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Fluorine in PDB 4bx2: Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride

Enzymatic activity of Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride

All present enzymatic activity of Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride:
3.1.3.3; 3.1.3.74;

Protein crystallography data

The structure of Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride, PDB code: 4bx2 was solved by G.Knobloch, A.Gohla, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.587 / 2.19
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 166.830, 166.830, 166.830, 90.00, 90.00, 90.00
R / Rfree (%) 16.78 / 21.23

Other elements in 4bx2:

The structure of Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride (pdb code 4bx2). 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 Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride, PDB code: 4bx2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4bx2

Go back to Fluorine Binding Sites List in 4bx2
Fluorine binding site 1 out of 6 in the Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride


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 Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:20.1
occ:1.00
 F1 A:BEF302 0.0 20.1 1.0
BE A:BEF302 1.5 22.9 1.0
MG A:MG301 1.9 25.1 1.0
HB2 A:ASP27 2.5 30.0 1.0
F3 A:BEF302 2.5 23.0 1.0
F2 A:BEF302 2.5 23.7 1.0
OD1 A:ASP25 2.7 17.2 1.0
O A:HOH2006 2.7 23.5 1.0
OD2 A:ASP25 2.8 20.4 1.0
O A:ASP27 2.8 29.4 1.0
O A:HOH2007 2.9 21.6 1.0
H A:ASP27 3.0 29.4 1.0
CG A:ASP25 3.1 23.9 1.0
O A:HOH2009 3.3 36.8 1.0
CB A:ASP27 3.3 25.0 1.0
N A:ASP27 3.4 24.5 1.0
C A:ASP27 3.5 24.8 1.0
CA A:ASP27 3.6 23.5 1.0
HZ2 A:LYS209 3.8 45.3 1.0
O A:HOH2074 3.8 24.3 1.0
O A:HOH2076 3.9 28.9 1.0
H A:CYS26 3.9 31.7 1.0
OD1 A:ASP234 3.9 26.7 1.0
HB3 A:ASP27 4.0 30.0 1.0
CG A:ASP27 4.2 34.6 1.0
H A:ASN59 4.3 27.5 1.0
HZ1 A:LYS209 4.4 45.3 1.0
C A:CYS26 4.4 22.8 1.0
NZ A:LYS209 4.4 37.8 1.0
N A:CYS26 4.4 26.4 1.0
HZ3 A:LYS209 4.4 45.3 1.0
OD2 A:ASP27 4.4 31.3 1.0
HA A:ASP27 4.6 28.2 1.0
HA A:SER58 4.6 27.5 1.0
CB A:ASP25 4.6 18.5 1.0
O A:HOH2010 4.7 30.4 1.0
HG21 A:VAL29 4.7 29.4 1.0
N A:GLY28 4.8 26.2 1.0
CG A:ASP234 4.9 26.4 1.0
OG A:SER58 4.9 25.5 1.0
O A:HOH2024 4.9 43.9 1.0
OD2 A:ASP239 4.9 26.6 1.0
CA A:CYS26 4.9 22.6 1.0

Fluorine binding site 2 out of 6 in 4bx2

Go back to Fluorine Binding Sites List in 4bx2
Fluorine binding site 2 out of 6 in the Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride


