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Fluorine in PDB 5uht: Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0

Protein crystallography data

The structure of Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0, PDB code: 5uht was solved by Y.Liu, J.Rose, L.Jiang, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.19 / 2.68
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 177.970, 98.380, 72.050, 90.00, 110.54, 90.00
R / Rfree (%) 18.2 / 22.2

Other elements in 5uht:

The structure of Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0 (pdb code 5uht). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0, PDB code: 5uht:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5uht

Go back to Fluorine Binding Sites List in 5uht
Fluorine binding site 1 out of 6 in the Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F53

b:41.2
occ:1.00
 F1 B:BFD53 0.0 41.2 1.0
BE B:BFD53 1.4 45.0 1.0
MG B:MG204 2.1 37.4 1.0
OD2 B:BFD53 2.2 33.0 1.0
F3 B:BFD53 2.2 35.9 1.0
F2 B:BFD53 2.3 40.0 1.0
OD1 B:BFD53 2.3 45.3 1.0
CG B:BFD53 2.6 32.1 1.0
O B:MET55 3.1 41.8 1.0
O B:HOH313 3.2 46.6 1.0
O B:HOH305 3.2 32.9 1.0
N B:MET55 3.6 45.1 1.0
CB B:MET55 3.8 42.1 1.0
OD1 B:ASP10 3.8 66.1 1.0
C B:MET55 3.9 45.4 1.0
CA B:MET55 4.0 45.2 1.0
NZ B:LYS105 4.0 28.0 1.0
CG B:MET55 4.1 51.6 1.0
CB B:BFD53 4.1 27.1 1.0
N B:ILE54 4.3 53.7 1.0
OD2 B:ASP9 4.5 41.4 1.0
OD2 B:ASP10 4.5 51.8 1.0
CE B:MET55 4.5 45.0 1.0
CG B:ASP10 4.6 56.3 1.0
C B:ILE54 4.7 45.1 1.0
OG1 B:THR83 4.7 35.6 1.0
N B:ALA84 4.9 35.9 1.0
CA B:BFD53 4.9 34.0 1.0
O A:HOH628 4.9 52.2 1.0
C B:BFD53 5.0 38.3 1.0

Fluorine binding site 2 out of 6 in 5uht

Go back to Fluorine Binding Sites List in 5uht
Fluorine binding site 2 out of 6 in the Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F53

b:40.0
occ:1.00
 F2 B:BFD53 0.0 40.0 1.0
BE B:BFD53 1.4 45.0 1.0
OD1 B:BFD53 2.3 45.3 1.0
F1 B:BFD53 2.3 41.2 1.0
F3 B:BFD53 2.3 35.9 1.0
N B:ALA84 2.8 35.9 1.0
NZ B:LYS105 2.9 28.0 1.0
CG B:BFD53 3.4 32.1 1.0
CA B:THR83 3.5 33.4 1.0
CD B:LYS105 3.5 41.6 1.0
OG1 B:THR83 3.6 35.6 1.0
C B:THR83 3.6 35.7 1.0
CB B:ALA84 3.6 40.4 1.0
CE B:LYS105 3.6 37.8 1.0
OD2 B:BFD53 3.7 33.0 1.0
CA B:ALA84 3.8 43.1 1.0
O B:HOH313 4.0 46.6 1.0
CB B:THR83 4.1 35.3 1.0
MG B:MG204 4.1 37.4 1.0
O B:LEU82 4.3 31.4 1.0
N B:THR83 4.6 35.9 1.0
OD2 B:ASP9 4.6 41.4 1.0
CB B:BFD53 4.6 27.1 1.0
O B:HOH310 4.7 38.9 1.0
N B:ILE54 4.7 53.7 1.0
O B:THR83 4.8 32.0 1.0
C B:ALA84 4.8 46.2 1.0
CE B:MET55 4.8 45.0 1.0
N B:LYS85 4.9 47.0 1.0
O A:HOH618 4.9 49.7 1.0
C B:LEU82 4.9 31.7 1.0
CG B:LYS105 4.9 35.6 1.0
O B:HOH305 5.0 32.9 1.0
N B:MET55 5.0 45.1 1.0

