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Fluorine in PDB 3zwv: 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: 3zwv 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) 30.00 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.146, 76.481, 141.366, 88.09, 90.88, 91.02
R / Rfree (%) 21.5 / 27.7

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 3zwv). 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: 3zwv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3zwv

Go back to Fluorine Binding Sites List in 3zwv
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:56.4
occ:1.00
 F2R A:AVU301 0.0 56.4 1.0
C2R A:AVU301 1.4 57.3 1.0
C1R A:AVU301 2.3 59.0 1.0
C3R A:AVU301 2.4 56.5 1.0
O4R A:AVU301 3.1 61.6 1.0
O3R A:AVU301 3.3 50.3 1.0
C4R A:AVU301 3.3 57.9 1.0
CD1 A:LEU97 3.4 39.0 1.0
OE2 A:GLU179 3.5 52.7 1.0
NE1 A:TRP77 3.7 44.5 1.0
CB A:LEU97 3.8 37.0 1.0
CG A:LEU97 4.0 39.7 1.0
C5R A:AVU301 4.2 60.4 1.0
CE2 A:TRP77 4.3 41.7 1.0
CD1 A:TRP77 4.4 40.2 1.0
CD A:GLU179 4.5 48.5 1.0
CE2 A:TYR147 4.6 39.6 1.0
CZ2 A:TRP77 4.7 47.4 1.0
N7 A:AVU301 4.7 78.5 1.0
OE2 A:GLU98 4.7 46.6 1.0
CD2 A:TYR147 4.7 35.7 1.0
OE1 A:GLU179 4.8 50.8 1.0
OG A:SER144 4.8 42.4 1.0
N A:LEU97 5.0 35.4 1.0
C8 A:AVU301 5.0 79.0 1.0
CA A:LEU97 5.0 36.4 1.0

Fluorine binding site 2 out of 8 in 3zwv

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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:40.4
occ:1.00
 F2R B:AVU301 0.0 40.4 1.0
C2R B:AVU301 1.4 37.5 1.0
C1R B:AVU301 2.3 34.5 1.0
C3R B:AVU301 2.4 37.2 1.0
O4R B:AVU301 3.1 39.1 1.0
C4R B:AVU301 3.2 38.6 1.0
CD2 B:LEU97 3.4 32.1 1.0
O3R B:AVU301 3.4 36.0 1.0
OE2 B:GLU179 3.6 39.1 1.0
CB B:LEU97 3.8 31.6 1.0
C5R B:AVU301 3.8 37.8 1.0
NE1 B:TRP77 4.0 39.9 1.0
CG B:LEU97 4.2 31.9 1.0
N7 B:AVU301 4.3 99.2 1.0
C8 B:AVU301 4.4 98.9 1.0
CE2 B:TRP77 4.4 39.2 1.0
CZ2 B:TRP77 4.5 43.4 1.0
CD B:GLU179 4.6 35.7 1.0
OE1 B:GLU179 4.8 35.2 1.0
OG B:SER144 4.8 30.4 1.0
CD1 B:TRP77 4.8 34.3 1.0
OE1 B:GLU98 4.9 28.9 1.0
OE2 B:GLU98 4.9 42.2 1.0

Fluorine binding site 3 out of 8 in 3zwv

Go back to Fluorine Binding Sites List in 3zwv
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:60.6
occ:1.00
 F2R C:AVU301 0.0 60.6 1.0
C2R C:AVU301 1.4 59.5 1.0
C1R C:AVU301 2.3 60.6 1.0
C3R C:AVU301 2.3 59.6 1.0
O4R C:AVU301 3.0 63.4 1.0
C4R C:AVU301 3.2 60.7 1.0
O3R C:AVU301 3.4 54.1 1.0
OE2 C:GLU179 3.6 54.6 1.0
CD2 C:LEU97 3.7 45.2 1.0
C5R C:AVU301 3.9 64.4 1.0
NE1 C:TRP77 3.9 46.9 1.0
CB C:LEU97 4.0 42.2 1.0
CE2 C:TRP77 4.2 45.2 1.0
CZ2 C:TRP77 4.3 48.8 1.0
CG C:LEU97 4.5 44.6 1.0
CD C:GLU179 4.6 53.4 1.0
OG C:SER144 4.7 46.5 1.0
CD1 C:TRP77 4.7 43.1 1.0
OE2 C:GLU98 4.7 49.6 1.0
C8 C:AVU301 4.7 94.3 1.0
N7 C:AVU301 4.7 94.2 1.0
OE1 C:GLU179 4.9 57.6 1.0
O5R C:AVU301 5.0 66.5 1.0

