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Fluorine in PDB 3zww: Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom

Enzymatic activity of Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom

All present enzymatic activity of Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom:
3.2.2.5;

Protein crystallography data

The structure of Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom, PDB code: 3zww was solved by M.Kotaka, R.Graeff, L.H.Zhang, H.C.Lee, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.86 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.962, 77.522, 140.503, 88.00, 89.16, 88.29
R / Rfree (%) 19.977 / 25.736

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom (pdb code 3zww). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom, PDB code: 3zww:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3zww

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Fluorine binding site 1 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom


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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:60.4
occ:1.00
F2R A:AVU301 0.0 60.4 1.0
C2R A:AVU301 1.4 55.6 1.0
C1R A:AVU301 2.3 55.9 1.0
C3R A:AVU301 2.4 54.9 1.0
OE2 A:GLU179 3.3 55.4 1.0
O4R A:AVU301 3.3 56.9 1.0
CD2 A:LEU97 3.3 40.6 1.0
C4R A:AVU301 3.3 56.1 1.0
O3R A:AVU301 3.4 50.5 1.0
CB A:LEU97 4.0 35.6 1.0
C5R A:AVU301 4.0 58.1 1.0
NE1 A:TRP77 4.1 41.1 1.0
OG A:SER144 4.2 43.4 1.0
CG A:LEU97 4.3 39.5 1.0
CE2 A:TRP77 4.4 38.8 1.0
CZ2 A:TRP77 4.4 43.3 1.0
CD A:GLU179 4.4 51.3 1.0
O2' A:AVU301 4.5 90.2 1.0
OE1 A:GLU179 4.9 51.0 1.0
CD1 A:TRP77 4.9 37.0 1.0

Fluorine binding site 2 out of 8 in 3zww

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Fluorine binding site 2 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom


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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:34.2
occ:1.00
F2R B:AVU301 0.0 34.2 1.0
C2R B:AVU301 1.4 35.2 1.0
C1R B:AVU301 2.3 33.5 1.0
C3R B:AVU301 2.3 35.1 1.0
O4R B:AVU301 2.8 34.6 1.0
C4R B:AVU301 3.1 36.3 1.0
O3R B:AVU301 3.4 30.8 1.0
CD2 B:LEU97 3.5 27.5 1.0
OE2 B:GLU179 3.6 35.0 1.0
C5R B:AVU301 3.7 40.3 1.0
CB B:LEU97 3.9 25.8 1.0
NE1 B:TRP77 4.2 33.8 1.0
CZ2 B:TRP77 4.3 35.2 1.0
CE2 B:TRP77 4.3 30.9 1.0
CG B:LEU97 4.3 27.8 1.0
CD B:GLU179 4.6 33.2 1.0
OG B:SER144 4.7 28.1 1.0
OE1 B:GLU179 4.7 39.9 1.0
C3' B:AVU301 4.8 81.9 1.0
OE2 B:GLU98 4.9 35.6 1.0
O5R B:AVU301 4.9 44.6 1.0
O3' B:AVU301 4.9 80.4 1.0

Fluorine binding site 3 out of 8 in 3zww

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Fluorine binding site 3 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom


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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:43.0
occ:1.00
F2R C:AVU301 0.0 43.0 1.0
C2R C:AVU301 1.4 41.0 1.0
C1R C:AVU301 2.2 39.9 1.0
C3R C:AVU301 2.3 43.0 1.0
O4R C:AVU301 3.0 43.0 1.0
C4R C:AVU301 3.1 43.4 1.0
OE2 C:GLU179 3.4 37.9 1.0
O3R C:AVU301 3.5 38.5 1.0
CD2 C:LEU97 3.6 27.5 1.0
C5R C:AVU301 3.6 43.3 1.0
NE1 C:TRP77 3.9 34.1 1.0
CZ2 C:TRP77 4.0 36.4 1.0
CB C:LEU97 4.0 29.2 1.0
CE2 C:TRP77 4.1 32.3 1.0
CG C:LEU97 4.4 31.0 1.0
CD C:GLU179 4.4 32.5 1.0
OE1 C:GLU179 4.6 36.5 1.0
OE2 C:GLU98 4.7 39.2 1.0
OG C:SER144 4.8 27.4 1.0
O5R C:AVU301 4.8 45.9 1.0
CD1 C:TRP77 4.9 29.0 1.0
CH2 C:TRP77 4.9 38.4 1.0
OE1 C:GLU98 5.0 33.2 1.0

