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Fluorine in PDB 4r84: Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound

Enzymatic activity of Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound

All present enzymatic activity of Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound:
2.4.99.1;

Protein crystallography data

The structure of Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound, PDB code: 4r84 was solved by A.J.Fisher, X.Chen, Y.Li, N.Huynh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.75 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.340, 81.450, 111.210, 99.02, 91.59, 101.20
R / Rfree (%) 17.2 / 20.3

Other elements in 4r84:

The structure of Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound (pdb code 4r84). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound, PDB code: 4r84:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4r84

Go back to Fluorine Binding Sites List in 4r84
Fluorine binding site 1 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound


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 Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:29.1
occ:1.00
 F3A A:CSF501 0.0 29.1 1.0
C3A A:CSF501 1.4 21.5 1.0
C2A A:CSF501 2.4 29.4 1.0
C4A A:CSF501 2.4 21.0 1.0
C1A A:CSF501 2.7 34.2 1.0
O4A A:CSF501 2.8 23.0 1.0
O6A A:CSF501 2.9 24.6 1.0
C5A A:CSF501 3.0 21.7 1.0
O A:HOH660 3.1 28.7 1.0
OAA A:CSF501 3.3 34.2 1.0
OBA A:CSF501 3.3 31.6 1.0
C6A A:CSF501 3.5 23.6 1.0
O1A A:CSF501 3.6 26.5 1.0
O A:HOH1236 3.7 65.1 1.0
O A:HOH773 4.2 36.1 1.0
N5A A:CSF501 4.3 26.0 1.0
O7A A:CSF501 4.4 25.7 1.0
O A:HOH642 4.4 26.4 1.0
C7A A:CSF501 4.6 21.9 1.0
O A:HOH738 4.9 34.7 1.0
O10 A:CSF501 4.9 35.8 1.0

Fluorine binding site 2 out of 4 in 4r84

Go back to Fluorine Binding Sites List in 4r84
Fluorine binding site 2 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound


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 Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:29.2
occ:1.00
 F3A B:CSF501 0.0 29.2 1.0
C3A B:CSF501 1.4 26.6 1.0
C2A B:CSF501 2.3 29.6 1.0
C4A B:CSF501 2.4 21.5 1.0
C1A B:CSF501 2.6 34.8 1.0
O4A B:CSF501 2.7 22.7 1.0
O6A B:CSF501 2.9 28.3 1.0
C5A B:CSF501 2.9 25.3 1.0
O B:HOH704 3.1 34.2 1.0
OBA B:CSF501 3.1 33.6 1.0
OAA B:CSF501 3.1 29.4 1.0
C6A B:CSF501 3.5 25.1 1.0
O1A B:CSF501 3.6 30.1 1.0
O B:HOH624 4.3 24.9 1.0
N5A B:CSF501 4.3 27.4 1.0
O7A B:CSF501 4.4 23.9 1.0
O B:HOH630 4.5 26.0 1.0
C7A B:CSF501 4.6 22.2 1.0
O B:HOH968 4.6 48.9 1.0
O10 B:CSF501 4.9 32.0 1.0
O B:HOH765 4.9 38.0 1.0

Fluorine binding site 3 out of 4 in 4r84

Go back to Fluorine Binding Sites List in 4r84
Fluorine binding site 3 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound


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 Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:30.3
occ:1.00
 F3A C:CSF501 0.0 30.3 1.0
C3A C:CSF501 1.4 31.1 1.0
C2A C:CSF501 2.3 33.5 1.0
C4A C:CSF501 2.4 29.0 1.0
C1A C:CSF501 2.7 41.1 1.0
O4A C:CSF501 2.8 27.8 1.0
O6A C:CSF501 2.8 32.6 1.0
C5A C:CSF501 2.9 25.4 1.0
O C:HOH723 2.9 33.5 1.0
OAA C:CSF501 3.2 43.2 1.0
OBA C:CSF501 3.3 30.8 1.0
C6A C:CSF501 3.4 28.8 1.0
O1A C:CSF501 3.6 33.7 1.0
O C:HOH814 4.0 39.0 1.0
N5A C:CSF501 4.2 27.7 1.0
O7A C:CSF501 4.4 25.9 1.0
O C:HOH686 4.5 31.6 1.0
C7A C:CSF501 4.5 21.3 1.0
O C:HOH936 4.8 45.4 1.0
O10 C:CSF501 4.8 35.7 1.0
O C:HOH1046 5.0 50.8 1.0
C10 C:CSF501 5.0 34.7 1.0

Fluorine binding site 4 out of 4 in 4r84

Go back to Fluorine Binding Sites List in 4r84
Fluorine binding site 4 out of 4 in the Crystal Structure of Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound


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 Sialyltransferase From Photobacterium Damsela with Cmp-3F(A)NEU5AC Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:27.9
occ:1.00
 F3A D:CSF501 0.0 27.9 1.0
C3A D:CSF501 1.4 24.8 1.0
C2A D:CSF501 2.3 33.3 1.0
C4A D:CSF501 2.4 25.4 1.0
C1A D:CSF501 2.7 39.8 1.0
O4A D:CSF501 2.8 25.6 1.0
O6A D:CSF501 2.8 29.3 1.0
C5A D:CSF501 2.9 19.1 1.0
O D:HOH646 3.1 29.7 1.0
OBA D:CSF501 3.1 33.6 1.0
OAA D:CSF501 3.3 28.4 1.0
C6A D:CSF501 3.4 18.8 1.0
O1A D:CSF501 3.6 28.4 1.0
N5A D:CSF501 4.2 26.2 1.0
O7A D:CSF501 4.3 26.1 1.0
O D:HOH612 4.4 24.4 1.0
C7A D:CSF501 4.5 23.3 1.0
O D:HOH698 4.6 34.0 1.0
O10 D:CSF501 4.8 33.3 1.0
C10 D:CSF501 5.0 36.4 1.0
PA D:CSF501 5.0 36.6 1.0

Reference:

N.Huynh, Y.Li, H.Yu, S.Huang, K.Lau, X.Chen, A.J.Fisher. Crystal Structures of Sialyltransferase From Photobacterium Damselae Febs Lett. 2014.
ISSN: ISSN 0014-5793
DOI: 10.1016/J.FEBSLET.2014.11.003
Page generated: Tue Jul 15 00:36:11 2025

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