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Fluorine in PDB 1rlt: Transition State Analogue of Ybiv From E. Coli K12

Protein crystallography data

The structure of Transition State Analogue of Ybiv From E. Coli K12, PDB code: 1rlt was solved by A.Roberts, S.Y.Lee, E.Mccullagh, R.E.Silversmith, D.E.Wemmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.93 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.761, 91.166, 183.850, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 26.4

Other elements in 1rlt:

The structure of Transition State Analogue of Ybiv From E. Coli K12 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Aluminium (Al) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Transition State Analogue of Ybiv From E. Coli K12 (pdb code 1rlt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Transition State Analogue of Ybiv From E. Coli K12, PDB code: 1rlt:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 1rlt

Go back to Fluorine Binding Sites List in 1rlt
Fluorine binding site 1 out of 12 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:43.7
occ:1.00
F1 A:AF3801 0.0 43.7 1.0
AL A:AF3801 1.7 44.1 1.0
NZ A:LYS192 2.7 12.7 1.0
N A:GLY45 2.8 22.2 1.0
F2 A:AF3801 2.9 41.0 1.0
F3 A:AF3801 2.9 47.0 1.0
OD1 A:ASP9 3.0 22.4 1.0
CA A:SER44 3.1 22.5 1.0
OG A:SER44 3.2 20.0 1.0
CE A:LYS192 3.4 20.7 1.0
CB A:SER44 3.4 20.9 1.0
O A:HOH911 3.5 45.5 1.0
C A:SER44 3.5 22.1 1.0
CA A:GLY45 4.0 18.5 1.0
O A:ALA43 4.0 26.5 1.0
CG A:ASP9 4.0 24.3 1.0
ND2 A:ASN218 4.1 22.1 1.0
OD1 A:ASN218 4.2 21.2 1.0
N A:SER44 4.3 23.2 1.0
O A:SER178 4.4 26.1 1.0
O A:HOH807 4.5 22.5 1.0
CG A:ASN218 4.5 19.5 1.0
OD2 A:ASP9 4.5 19.8 1.0
C A:ALA43 4.6 26.2 1.0
N A:ASN46 4.6 18.5 1.0
O A:SER44 4.7 23.7 1.0
N A:MET10 4.7 21.4 1.0
MG A:MG805 4.8 26.0 1.0
C A:GLY45 4.8 16.8 1.0
CD A:LYS192 4.9 16.5 1.0
OD1 A:ASP219 5.0 25.1 1.0

Fluorine binding site 2 out of 12 in 1rlt

Go back to Fluorine Binding Sites List in 1rlt
Fluorine binding site 2 out of 12 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:41.0
occ:1.00
F2 A:AF3801 0.0 41.0 1.0
AL A:AF3801 1.7 44.1 1.0
N A:ASP11 2.7 20.9 1.0
F3 A:AF3801 2.9 47.0 1.0
N A:MET10 2.9 21.4 1.0
F1 A:AF3801 2.9 43.7 1.0
CB A:MET10 2.9 22.5 1.0
OG A:SER44 3.0 20.0 1.0
CA A:MET10 3.2 18.1 1.0
OD1 A:ASP11 3.2 21.6 1.0
C A:MET10 3.4 21.6 1.0
ND2 A:ASN46 3.6 16.0 1.0
OD1 A:ASP9 3.6 22.4 1.0
CB A:SER44 3.6 20.9 1.0
O A:HOH911 3.7 45.5 1.0
CG A:ASP11 3.8 24.2 1.0
CA A:ASP11 3.9 22.6 1.0
CG A:MET10 3.9 25.4 1.0
CB A:ASP11 3.9 21.8 1.0
CG A:ASP9 4.0 24.3 1.0
OD2 A:ASP9 4.0 19.8 1.0
C A:ASP9 4.1 20.1 1.0
MG A:MG805 4.3 26.0 1.0
CA A:SER44 4.5 22.5 1.0
O A:HOH825 4.6 25.8 1.0
O A:ASP11 4.6 23.9 1.0
O A:MET10 4.6 22.6 1.0
CG A:ASN46 4.6 20.3 1.0
CA A:ASP9 4.7 19.8 1.0
C A:ASP11 4.7 23.5 1.0
N A:GLY45 4.8 22.2 1.0
OD2 A:ASP11 4.9 25.3 1.0
CB A:ASP9 4.9 23.9 1.0
NZ A:LYS192 5.0 12.7 1.0