Fluorine binding site 4 out of 8 in 3zww

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Fluorine binding site 4 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom


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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:51.4
occ:1.00
F2R D:AVU301 0.0 51.4 1.0
C2R D:AVU301 1.4 49.4 1.0
C1R D:AVU301 2.4 46.6 1.0
C3R D:AVU301 2.4 47.3 1.0
CD2 D:LEU97 3.2 34.3 1.0
O4R D:AVU301 3.2 46.8 1.0
O3R D:AVU301 3.2 42.8 1.0
C4R D:AVU301 3.4 46.5 1.0
OE2 D:GLU179 3.6 40.7 1.0
CB D:LEU97 3.8 31.0 1.0
NE1 D:TRP77 3.9 31.4 1.0
C5R D:AVU301 4.1 49.0 1.0
CG D:LEU97 4.2 34.4 1.0
CE2 D:TRP77 4.3 31.3 1.0
CZ2 D:TRP77 4.4 38.9 1.0
CD D:GLU179 4.5 40.3 1.0
OG D:SER144 4.5 34.2 1.0
CD1 D:TRP77 4.6 27.9 1.0
N7 D:AVU301 4.7 85.9 1.0
CE2 D:TYR147 4.8 26.2 1.0
OE1 D:GLU179 4.8 42.3 1.0
CD2 D:TYR147 4.8 25.3 1.0

Fluorine binding site 5 out of 8 in 3zww

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Fluorine binding site 5 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom


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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F301

b:39.8
occ:1.00
F2R E:AVU301 0.0 39.8 1.0
C2R E:AVU301 1.4 38.2 1.0
C1R E:AVU301 2.2 36.8 1.0
C3R E:AVU301 2.3 39.7 1.0
O4R E:AVU301 3.1 41.2 1.0
C4R E:AVU301 3.2 40.8 1.0
OE2 E:GLU179 3.4 32.4 1.0
O3R E:AVU301 3.4 37.3 1.0
CD2 E:LEU97 3.8 32.8 1.0
CB E:LEU97 3.8 27.2 1.0
C5R E:AVU301 3.8 42.6 1.0
NE1 E:TRP77 4.2 32.6 1.0
CD E:GLU179 4.3 31.8 1.0
CZ2 E:TRP77 4.4 32.1 1.0
CG E:LEU97 4.4 29.3 1.0
CE2 E:TRP77 4.4 31.5 1.0
OE1 E:GLU179 4.5 35.7 1.0
OG E:SER144 4.6 22.2 1.0
CE2 E:TYR147 4.9 25.8 1.0
CD2 E:TYR147 5.0 25.2 1.0

Fluorine binding site 6 out of 8 in 3zww

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Fluorine binding site 6 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom


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 Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F301

b:67.4
occ:1.00
F2R F:AVU301 0.0 67.4 1.0
C2R F:AVU301 1.3 67.0 1.0
C1R F:AVU301 2.2 68.5 1.0
C3R F:AVU301 2.3 66.8 1.0
O4R F:AVU301 2.7 69.0 1.0
C4R F:AVU301 3.1 68.4 1.0
OE2 F:GLU179 3.4 67.4 1.0
O3R F:AVU301 3.4 68.4 1.0
CD2 F:LEU97 3.6 54.7 1.0
OG F:SER144 3.8 55.8 1.0
NE1 F:TRP77 4.0 47.4 1.0
C5R F:AVU301 4.0 67.2 1.0
CB F:LEU97 4.2 51.5 1.0
CE2 F:TRP77 4.3 48.3 1.0
CD F:GLU179 4.4 67.0 1.0
CZ2 F:TRP77 4.4 51.4 1.0
CG F:LEU97 4.5 53.1 1.0
OE1 F:GLU179 4.6 67.6 1.0
C8 F:AVU301 4.7 93.5 1.0
CD1 F:TRP77 4.7 46.9 1.0
CB F:SER144 4.8 55.3 1.0
N7 F:AVU301 4.9 93.2 1.0

