Fluorine in PDB 8pno: The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx

Enzymatic activity of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx

All present enzymatic activity of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx:
3.1.3.10;

Protein crystallography data

The structure of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx, PDB code: 8pno was solved by P.Baumann, D.Zappala, Y.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.04 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.259, 79.325, 80.297, 90, 108.52, 90
R / Rfree (%) 21.2 / 25.7

Other elements in 8pno:

The structure of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Calcium (Ca) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx (pdb code 8pno). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx, PDB code: 8pno:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8pno

Go back to Fluorine Binding Sites List in 8pno
Fluorine binding site 1 out of 6 in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:34.3
occ:1.00
 F1 A:KQB302 0.0 34.3 1.0
MG1 A:KQB302 1.8 31.3 1.0
MG A:MG306 2.0 35.8 1.0
O1 A:KQB302 2.5 35.2 1.0
F3 A:KQB302 2.7 30.9 1.0
O A:HOH429 2.7 28.3 1.0
OD1 A:ASP6 2.8 34.8 1.0
O A:HOH445 2.8 33.5 1.0
OD2 A:ASP6 2.8 32.4 1.0
O A:GLY8 2.9 36.8 1.0
O A:HOH405 3.1 29.5 1.0
N A:GLY8 3.1 34.8 1.0
CA A:GLY8 3.1 36.1 1.0
CG A:ASP6 3.2 36.0 1.0
C A:GLY8 3.4 36.9 1.0
F2 A:KQB302 3.6 34.6 1.0
O1 A:GOL308 3.6 51.0 1.0
O A:HOH452 3.7 48.8 1.0
OD1 A:ASP166 4.0 38.1 1.0
C1 A:GOL308 4.0 56.9 1.0
C A:LEU7 4.3 34.1 1.0
N A:LEU7 4.4 37.3 1.0
CB A:ASP6 4.7 35.3 1.0
O2 A:EDO305 4.7 39.7 1.0
N A:ASN9 4.7 36.9 1.0
CA A:LEU7 4.9 36.2 1.0

Fluorine binding site 2 out of 6 in 8pno

Go back to Fluorine Binding Sites List in 8pno
Fluorine binding site 2 out of 6 in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:34.6
occ:1.00
 F2 A:KQB302 0.0 34.6 1.0
MG1 A:KQB302 1.8 31.3 1.0
F3 A:KQB302 2.5 30.9 1.0
O1 A:KQB302 2.5 35.2 1.0
O A:HOH429 2.6 28.3 1.0
N A:ASN108 2.6 32.0 1.0
OD1 A:ASP6 2.7 34.8 1.0
NZ A:LYS141 2.8 34.8 1.0
CA A:SER107 3.1 29.2 1.0
CE A:LYS141 3.2 32.6 1.0
C A:SER107 3.3 33.0 1.0
OG A:SER107 3.5 28.6 1.0
CA A:ASN108 3.5 30.5 1.0
O A:ASN108 3.6 31.0 1.0
CB A:ASN108 3.6 30.4 1.0
F1 A:KQB302 3.6 34.3 1.0
CB A:SER107 3.8 28.8 1.0
O2 A:EDO305 3.9 39.7 1.0
CG A:ASP6 3.9 36.0 1.0
O A:LEU106 3.9 27.2 1.0
C A:ASN108 4.0 33.6 1.0
N A:SER107 4.2 28.6 1.0
CG A:ASN108 4.3 32.2 1.0
C A:LEU106 4.5 28.0 1.0
O A:SER107 4.6 34.2 1.0
OD2 A:ASP6 4.6 32.4 1.0
OD1 A:ASN108 4.7 31.4 1.0
N A:LEU7 4.7 37.3 1.0
CD A:LYS141 4.7 30.4 1.0
CB A:ASP6 4.9 35.3 1.0
O A:HOH405 4.9 29.5 1.0
OD2 A:ASP165 5.0 36.4 1.0