Fluorine binding site 3 out of 12 in 1rlt

Go back to Fluorine Binding Sites List in 1rlt
Fluorine binding site 3 out of 12 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:47.0
occ:1.00
F3 A:AF3801 0.0 47.0 1.0
AL A:AF3801 1.7 44.1 1.0
MG A:MG805 2.0 26.0 1.0
O A:HOH807 2.8 22.5 1.0
OD2 A:ASP9 2.8 19.8 1.0
F2 A:AF3801 2.9 41.0 1.0
F1 A:AF3801 2.9 43.7 1.0
OD1 A:ASP9 3.0 22.4 1.0
O A:HOH892 3.2 26.5 1.0
CG A:ASP9 3.3 24.3 1.0
O A:ASP11 3.3 23.9 1.0
O A:HOH911 3.6 45.5 1.0
CA A:GLY179 3.6 24.4 1.0
CB A:ASP11 3.7 21.8 1.0
N A:ASP11 3.7 20.9 1.0
CA A:ASP11 4.0 22.6 1.0
C A:ASP11 4.1 23.5 1.0
O A:GLY179 4.1 26.9 1.0
OD1 A:ASP11 4.1 21.6 1.0
OD1 A:ASP215 4.2 19.0 1.0
C A:GLY179 4.2 28.0 1.0
O A:SER178 4.4 26.1 1.0
CG A:ASP11 4.4 24.2 1.0
N A:MET10 4.4 21.4 1.0
NZ A:LYS192 4.4 12.7 1.0
ND2 A:ASN218 4.5 22.1 1.0
OG A:SER216 4.5 32.5 1.0
C A:MET10 4.6 21.6 1.0
OD1 A:ASN218 4.7 21.2 1.0
CB A:ASP9 4.7 23.9 1.0
N A:GLY179 4.8 27.4 1.0
OD2 A:ASP219 4.9 28.5 1.0

Fluorine binding site 4 out of 12 in 1rlt

Go back to Fluorine Binding Sites List in 1rlt
Fluorine binding site 4 out of 12 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:52.3
occ:1.00
F1 B:AF3802 0.0 52.3 1.0
AL B:AF3802 1.7 51.8 1.0
NZ B:LYS192 2.5 20.6 1.0
OD1 B:ASP9 2.7 27.5 1.0
F2 B:AF3802 2.9 52.1 1.0
F3 B:AF3802 2.9 52.4 1.0
CE B:LYS192 3.2 25.4 1.0
N B:GLY45 3.2 25.7 1.0
CA B:SER44 3.4 25.0 1.0
O B:HOH857 3.5 52.7 1.0
OG B:SER44 3.6 26.1 1.0
ND2 B:ASN218 3.7 35.7 1.0
OD1 B:ASN218 3.8 35.1 1.0
C B:SER44 3.8 24.6 1.0
CG B:ASP9 3.8 28.5 1.0
CB B:SER44 3.8 24.6 1.0
O B:HOH816 4.0 29.9 1.0
O B:ALA43 4.1 26.3 1.0
CG B:ASN218 4.1 34.9 1.0
OD2 B:ASP9 4.2 26.6 1.0
CA B:GLY45 4.3 22.9 1.0
MG B:MG806 4.4 37.3 1.0
OD1 B:ASP219 4.5 22.8 1.0
N B:SER44 4.5 26.1 1.0
O B:SER178 4.6 53.9 1.0
CD B:LYS192 4.6 25.9 1.0
N B:MET10 4.7 20.3 1.0
CA B:GLY179 4.7 61.4 1.0
C B:ALA43 4.7 26.4 1.0
O B:SER44 5.0 24.8 1.0

