 52.3 1.0
F3 A:BFD57 2.5 52.3 1.0
OD1 A:BFD57 2.5 26.1 1.0
OD2 A:BFD57 2.6 32.2 1.0
CG A:BFD57 2.9 33.0 1.0
O A:ASN59 3.1 32.8 1.0
O A:HOH221 3.3 42.6 1.0
O A:HOH196 3.3 44.5 1.0
N A:ASN59 3.4 43.2 1.0
CB A:ASN59 3.5 51.6 1.0
O A:HOH269 3.6 67.1 1.0
O A:HOH250 3.6 64.5 1.0
CA A:ASN59 3.7 43.9 1.0
C A:ASN59 3.8 43.7 1.0
OD1 A:ASP13 4.2 53.4 1.0
NZ A:LYS109 4.2 40.5 1.0
N A:TRP58 4.3 40.2 1.0
CB A:BFD57 4.4 33.4 1.0
C A:TRP58 4.5 42.1 1.0
CG A:ASN59 4.6 71.9 1.0
ND2 A:ASN59 4.7 77.0 1.0
CA A:TRP58 4.9 43.0 1.0
OG1 A:THR87 4.9 34.7 1.0

Fluorine binding site 2 out of 6 in 1zdm

Go back to Fluorine Binding Sites List in 1zdm
Fluorine binding site 2 out of 6 in the Crystal Structure of Activated Chey Bound to Xe


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 Activated Chey Bound to Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F57

b:52.3
occ:1.00
 F2 A:BFD57 0.0 52.3 1.0
BE A:BFD57 1.5 40.3 1.0
OD1 A:BFD57 2.4 26.1 1.0
F1 A:BFD57 2.5 52.3 1.0
F3 A:BFD57 2.5 52.3 1.0
OG1 A:THR87 2.5 34.7 1.0
O A:HOH250 2.9 64.5 1.0
N A:ASN59 3.0 43.2 1.0
N A:TRP58 3.2 40.2 1.0
CB A:THR87 3.3 26.5 1.0
CB A:TRP58 3.4 37.9 1.0
CG A:BFD57 3.5 33.0 1.0
CA A:TRP58 3.6 43.0 1.0
N A:ALA88 3.8 30.7 1.0
C A:TRP58 3.8 42.1 1.0
CA A:THR87 3.8 36.5 1.0
CB A:ASN59 3.9 51.6 1.0
OD2 A:BFD57 4.0 32.2 1.0
CA A:ASN59 4.0 43.9 1.0
C A:THR87 4.4 36.0 1.0
C A:BFD57 4.4 38.7 1.0
CG A:GLU89 4.4 54.4 1.0
MN A:MN192 4.5 39.9 1.0
CG A:TRP58 4.5 46.6 1.0
N A:GLU89 4.6 32.4 1.0
CB A:BFD57 4.7 33.4 1.0
CA A:BFD57 4.7 36.6 1.0
O A:ASN59 4.7 32.8 1.0
CG2 A:THR87 4.7 30.3 1.0
O A:HOH269 4.8 67.1 1.0
CA A:ALA88 4.8 36.4 1.0
NZ A:LYS109 4.8 40.5 1.0
C A:ASN59 4.8 43.7 1.0
CB A:ALA88 4.9 28.7 1.0

Fluorine binding site 3 out of 6 in 1zdm

Go back to Fluorine Binding Sites List in 1zdm
Fluorine binding site 3 out of 6 in the Crystal Structure of Activated Chey Bound to Xe


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 Activated Chey Bound to Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F57

b:52.3
occ:1.00
 F3 A:BFD57 0.0 52.3 1.0
BE A:BFD57 1.5 40.3 1.0
OD1 A:BFD57 2.5 26.1 1.0
F1 A:BFD57 2.5 52.3 1.0
F2 A:BFD57 2.5 52.3 1.0
NZ A:LYS109 2.7 40.5 1.0
N A:ALA88 3.2 30.7 1.0
CE A:LYS109 3.4 37.4 1.0
CG A:BFD57 3.5 33.0 1.0
CD A:LYS109 3.6 40.0 1.0
CA A:THR87 3.6 36.5 1.0
O A:HOH196 3.8 44.5 1.0
OG1 A:THR87 3.8 34.7 1.0
CB A:ALA88 3.9 28.7 1.0
C A:THR87 3.9 36.0 1.0
OD2 A:BFD57 3.9 32.2 1.0
MN A:MN192 4.1 39.9 1.0
CA A:ALA88 4.1 36.4 1.0
CB A:THR87 4.2 26.5 1.0
O A:HOH250 4.3 64.5 1.0
O A:VAL86 4.5 37.0 1.0
CG A:LYS109 4.6 37.5 1.0
O A:HOH269 4.7 67.1 1.0
CB A:BFD57 4.7 33.4 1.0
O A:HOH202 4.7 46.5 1.0
OD2 A:ASP12 4.8 38.6 1.0
N A:THR87 4.8 38.7 1.0
N A:TRP58 4.8 40.2 1.0

Fluorine binding site 4 out of 6 in 1zdm

Go back to Fluorine Binding Sites List in 1zdm
Fluorine binding site 4 out of 6 in the Crystal Structure of Activated Chey Bound to Xe