Fluorine binding site 3 out of 6 in 8pno

Go back to Fluorine Binding Sites List in 8pno
Fluorine binding site 3 out of 6 in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:30.9
occ:1.00
 F3 A:KQB302 0.0 30.9 1.0
MG1 A:KQB302 1.8 31.3 1.0
OD1 A:ASP6 2.4 34.8 1.0
F2 A:KQB302 2.5 34.6 1.0
O A:HOH429 2.6 28.3 1.0
F1 A:KQB302 2.7 34.3 1.0
OG A:SER107 2.9 28.6 1.0
N A:GLY8 2.9 34.8 1.0
N A:LEU7 3.0 37.3 1.0
CB A:LEU7 3.2 41.3 1.0
CA A:LEU7 3.5 36.2 1.0
CG A:ASP6 3.5 36.0 1.0
O1 A:KQB302 3.6 35.2 1.0
C1 A:GOL308 3.7 56.9 1.0
CB A:SER107 3.7 28.8 1.0
C A:LEU7 3.7 34.1 1.0
CA A:SER107 3.9 29.2 1.0
CA A:GLY8 3.9 36.1 1.0
OD2 A:ASP6 4.1 32.4 1.0
O1 A:GOL308 4.2 51.0 1.0
O A:ASN108 4.2 31.0 1.0
C A:ASP6 4.2 37.4 1.0
MG A:MG306 4.3 35.8 1.0
C2 A:GOL308 4.4 56.4 1.0
N A:ASN108 4.4 32.0 1.0
O2 A:GOL308 4.4 62.2 1.0
NZ A:LYS141 4.5 34.8 1.0
CG A:LEU7 4.5 41.9 1.0
CA A:ASP6 4.5 38.2 1.0
CB A:ASP6 4.6 35.3 1.0
O A:LEU106 4.6 27.2 1.0
C A:SER107 4.6 33.0 1.0
O A:GLY8 4.7 36.8 1.0
C A:GLY8 4.8 36.9 1.0
O A:LEU7 4.9 28.3 1.0
C A:ASN108 5.0 33.6 1.0

Fluorine binding site 4 out of 6 in 8pno

Go back to Fluorine Binding Sites List in 8pno
Fluorine binding site 4 out of 6 in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:34.8
occ:1.00
 F1 B:KQB302 0.0 34.8 1.0
MG1 B:KQB302 1.8 28.9 1.0
MG B:MG305 2.0 36.2 1.0
O1 B:KQB302 2.5 35.7 1.0
F3 B:KQB302 2.6 27.6 1.0
OD1 B:ASP6 2.7 34.8 1.0
O B:HOH438 2.8 24.7 1.0
OD2 B:ASP6 2.8 31.7 1.0
O B:HOH427 2.8 26.8 1.0
O B:GLY8 2.8 38.0 1.0
O B:HOH407 3.0 35.1 1.0
CG B:ASP6 3.1 35.7 1.0
N B:GLY8 3.2 33.8 1.0
CA B:GLY8 3.3 33.5 1.0
C B:GLY8 3.5 36.4 1.0
F2 B:KQB302 3.6 34.9 1.0
O4 B:PEG304 3.6 67.6 1.0
C3 B:PEG304 3.8 60.7 1.0
OD1 B:ASP166 3.9 39.3 1.0
C4 B:PEG304 4.1 62.2 1.0
C B:LEU7 4.3 31.7 1.0
N B:LEU7 4.3 34.9 1.0
CB B:ASP6 4.6 35.0 1.0
N B:ASN9 4.8 34.2 1.0
O2 B:EDO303 4.8 45.6 1.0
C2 B:EDO303 4.9 50.6 1.0
CA B:LEU7 4.9 33.5 1.0
OD1 B:ASP165 5.0 33.8 1.0
CG B:ASP166 5.0 40.3 1.0
O2 B:PEG304 5.0 69.3 1.0