Fluorine binding site 5 out of 12 in 1rlt

Go back to Fluorine Binding Sites List in 1rlt
Fluorine binding site 5 out of 12 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:52.1
occ:1.00
F2 B:AF3802 0.0 52.1 1.0
AL B:AF3802 1.7 51.8 1.0
N B:ASP11 2.7 24.1 1.0
N B:MET10 2.8 20.3 1.0
CB B:MET10 2.8 24.3 1.0
OG B:SER44 2.9 26.1 1.0
F3 B:AF3802 2.9 52.4 1.0
F1 B:AF3802 2.9 52.3 1.0
CA B:MET10 3.1 22.7 1.0
C B:MET10 3.3 23.5 1.0
CB B:SER44 3.4 24.6 1.0
OD1 B:ASP11 3.6 33.0 1.0
OD1 B:ASP9 3.6 27.5 1.0
O B:HOH857 3.8 52.7 1.0
CA B:ASP11 3.9 26.2 1.0
CB B:ASP11 4.0 25.6 1.0
ND2 B:ASN46 4.0 21.5 1.0
CG B:ASP11 4.0 29.6 1.0
CG B:ASP9 4.0 28.5 1.0
CG B:MET10 4.0 26.9 1.0
C B:ASP9 4.1 20.8 1.0
CA B:SER44 4.1 25.0 1.0
OD2 B:ASP9 4.1 26.6 1.0
MG B:MG806 4.3 37.3 1.0
O B:MET10 4.6 23.2 1.0
O B:ASP11 4.6 27.9 1.0
CA B:ASP9 4.6 23.1 1.0
N B:GLY45 4.6 25.7 1.0
O B:HOH833 4.7 29.1 1.0
C B:ASP11 4.7 25.9 1.0
NZ B:LYS192 4.8 20.6 1.0
CG B:ASN46 4.9 23.1 1.0
OD2 B:ASP11 4.9 31.6 1.0
O B:ALA43 4.9 26.3 1.0
CB B:ASP9 4.9 25.1 1.0
C B:SER44 5.0 24.6 1.0

Fluorine binding site 6 out of 12 in 1rlt

Go back to Fluorine Binding Sites List in 1rlt
Fluorine binding site 6 out of 12 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:52.4
occ:1.00
F3 B:AF3802 0.0 52.4 1.0
AL B:AF3802 1.7 51.8 1.0
MG B:MG806 1.9 37.3 1.0
O B:HOH816 2.8 29.9 1.0
F2 B:AF3802 2.9 52.1 1.0
F1 B:AF3802 2.9 52.3 1.0
OD2 B:ASP9 3.0 26.6 1.0
O B:ASP11 3.1 27.9 1.0
O B:HOH889 3.1 34.5 1.0
OD1 B:ASP9 3.3 27.5 1.0
CB B:ASP11 3.4 25.6 1.0
O B:HOH857 3.4 52.7 1.0
N B:ASP11 3.5 24.1 1.0
CG B:ASP9 3.5 28.5 1.0
CA B:GLY179 3.7 61.4 1.0
CA B:ASP11 3.7 26.2 1.0
C B:ASP11 3.8 25.9 1.0
O B:GLY179 3.9 65.1 1.0
OD1 B:ASP11 4.0 33.0 1.0
OD1 B:ASP215 4.0 25.4 1.0
CG B:ASP11 4.2 29.6 1.0
C B:GLY179 4.3 65.6 1.0
N B:MET10 4.4 20.3 1.0
C B:MET10 4.4 23.5 1.0
OG B:SER216 4.6 38.5 1.0
NZ B:LYS192 4.7 20.6 1.0
OD1 B:ASN218 4.8 35.1 1.0
ND2 B:ASN218 4.8 35.7 1.0
OD2 B:ASP219 4.9 29.8 1.0
CA B:MET10 4.9 22.7 1.0
CB B:ASP9 4.9 25.1 1.0
N B:GLY179 4.9 56.7 1.0