Fluorine binding site 3 out of 6 in 5uht

Go back to Fluorine Binding Sites List in 5uht
Fluorine binding site 3 out of 6 in the Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F53

b:35.9
occ:1.00
 F3 B:BFD53 0.0 35.9 1.0
BE B:BFD53 1.4 45.0 1.0
F1 B:BFD53 2.2 41.2 1.0
OD1 B:BFD53 2.3 45.3 1.0
F2 B:BFD53 2.3 40.0 1.0
OG1 B:THR83 2.5 35.6 1.0
N B:MET55 3.0 45.1 1.0
CG B:MET55 3.2 51.6 1.0
N B:ILE54 3.2 53.7 1.0
CG B:BFD53 3.3 32.1 1.0
CB B:THR83 3.6 35.3 1.0
CB B:ILE54 3.7 45.9 1.0
OD2 B:BFD53 3.7 33.0 1.0
CA B:ILE54 3.7 48.9 1.0
N B:ALA84 3.7 35.9 1.0
CB B:MET55 3.7 42.1 1.0
C B:ILE54 3.8 45.1 1.0
CA B:MET55 3.9 45.2 1.0
CA B:THR83 3.9 33.4 1.0
CE B:MET55 4.1 45.0 1.0
MG B:MG204 4.2 37.4 1.0
C B:BFD53 4.3 38.3 1.0
C B:THR83 4.3 35.7 1.0
O B:MET55 4.4 41.8 1.0
SD B:MET55 4.4 50.5 1.0
CB B:BFD53 4.5 27.1 1.0
C B:MET55 4.5 45.4 1.0
N B:LYS85 4.6 47.0 1.0
CG1 B:ILE54 4.6 40.7 1.0
CA B:BFD53 4.6 34.0 1.0
CG2 B:ILE54 4.7 40.6 1.0
CA B:ALA84 4.7 43.1 1.0
CB B:ALA84 4.8 40.4 1.0
CG2 B:THR83 4.9 31.7 1.0
O B:LEU82 4.9 31.4 1.0
NZ B:LYS105 4.9 28.0 1.0
O B:ILE54 5.0 43.7 1.0

Fluorine binding site 4 out of 6 in 5uht

Go back to Fluorine Binding Sites List in 5uht
Fluorine binding site 4 out of 6 in the Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F53

b:54.6
occ:1.00
 F1 D:BFD53 0.0 54.6 1.0
BE D:BFD53 1.4 50.9 1.0
OD2 D:BFD53 2.1 34.9 1.0
MG D:MG202 2.1 32.6 1.0
F3 D:BFD53 2.2 43.5 1.0
F2 D:BFD53 2.3 46.1 1.0
OD1 D:BFD53 2.3 47.9 1.0
CG D:BFD53 2.5 35.7 1.0
O D:HOH307 2.9 48.0 1.0
O D:MET55 3.0 41.2 1.0
O D:HOH305 3.3 40.0 1.0
N D:MET55 3.4 39.8 1.0
CB D:MET55 3.6 42.9 1.0
C D:MET55 3.7 50.8 1.0
CA D:MET55 3.8 44.5 1.0
OD1 D:ASP10 3.8 57.0 1.0
CB D:BFD53 4.0 28.8 1.0
N D:ILE54 4.2 65.9 1.0
CG D:MET55 4.3 51.6 1.0
NZ D:LYS105 4.5 27.7 1.0
C D:ILE54 4.5 55.1 1.0
OD2 D:ASP9 4.5 42.9 1.0
OD2 D:ASP10 4.5 56.3 1.0
CG D:ASP10 4.6 52.8 1.0
SD D:MET55 4.7 57.4 1.0
OG1 D:THR83 4.7 41.9 1.0
CA D:BFD53 4.8 36.1 1.0
C D:BFD53 4.8 42.0 1.0
CA D:ILE54 4.8 53.6 1.0
CE D:LYS105 4.9 31.2 1.0
N D:ALA84 5.0 36.2 1.0