Fluorine binding site 5 out of 6 in 8pno

Go back to Fluorine Binding Sites List in 8pno
Fluorine binding site 5 out of 6 in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:34.9
occ:1.00
 F2 B:KQB302 0.0 34.9 1.0
MG1 B:KQB302 1.8 28.9 1.0
F3 B:KQB302 2.4 27.6 1.0
O1 B:KQB302 2.6 35.7 1.0
O B:HOH438 2.6 24.7 1.0
N B:ASN108 2.6 33.6 1.0
OD1 B:ASP6 2.7 34.8 1.0
NZ B:LYS141 2.8 36.3 1.0
CA B:SER107 3.1 32.1 1.0
CE B:LYS141 3.2 35.4 1.0
C B:SER107 3.3 33.4 1.0
OG B:SER107 3.5 26.3 1.0
CA B:ASN108 3.6 30.1 1.0
O B:ASN108 3.6 30.3 1.0
F1 B:KQB302 3.6 34.8 1.0
CB B:ASN108 3.7 31.6 1.0
O B:LEU106 3.8 26.9 1.0
CB B:SER107 3.8 30.6 1.0
CG B:ASP6 3.9 35.7 1.0
C B:ASN108 4.0 30.4 1.0
O2 B:EDO303 4.1 45.6 1.0
N B:SER107 4.1 30.0 1.0
CG B:ASN108 4.3 33.1 1.0
C B:LEU106 4.4 29.8 1.0
O B:SER107 4.6 32.3 1.0
OD1 B:ASN108 4.7 31.9 1.0
OD2 B:ASP6 4.7 31.7 1.0
N B:LEU7 4.7 34.9 1.0
CD B:LYS141 4.7 34.2 1.0
CB B:ASP6 4.8 35.0 1.0
OD2 B:ASP165 4.9 43.2 1.0
O B:HOH407 4.9 35.1 1.0
ND2 B:ASN170 4.9 31.9 1.0
ND2 B:ASN108 4.9 29.2 1.0
CA B:ASP6 5.0 35.1 1.0

Fluorine binding site 6 out of 6 in 8pno

Go back to Fluorine Binding Sites List in 8pno
Fluorine binding site 6 out of 6 in the The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The MGF3(H2O) Transition State Analog Complex of E. Coli Yihx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:27.6
occ:1.00
 F3 B:KQB302 0.0 27.6 1.0
MG1 B:KQB302 1.8 28.9 1.0
OD1 B:ASP6 2.4 34.8 1.0
F2 B:KQB302 2.4 34.9 1.0
O B:HOH438 2.6 24.7 1.0
F1 B:KQB302 2.6 34.8 1.0
OG B:SER107 2.9 26.3 1.0
N B:GLY8 3.0 33.8 1.0
N B:LEU7 3.1 34.9 1.0
CB B:LEU7 3.3 36.9 1.0
CG B:ASP6 3.4 35.7 1.0
O1 B:KQB302 3.5 35.7 1.0
CA B:LEU7 3.6 33.5 1.0
CB B:SER107 3.6 30.6 1.0
C3 B:PEG304 3.7 60.7 1.0
C B:LEU7 3.8 31.7 1.0
CA B:SER107 3.8 32.1 1.0
CA B:GLY8 4.0 33.5 1.0
OD2 B:ASP6 4.1 31.7 1.0
O B:ASN108 4.1 30.3 1.0
C B:ASP6 4.2 36.6 1.0
N B:ASN108 4.3 33.6 1.0
O2 B:PEG304 4.3 69.3 1.0
MG B:MG305 4.4 36.2 1.0
NZ B:LYS141 4.5 36.3 1.0
CA B:ASP6 4.5 35.1 1.0
CG B:LEU7 4.5 39.3 1.0
CB B:ASP6 4.5 35.0 1.0
O B:LEU106 4.5 26.9 1.0
C B:SER107 4.6 33.4 1.0
O B:HOH440 4.6 33.8 1.0
O B:GLY8 4.7 38.0 1.0
C4 B:PEG304 4.9 62.2 1.0
C B:GLY8 4.9 36.4 1.0
O B:LEU7 4.9 30.0 1.0
C B:ASN108 5.0 30.4 1.0
N B:SER107 5.0 30.0 1.0

Reference:

P.Baumann, D.Zappala, Y.Jin. The MGF3(H2O)- Transition State Analog Complex of E. Coli Yihx To Be Published.
Page generated: Fri Aug 2 22:18:26 2024

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