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 Activated Chey Bound to Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F57

b:52.3
occ:1.00
 F1 B:BFD57 0.0 52.3 1.0
BE B:BFD57 1.5 50.9 1.0
MN B:MN191 2.1 42.9 1.0
F2 B:BFD57 2.4 52.3 1.0
F3 B:BFD57 2.5 52.3 1.0
OD1 B:BFD57 2.5 33.3 1.0
OD2 B:BFD57 2.6 23.4 1.0
CG B:BFD57 2.9 35.3 1.0
O B:HOH251 3.1 71.3 1.0
O B:HOH195 3.1 44.1 1.0
O B:HOH228 3.1 55.8 1.0
O B:ASN59 3.2 38.5 1.0
CB B:ASN59 3.6 49.8 1.0
N B:ASN59 3.6 30.6 1.0
CA B:ASN59 3.8 35.8 1.0
C B:ASN59 3.9 40.6 1.0
NZ B:LYS109 4.1 40.5 1.0
OD1 B:ASP13 4.3 41.7 1.0
ND2 B:ASN59 4.3 62.2 1.0
CG B:ASN59 4.4 60.6 1.0
CB B:BFD57 4.4 29.3 1.0
N B:TRP58 4.4 39.7 1.0
O B:HOH220 4.5 71.0 1.0
C B:TRP58 4.6 40.4 1.0
OG1 B:THR87 4.7 37.0 1.0

Fluorine binding site 5 out of 6 in 1zdm

Go back to Fluorine Binding Sites List in 1zdm
Fluorine binding site 5 out of 6 in the Crystal Structure of Activated Chey Bound to Xe


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 Activated Chey Bound to Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F57

b:52.3
occ:1.00
 F2 B:BFD57 0.0 52.3 1.0
BE B:BFD57 1.5 50.9 1.0
OG1 B:THR87 2.4 37.0 1.0
F1 B:BFD57 2.4 52.3 1.0
OD1 B:BFD57 2.5 33.3 1.0
F3 B:BFD57 2.5 52.3 1.0
N B:ASN59 2.9 30.6 1.0
N B:TRP58 3.3 39.7 1.0
CB B:TRP58 3.4 50.5 1.0
CB B:THR87 3.4 30.4 1.0
CG B:BFD57 3.4 35.3 1.0
CA B:TRP58 3.6 37.6 1.0
CB B:ASN59 3.7 49.8 1.0
N B:ALA88 3.7 41.2 1.0
C B:TRP58 3.8 40.4 1.0
OD2 B:BFD57 3.8 23.4 1.0
CA B:ASN59 3.9 35.8 1.0
O B:HOH251 3.9 71.3 1.0
CA B:THR87 3.9 33.8 1.0
C B:THR87 4.4 34.5 1.0
MN B:MN191 4.4 42.9 1.0
C B:BFD57 4.4 38.2 1.0
N B:GLU89 4.5 45.3 1.0
O B:ASN59 4.6 38.5 1.0
CG B:TRP58 4.6 48.8 1.0
C B:ASN59 4.7 40.6 1.0
CB B:BFD57 4.7 29.3 1.0
CB B:ALA88 4.7 25.7 1.0
CA B:ALA88 4.7 43.3 1.0
CG2 B:THR87 4.7 34.9 1.0
CA B:BFD57 4.8 33.1 1.0
NZ B:LYS109 4.9 40.5 1.0
O B:TRP58 5.0 41.5 1.0
CB B:GLU89 5.0 45.2 1.0

Fluorine binding site 6 out of 6 in 1zdm

Go back to Fluorine Binding Sites List in 1zdm
Fluorine binding site 6 out of 6 in the Crystal Structure of Activated Chey Bound to Xe


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 Activated Chey Bound to Xe within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F57

b:52.3
occ:1.00
 F3 B:BFD57 0.0 52.3 1.0
BE B:BFD57 1.5 50.9 1.0
F1 B:BFD57 2.5 52.3 1.0
F2 B:BFD57 2.5 52.3 1.0
OD1 B:BFD57 2.5 33.3 1.0
NZ B:LYS109 2.8 40.5 1.0
N B:ALA88 3.0 41.2 1.0
CE B:LYS109 3.3 44.8 1.0
CD B:LYS109 3.4 39.7 1.0
CB B:ALA88 3.5 25.7 1.0
CG B:BFD57 3.6 35.3 1.0
OG1 B:THR87 3.6 37.0 1.0
CA B:THR87 3.7 33.8 1.0
C B:THR87 3.8 34.5 1.0
CA B:ALA88 3.8 43.3 1.0
O B:HOH251 3.9 71.3 1.0
O B:HOH195 3.9 44.1 1.0
OD2 B:BFD57 4.0 23.4 1.0
CB B:THR87 4.2 30.4 1.0
MN B:MN191 4.3 42.9 1.0
CG B:LYS109 4.5 44.1 1.0
O B:VAL86 4.5 41.4 1.0
CB B:BFD57 4.8 29.3 1.0
N B:THR87 4.9 38.5 1.0
O B:THR87 4.9 43.6 1.0
N B:TRP58 4.9 39.7 1.0
C B:ALA88 4.9 43.0 1.0
N B:GLU89 4.9 45.3 1.0
O B:HOH193 5.0 56.0 1.0

Reference:

T.J.Lowery, M.Doucleff, E.J.Ruiz, S.M.Rubin, A.Pines, D.E.Wemmer. Distinguishing Multiple Chemotaxis Y Protein Conformations with Laser-Polarized 129XE uc(Nmr). Protein Sci. V. 14 848 2005.
ISSN: ISSN 0961-8368
PubMed: 15741343
DOI: 10.1110/PS.041231005
Page generated: Wed Jul 31 13:37:22 2024

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