Fluorine binding site 5 out of 6 in 5uht

Go back to Fluorine Binding Sites List in 5uht
Fluorine binding site 5 out of 6 in the Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F53

b:46.1
occ:1.00
 F2 D:BFD53 0.0 46.1 1.0
BE D:BFD53 1.4 50.9 1.0
F1 D:BFD53 2.3 54.6 1.0
OD1 D:BFD53 2.3 47.9 1.0
F3 D:BFD53 2.3 43.5 1.0
N D:ALA84 2.9 36.2 1.0
CE D:LYS105 3.1 31.2 1.0
NZ D:LYS105 3.3 27.7 1.0
CG D:BFD53 3.4 35.7 1.0
CA D:THR83 3.5 41.2 1.0
OG1 D:THR83 3.6 41.9 1.0
C D:THR83 3.7 41.6 1.0
CB D:ALA84 3.7 33.7 1.0
OD2 D:BFD53 3.7 34.9 1.0
O D:HOH307 3.8 48.0 1.0
CA D:ALA84 3.9 41.4 1.0
MG D:MG202 4.1 32.6 1.0
CB D:THR83 4.1 43.9 1.0
CD D:LYS105 4.2 28.1 1.0
O D:LEU82 4.4 34.4 1.0
CG D:LYS105 4.5 31.0 1.0
N D:THR83 4.6 37.5 1.0
N D:ILE54 4.6 65.9 1.0
OD2 D:ASP9 4.7 42.9 1.0
CB D:BFD53 4.7 28.8 1.0
O D:HOH312 4.7 35.7 1.0
N D:MET55 4.8 39.8 1.0
O D:THR83 4.8 34.9 1.0
C D:ALA84 4.9 47.4 1.0
N D:LYS85 4.9 45.6 1.0
C D:LEU82 5.0 36.1 1.0

Fluorine binding site 6 out of 6 in 5uht

Go back to Fluorine Binding Sites List in 5uht
Fluorine binding site 6 out of 6 in the Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the Thermotoga Maritima HK853-BEF3-RR468 Complex at pH 5.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F53

b:43.5
occ:1.00
 F3 D:BFD53 0.0 43.5 1.0
BE D:BFD53 1.4 50.9 1.0
F1 D:BFD53 2.2 54.6 1.0
F2 D:BFD53 2.3 46.1 1.0
OD1 D:BFD53 2.3 47.9 1.0
OG1 D:THR83 2.6 41.9 1.0
N D:MET55 2.8 39.8 1.0
N D:ILE54 3.1 65.9 1.0
CG D:BFD53 3.2 35.7 1.0
CB D:ILE54 3.5 46.0 1.0
CG D:MET55 3.5 51.6 1.0
CA D:ILE54 3.5 53.6 1.0
OD2 D:BFD53 3.5 34.9 1.0
C D:ILE54 3.6 55.1 1.0
CB D:MET55 3.6 42.9 1.0
CB D:THR83 3.7 43.9 1.0
CA D:MET55 3.7 44.5 1.0
N D:ALA84 3.9 36.2 1.0
CA D:THR83 3.9 41.2 1.0
SD D:MET55 4.1 57.4 1.0
C D:BFD53 4.2 42.0 1.0
MG D:MG202 4.2 32.6 1.0
O D:MET55 4.3 41.2 1.0
C D:MET55 4.4 50.8 1.0
CG1 D:ILE54 4.4 43.7 1.0
C D:THR83 4.4 41.6 1.0
CB D:BFD53 4.5 28.8 1.0
CG2 D:ILE54 4.5 45.3 1.0
CA D:BFD53 4.5 36.1 1.0
CG D:LYS85 4.6 47.9 1.0
N D:LYS85 4.7 45.6 1.0
O D:ILE54 4.8 43.2 1.0
CA D:ALA84 4.8 41.4 1.0
CB D:ALA84 4.9 33.7 1.0
O D:LEU82 5.0 34.4 1.0
O D:HOH307 5.0 48.0 1.0

Reference:

Y.Liu, J.Rose, S.Huang, Y.Hu, Q.Wu, D.Wang, C.Li, M.Liu, P.Zhou, L.Jiang. A pH-Gated Conformational Switch Regulates the Phosphatase Activity of Bifunctional Hiska-Family Histidine Kinases. Nat Commun V. 8 2104 2017.
ISSN: ESSN 2041-1723
PubMed: 29235472
DOI: 10.1038/S41467-017-02310-9
Page generated: Thu Aug 1 15:40:11 2024

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