Fluorine binding site 7 out of 12 in 1rlt

Go back to Fluorine Binding Sites List in 1rlt
Fluorine binding site 7 out of 12 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:58.8
occ:1.00
F1 C:AF3803 0.0 58.8 1.0
AL C:AF3803 1.7 58.7 1.0
OG C:SER44 2.7 29.6 1.0
F3 C:AF3803 2.9 58.6 1.0
F2 C:AF3803 2.9 58.4 1.0
N C:ASP11 3.1 33.4 1.0
N C:MET10 3.2 33.4 1.0
CB C:MET10 3.3 29.5 1.0
CB C:SER44 3.4 25.8 1.0
OD1 C:ASP9 3.4 33.3 1.0
CA C:MET10 3.6 34.4 1.0
OD1 C:ASP11 3.6 36.6 1.0
O C:HOH811 3.7 50.0 1.0
ND2 C:ASN46 3.8 29.4 1.0
C C:MET10 3.8 34.1 1.0
CB C:ASP11 3.9 33.8 1.0
CG C:ASP9 3.9 31.4 1.0
CG C:ASP11 4.0 36.7 1.0
CA C:ASP11 4.1 33.9 1.0
CA C:SER44 4.1 26.4 1.0
OD2 C:ASP9 4.1 28.8 1.0
CG C:MET10 4.1 28.3 1.0
N C:GLY45 4.4 27.4 1.0
C C:ASP9 4.4 33.6 1.0
MG C:MG807 4.4 39.2 1.0
O C:ASP11 4.7 37.4 1.0
CG C:ASN46 4.8 29.3 1.0
NZ C:LYS192 4.8 41.8 1.0
C C:SER44 4.8 25.7 1.0
CA C:ASP9 4.8 32.3 1.0
O C:ALA43 4.8 30.4 1.0
O C:HOH836 4.9 34.6 1.0
C C:ASP11 4.9 34.7 1.0
OD2 C:ASP11 4.9 36.5 1.0

Fluorine binding site 8 out of 12 in 1rlt

Go back to Fluorine Binding Sites List in 1rlt
Fluorine binding site 8 out of 12 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:58.4
occ:1.00
F2 C:AF3803 0.0 58.4 1.0
AL C:AF3803 1.7 58.7 1.0
NZ C:LYS192 2.9 41.8 1.0
F3 C:AF3803 2.9 58.6 1.0
F1 C:AF3803 2.9 58.8 1.0
N C:GLY45 2.9 27.4 1.0
ND2 C:ASN218 2.9 46.0 1.0
OD1 C:ASP9 3.2 33.3 1.0
CE C:LYS192 3.4 41.3 1.0
CA C:SER44 3.6 26.4 1.0
O C:HOH811 3.6 50.0 1.0
OG C:SER44 3.6 29.6 1.0
C C:SER44 3.7 25.7 1.0
CG C:ASN218 3.8 46.9 1.0
CA C:GLY45 3.9 27.4 1.0
CB C:SER44 4.0 25.8 1.0
OD1 C:ASN218 4.0 48.5 1.0
CG C:ASP9 4.3 31.4 1.0
O3 C:GOL759 4.3 48.6 1.0
OG C:SER178 4.4 79.5 1.0
O C:ALA43 4.5 30.4 1.0
OD2 C:ASP9 4.6 28.8 1.0
MG C:MG807 4.7 39.2 1.0
N C:SER44 4.8 26.8 1.0
OD1 C:ASN68 4.8 41.1 1.0
OD1 C:ASP219 4.8 35.1 1.0
N C:ASN46 4.9 27.8 1.0
O C:SER44 4.9 23.7 1.0
C C:GLY45 4.9 28.4 1.0
CD C:LYS192 4.9 41.4 1.0