Fluorine binding site 7 out of 8 in 3zww

Go back to Fluorine Binding Sites List in 3zww
Fluorine binding site 7 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F301

b:44.5
occ:1.00
F2R G:AVU301 0.0 44.5 1.0
C2R G:AVU301 1.4 40.9 1.0
C1R G:AVU301 2.3 36.9 1.0
C3R G:AVU301 2.3 40.4 1.0
O4R G:AVU301 3.1 38.5 1.0
C4R G:AVU301 3.1 39.7 1.0
O3R G:AVU301 3.4 37.0 1.0
OE2 G:GLU179 3.5 34.3 1.0
CD2 G:LEU97 3.7 31.0 1.0
C5R G:AVU301 3.7 40.0 1.0
CB G:LEU97 3.8 27.4 1.0
NE1 G:TRP77 3.9 32.4 1.0
CE2 G:TRP77 4.3 30.3 1.0
CZ2 G:TRP77 4.3 33.0 1.0
CG G:LEU97 4.4 30.7 1.0
CD G:GLU179 4.5 29.6 1.0
OE1 G:GLU179 4.6 32.0 1.0
OG G:SER144 4.7 27.1 1.0
CD1 G:TRP77 4.8 27.6 1.0
O5R G:AVU301 4.9 44.4 1.0
OE1 G:GLU98 4.9 42.1 1.0
CE2 G:TYR147 5.0 25.4 1.0

Fluorine binding site 8 out of 8 in 3zww

Go back to Fluorine Binding Sites List in 3zww
Fluorine binding site 8 out of 8 in the Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Adp-Ribosyl Cyclase Complexed with Ara-2'F-Adp-Ribose at 2.3 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F301

b:62.3
occ:1.00
F2R H:AVU301 0.0 62.3 1.0
C2R H:AVU301 1.4 57.9 1.0
C3R H:AVU301 2.3 57.0 1.0
C1R H:AVU301 2.4 59.1 1.0
C4R H:AVU301 3.3 57.2 1.0
O4R H:AVU301 3.3 59.1 1.0
O3R H:AVU301 3.3 55.2 1.0
NE1 H:TRP77 3.5 41.3 1.0
OE2 H:GLU179 3.6 56.6 1.0
CD2 H:LEU97 3.7 46.5 1.0
C5R H:AVU301 3.8 55.9 1.0
CB H:LEU97 3.8 42.4 1.0
CE2 H:TRP77 4.0 40.2 1.0
CZ2 H:TRP77 4.2 43.8 1.0
CD1 H:TRP77 4.2 39.9 1.0
C2 H:AVU301 4.3 79.1 1.0
OG H:SER144 4.4 47.7 1.0
CG H:LEU97 4.4 44.5 1.0
CD H:GLU179 4.5 53.5 1.0
OE1 H:GLU179 4.6 52.3 1.0
N1 H:AVU301 4.8 79.8 1.0
CD2 H:TRP77 4.9 38.2 1.0
O5R H:AVU301 4.9 54.9 1.0

Reference:

M.Kotaka, R.Graeff, Z.Chen, L.H.Zhang, H.C.Lee, Q.Hao. Structural Studies of Intermediates Along the Cyclization Pathway of Aplysia Adp-Ribosyl Cyclase. J.Mol.Biol. V. 415 514 2012.
ISSN: ISSN 0022-2836
PubMed: 22138343
DOI: 10.1016/J.JMB.2011.11.022
Page generated: Mon Jul 14 20:19:58 2025

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