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 Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:23.7
occ:1.00
 F2 A:BEF302 0.0 23.7 1.0
BE A:BEF302 1.5 22.9 1.0
H A:ASN59 1.9 27.5 1.0
HZ2 A:LYS209 1.9 45.3 1.0
OD1 A:ASP25 2.4 17.2 1.0
F3 A:BEF302 2.4 23.0 1.0
F1 A:BEF302 2.5 20.1 1.0
HA A:SER58 2.6 27.5 1.0
N A:ASN59 2.8 22.9 1.0
NZ A:LYS209 2.8 37.8 1.0
HZ1 A:LYS209 3.0 45.3 1.0
HZ3 A:LYS209 3.2 45.3 1.0
HB2 A:ASN59 3.2 22.1 1.0
CA A:SER58 3.4 22.9 1.0
O A:HOH2074 3.4 24.3 1.0
O A:HOH2009 3.5 36.8 1.0
C A:SER58 3.5 29.8 1.0
OG A:SER58 3.5 25.5 1.0
CG A:ASP25 3.6 23.9 1.0
H A:ASN60 3.7 26.8 1.0
O A:HOH2006 3.8 23.5 1.0
HE2 A:LYS209 3.8 36.4 1.0
CE A:LYS209 3.8 30.4 1.0
CA A:ASN59 3.8 20.6 1.0
O A:HOH2024 3.9 43.9 1.0
CB A:ASN59 3.9 18.4 1.0
HE3 A:LYS209 3.9 36.4 1.0
H A:CYS26 4.0 31.7 1.0
CB A:SER58 4.0 20.9 1.0
OD2 A:ASP25 4.1 20.4 1.0
MG A:MG301 4.1 25.1 1.0
H A:ASP27 4.1 29.4 1.0
HG A:SER58 4.2 30.6 1.0
HB2 A:ASP27 4.3 30.0 1.0
HB2 A:SER58 4.3 25.1 1.0
N A:ASN60 4.3 22.3 1.0
O A:VAL57 4.4 32.9 1.0
CG A:ASN59 4.5 26.2 1.0
C A:ASN59 4.6 26.7 1.0
HA A:ASN59 4.6 24.7 1.0
N A:SER58 4.6 22.9 1.0
HB3 A:ASN59 4.7 22.1 1.0
O A:SER58 4.8 23.2 1.0
N A:CYS26 4.8 26.4 1.0
CB A:ASP25 4.8 18.5 1.0
OD2 A:ASP175 4.8 32.6 1.0
HB2 A:ASP25 4.8 22.2 1.0
OD1 A:ASP239 4.8 26.6 1.0
HD21 A:ASN59 4.9 33.2 1.0
N A:ASP27 4.9 24.5 1.0
C A:VAL57 4.9 26.7 1.0
HB2 A:ASN60 4.9 35.9 1.0
O A:HOH2076 4.9 28.9 1.0
HA A:ASP25 4.9 18.7 1.0
HB3 A:SER58 4.9 25.1 1.0
ND2 A:ASN59 4.9 27.7 1.0

Fluorine binding site 3 out of 6 in 4bx2

Go back to Fluorine Binding Sites List in 4bx2
Fluorine binding site 3 out of 6 in the Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride


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 Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:23.0
occ:1.00
 F3 A:BEF302 0.0 23.0 1.0
BE A:BEF302 1.5 22.9 1.0
H A:ASP27 1.9 29.4 1.0
H A:CYS26 2.3 31.7 1.0
F2 A:BEF302 2.4 23.7 1.0
F1 A:BEF302 2.5 20.1 1.0
OD1 A:ASP25 2.6 17.2 1.0
N A:ASP27 2.7 24.5 1.0
HB2 A:CYS26 2.8 29.4 1.0
OG A:SER58 2.8 25.5 1.0
HA A:SER58 2.8 27.5 1.0
N A:CYS26 3.0 26.4 1.0
HB2 A:SER58 3.1 25.1 1.0
HG A:SER58 3.1 30.6 1.0
HB2 A:ASP27 3.2 30.0 1.0
CB A:SER58 3.3 20.9 1.0
CA A:CYS26 3.4 22.6 1.0
CG A:ASP25 3.4 23.9 1.0
C A:CYS26 3.5 22.8 1.0
CA A:SER58 3.5 22.9 1.0
CB A:CYS26 3.5 24.5 1.0
H A:ASN59 3.6 27.5 1.0
CB A:ASP27 3.6 25.0 1.0
CG A:ASP27 3.7 34.6 1.0
CA A:ASP27 3.7 23.5 1.0
OD2 A:ASP25 3.7 20.4 1.0
OD2 A:ASP27 3.9 31.3 1.0
O A:VAL57 3.9 32.9 1.0
HZ2 A:LYS209 3.9 45.3 1.0
O A:HOH2009 4.0 36.8 1.0
MG A:MG301 4.1 25.1 1.0
OD1 A:ASP27 4.1 34.8 1.0
C A:ASP25 4.1 14.4 1.0
N A:ASN59 4.2 22.9 1.0
O A:ASP27 4.2 29.4 1.0
H A:ASN60 4.2 26.8 1.0
HB3 A:CYS26 4.2 29.4 1.0
HB3 A:SER58 4.2 25.1 1.0
O A:HOH2008 4.2 24.7 1.0
HZ1 A:LYS209 4.3 45.3 1.0
C A:SER58 4.4 29.8 1.0
HA A:ASP25 4.4 18.7 1.0
HB2 A:ASN60 4.4 35.9 1.0
HA A:CYS26 4.4 27.2 1.0
C A:ASP27 4.4 24.8 1.0
HA A:ASP27 4.4 28.2 1.0
NZ A:LYS209 4.6 37.8 1.0
HB3 A:ASP27 4.6 30.0 1.0
CA A:ASP25 4.6 15.6 1.0
CB A:ASP25 4.6 18.5 1.0
N A:SER58 4.6 22.9 1.0
SG A:CYS26 4.6 25.7 1.0
O A:CYS26 4.7 23.4 1.0
C A:VAL57 4.7 26.7 1.0
O A:HOH2006 4.9 23.5 1.0
N A:ASN60 5.0 22.3 1.0