Fluorine binding site 9 out of 12 in 1rlt

Go back to Fluorine Binding Sites List in 1rlt
Fluorine binding site 9 out of 12 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:58.6
occ:1.00
F3 C:AF3803 0.0 58.6 1.0
AL C:AF3803 1.7 58.7 1.0
MG C:MG807 1.9 39.2 1.0
OD2 C:ASP9 2.6 28.8 1.0
F1 C:AF3803 2.9 58.8 1.0
F2 C:AF3803 2.9 58.4 1.0
OD1 C:ASP9 2.9 33.3 1.0
CG C:ASP9 3.1 31.4 1.0
O C:ASP11 3.2 37.4 1.0
O C:HOH839 3.2 46.7 1.0
OD1 C:ASP215 3.5 36.8 1.0
O C:HOH811 3.5 50.0 1.0
CB C:ASP11 3.6 33.8 1.0
N C:ASP11 3.8 33.4 1.0
C C:ASP11 4.0 34.7 1.0
CA C:ASP11 4.0 33.9 1.0
OD1 C:ASN218 4.4 48.5 1.0
OD1 C:ASP11 4.4 36.6 1.0
NZ C:LYS192 4.4 41.8 1.0
CG C:ASP11 4.5 36.7 1.0
ND2 C:ASN218 4.5 46.0 1.0
CG C:ASP215 4.5 39.3 1.0
O C:SER178 4.5 92.9 1.0
N C:MET10 4.5 33.4 1.0
OD2 C:ASP219 4.6 38.5 1.0
CB C:ASP9 4.6 32.3 1.0
C C:MET10 4.7 34.1 1.0
OD2 C:ASP215 4.7 39.1 1.0
OG C:SER178 4.8 79.5 1.0
OG C:SER216 4.8 53.0 1.0
CG C:ASN218 4.9 46.9 1.0

Fluorine binding site 10 out of 12 in 1rlt

Go back to Fluorine Binding Sites List in 1rlt
Fluorine binding site 10 out of 12 in the Transition State Analogue of Ybiv From E. Coli K12


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Transition State Analogue of Ybiv From E. Coli K12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F804

b:55.5
occ:1.00
F1 D:AF3804 0.0 55.5 1.0
AL D:AF3804 1.7 55.4 1.0
ND2 D:ASN218 2.8 74.7 1.0
NZ D:LYS192 2.8 26.7 1.0
F3 D:AF3804 2.9 56.8 1.0
F2 D:AF3804 2.9 54.8 1.0
OD1 D:ASP9 2.9 33.8 1.0
N D:GLY45 3.3 25.6 1.0
O D:HOH889 3.4 55.0 1.0
CE D:LYS192 3.4 32.2 1.0
CA D:SER44 3.6 23.3 1.0
CG D:ASN218 3.8 68.5 1.0
OG D:SER44 3.8 22.8 1.0
C D:SER44 3.9 24.6 1.0
CG D:ASP9 3.9 31.6 1.0
OD1 D:ASN218 4.0 74.8 1.0
CB D:SER44 4.0 22.8 1.0
O D:HOH899 4.2 40.9 1.0
OD2 D:ASP9 4.3 28.7 1.0
CA D:GLY45 4.3 25.2 1.0
O D:ALA43 4.4 23.3 1.0
OD1 D:ASP219 4.4 28.1 1.0
MG D:MG808 4.5 32.9 1.0
OD1 D:ASN68 4.7 39.5 1.0
N D:SER44 4.8 24.0 1.0
CD D:LYS192 4.9 32.9 1.0
N D:MET10 4.9 27.5 1.0

Reference:

A.Roberts, S.Y.Lee, E.Mccullagh, R.E.Silversmith, D.E.Wemmer. Ybiv From Escherichia Coli K12 Is A Had Phosphatase. Proteins V. 58 790 2005.
ISSN: ISSN 0887-3585
PubMed: 15657928
DOI: 10.1002/PROT.20267
Page generated: Wed Jul 31 12:41:18 2024

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