Fluorine binding site 4 out of 6 in 4bx2

Go back to Fluorine Binding Sites List in 4bx2
Fluorine binding site 4 out of 6 in the Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride


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 Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:29.5
occ:1.00
 F1 B:BEF302 0.0 29.5 1.0
BE B:BEF302 1.5 30.0 1.0
HZ2 B:LYS209 2.0 48.7 1.0
H B:ASN59 2.0 31.9 1.0
F3 B:BEF302 2.5 24.5 1.0
OD1 B:ASP25 2.5 35.5 1.0
F2 B:BEF302 2.6 32.6 1.0
HA B:SER58 2.7 39.6 1.0
N B:ASN59 2.8 26.6 1.0
NZ B:LYS209 2.8 40.5 1.0
O B:HOH2065 3.0 28.1 1.0
HZ3 B:LYS209 3.1 48.7 1.0
HB2 B:ASN59 3.2 30.3 1.0
HZ1 B:LYS209 3.3 48.7 1.0
CA B:SER58 3.5 33.0 1.0
O B:HOH2007 3.6 45.4 1.0
CG B:ASP25 3.6 36.2 1.0
C B:SER58 3.6 38.0 1.0
OG B:SER58 3.6 30.4 1.0
HE3 B:LYS209 3.7 45.9 1.0
CE B:LYS209 3.7 38.3 1.0
O B:HOH2003 3.8 28.6 1.0
HE2 B:LYS209 3.8 45.9 1.0
CA B:ASN59 3.8 25.3 1.0
H B:ASN60 3.8 30.6 1.0
CB B:ASN59 3.9 25.3 1.0
O B:HOH2016 4.0 34.4 1.0
H B:CYS26 4.1 49.5 1.0
OD2 B:ASP25 4.1 33.6 1.0
CB B:SER58 4.1 34.3 1.0
MG B:MG301 4.1 29.6 1.0
H B:ASP27 4.2 38.6 1.0
O B:VAL57 4.3 39.1 1.0
HG B:SER58 4.3 36.5 1.0
HB2 B:ASP27 4.3 36.2 1.0
HB2 B:SER58 4.4 41.1 1.0
N B:ASN60 4.4 25.5 1.0
CG B:ASN59 4.5 25.9 1.0
OD1 B:ASP239 4.5 37.2 1.0
C B:ASN59 4.6 26.8 1.0
HA B:ASN59 4.6 30.4 1.0
N B:SER58 4.6 32.8 1.0
HB2 B:ASP25 4.7 42.1 1.0
HG1 B:THR238 4.7 63.5 1.0
HB3 B:ASN59 4.7 30.3 1.0
CB B:ASP25 4.7 35.0 1.0
HA B:ASP25 4.8 42.5 1.0
O B:SER58 4.8 29.9 1.0
OD2 B:ASP175 4.9 28.0 1.0
N B:CYS26 4.9 41.2 1.0
C B:VAL57 4.9 39.8 1.0
O B:HOH2066 4.9 41.6 1.0
HB3 B:SER58 4.9 41.1 1.0
OD2 B:ASP27 5.0 30.0 1.0
HB2 B:ASN60 5.0 37.1 1.0
N B:ASP27 5.0 32.1 1.0
OD1 B:ASN59 5.0 26.2 1.0

Fluorine binding site 5 out of 6 in 4bx2

Go back to Fluorine Binding Sites List in 4bx2
Fluorine binding site 5 out of 6 in the Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride


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 Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:32.6
occ:1.00
 F2 B:BEF302 0.0 32.6 1.0
BE B:BEF302 1.6 30.0 1.0
H B:ASP27 1.9 38.6 1.0
H B:CYS26 2.4 49.5 1.0
F3 B:BEF302 2.5 24.5 1.0
F1 B:BEF302 2.6 29.5 1.0
OD1 B:ASP25 2.6 35.5 1.0
OG B:SER58 2.6 30.4 1.0
HB2 B:CYS26 2.7 47.4 1.0
N B:ASP27 2.7 32.1 1.0
HG B:SER58 2.9 36.5 1.0
HA B:SER58 3.0 39.6 1.0
HB2 B:SER58 3.1 41.1 1.0
HB2 B:ASP27 3.1 36.2 1.0
N B:CYS26 3.2 41.2 1.0
CB B:SER58 3.2 34.3 1.0
CG B:ASP27 3.5 32.9 1.0
CB B:CYS26 3.5 39.5 1.0
CG B:ASP25 3.5 36.2 1.0
CA B:CYS26 3.5 34.1 1.0
CB B:ASP27 3.5 30.2 1.0
CA B:SER58 3.6 33.0 1.0
C B:CYS26 3.6 36.0 1.0
OD2 B:ASP27 3.6 30.0 1.0
H B:ASN59 3.7 31.9 1.0
CA B:ASP27 3.7 32.0 1.0
O B:HOH2007 3.8 45.4 1.0
HZ2 B:LYS209 3.9 48.7 1.0
OD2 B:ASP25 3.9 33.6 1.0
OD1 B:ASP27 3.9 38.1 1.0
H B:ASN60 4.1 30.6 1.0
O B:HOH2006 4.1 24.1 1.0
HB3 B:CYS26 4.1 47.4 1.0
HB3 B:SER58 4.1 41.1 1.0
HB2 B:ASN60 4.2 37.1 1.0
N B:ASN59 4.2 26.6 1.0
O B:ASP27 4.2 33.3 1.0
MG B:MG301 4.2 29.6 1.0
C B:ASP25 4.3 36.7 1.0
HA B:ASP25 4.4 42.5 1.0
C B:SER58 4.4 38.0 1.0
HA B:ASP27 4.4 38.4 1.0
C B:ASP27 4.5 41.7 1.0
HB3 B:ASP27 4.5 36.2 1.0
HA B:CYS26 4.5 41.0 1.0
O B:VAL57 4.5 39.1 1.0
HZ1 B:LYS209 4.6 48.7 1.0
NZ B:LYS209 4.6 40.5 1.0
CA B:ASP25 4.7 35.4 1.0
CB B:ASP25 4.7 35.0 1.0
N B:SER58 4.7 32.8 1.0
SG B:CYS26 4.7 37.0 1.0
O B:CYS26 4.8 42.3 1.0
N B:ASN60 4.8 25.5 1.0
HZ3 B:LYS209 4.9 48.7 1.0
C B:VAL57 5.0 39.8 1.0

Fluorine binding site 6 out of 6 in 4bx2

Go back to Fluorine Binding Sites List in 4bx2
Fluorine binding site 6 out of 6 in the Crystal Structure of Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride


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 Murine Chronophin (Pyridoxal Phosphate Phosphatase) in Complex with Beryllium Trifluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:24.5
occ:1.00
 F3 B:BEF302 0.0 24.5 1.0
BE B:BEF302 1.5 30.0 1.0
MG B:MG301 2.0 29.6 1.0
HB2 B:ASP27 2.4 36.2 1.0
F1 B:BEF302 2.5 29.5 1.0
F2 B:BEF302 2.5 32.6 1.0
OD1 B:ASP25 2.7 35.5 1.0
OD2 B:ASP25 2.7 33.6 1.0
O B:HOH2003 2.9 28.6 1.0
O B:ASP27 2.9 33.3 1.0
O B:HOH2004 3.0 32.2 1.0
H B:ASP27 3.0 38.6 1.0
CG B:ASP25 3.1 36.2 1.0
O B:HOH2007 3.2 45.4 1.0
CB B:ASP27 3.3 30.2 1.0
O B:HOH2065 3.5 28.1 1.0
N B:ASP27 3.5 32.1 1.0
C B:ASP27 3.6 41.7 1.0
CA B:ASP27 3.6 32.0 1.0
O B:HOH2066 3.8 41.6 1.0
H B:CYS26 3.9 49.5 1.0
HZ2 B:LYS209 3.9 48.7 1.0
HB3 B:ASP27 3.9 36.2 1.0
OD1 B:ASP234 4.0 36.1 1.0
CG B:ASP27 4.1 32.9 1.0
OD2 B:ASP27 4.2 30.0 1.0
H B:ASN59 4.3 31.9 1.0
N B:CYS26 4.5 41.2 1.0
C B:CYS26 4.5 36.0 1.0
HZ3 B:LYS209 4.5 48.7 1.0
CB B:ASP25 4.6 35.0 1.0
HA B:SER58 4.6 39.6 1.0
HA B:ASP27 4.6 38.4 1.0
NZ B:LYS209 4.6 40.5 1.0
O B:HOH2016 4.7 34.4 1.0
OG B:SER58 4.8 30.4 1.0
N B:GLY28 4.9 34.4 1.0
HB2 B:ASP25 4.9 42.1 1.0
OD2 B:ASP239 4.9 35.9 1.0
HZ1 B:LYS209 4.9 48.7 1.0
HB2 B:CYS26 5.0 47.4 1.0

Reference:

C.Kestler, G.Knobloch, I.Tessmer, E.Jeanclos, H.Schindelin, A.Gohla. Chronophin Dimerization Is Required For Proper Positioning of Its Substrate Specificity Loop. J.Biol.Chem. V. 289 3094 2014.
ISSN: ISSN 0021-9258
PubMed: 24338687
DOI: 10.1074/JBC.M113.536482
Page generated: Thu Aug 1 00:26:51 2024

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