Fluorine binding site 4 out of 8 in 3zwv

Go back to Fluorine Binding Sites List in 3zwv
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:44.6
occ:1.00
 F2R D:AVU301 0.0 44.6 1.0
C2R D:AVU301 1.4 41.1 1.0
C1R D:AVU301 2.3 40.7 1.0
C3R D:AVU301 2.3 40.8 1.0
O4R D:AVU301 2.9 45.5 1.0
C4R D:AVU301 3.2 43.9 1.0
CD2 D:LEU97 3.3 33.6 1.0
O3R D:AVU301 3.4 38.3 1.0
OE2 D:GLU179 3.5 35.5 1.0
C2 D:AVU301 3.6 0.5 1.0
NE1 D:TRP77 3.7 38.6 1.0
CB D:LEU97 3.8 33.2 1.0
C5R D:AVU301 3.9 42.8 1.0
N1 D:AVU301 4.0 0.2 1.0
CE2 D:TRP77 4.1 37.9 1.0
CG D:LEU97 4.3 32.5 1.0
CZ2 D:TRP77 4.3 41.4 1.0
CD D:GLU179 4.5 33.2 1.0
CD1 D:TRP77 4.5 37.3 1.0
OE1 D:GLU179 4.6 36.0 1.0
OE2 D:GLU98 4.7 41.1 1.0
N3 D:AVU301 4.7 0.8 1.0
CE2 D:TYR147 4.8 34.2 1.0
CD2 D:TYR147 4.9 32.2 1.0
N D:LEU97 4.9 34.0 1.0

Fluorine binding site 5 out of 8 in 3zwv

Go back to Fluorine Binding Sites List in 3zwv
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:39.7
occ:1.00
 F2R E:AVU301 0.0 39.7 1.0
C2R E:AVU301 1.4 36.6 1.0
C1R E:AVU301 2.2 36.9 1.0
C3R E:AVU301 2.3 38.5 1.0
O4R E:AVU301 2.9 37.9 1.0
C4R E:AVU301 3.1 36.7 1.0
OE2 E:GLU179 3.4 34.4 1.0
O3R E:AVU301 3.4 36.3 1.0
CD2 E:LEU97 3.6 33.6 1.0
C5R E:AVU301 3.8 37.3 1.0
CB E:LEU97 3.9 31.2 1.0
NE1 E:TRP77 4.1 37.0 1.0
CE2 E:TRP77 4.4 35.7 1.0
CZ2 E:TRP77 4.4 40.9 1.0
CD E:GLU179 4.4 33.1 1.0
CG E:LEU97 4.4 31.6 1.0
OE1 E:GLU179 4.6 34.6 1.0
CD2 E:TYR147 4.8 33.2 1.0
OG E:SER144 4.8 31.3 1.0
CE2 E:TYR147 4.8 33.6 1.0
O5R E:AVU301 4.9 42.4 1.0
CD1 E:TRP77 4.9 33.9 1.0

Fluorine binding site 6 out of 8 in 3zwv

Go back to Fluorine Binding Sites List in 3zwv
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:70.9
occ:1.00
 F2R F:AVU301 0.0 70.9 1.0
C2R F:AVU301 1.3 67.1 1.0
C1R F:AVU301 2.2 68.2 1.0
C3R F:AVU301 2.3 66.4 1.0
O4R F:AVU301 2.6 68.3 1.0
C4R F:AVU301 2.8 66.4 1.0
C5R F:AVU301 3.3 64.3 1.0
O3R F:AVU301 3.5 66.3 1.0
NE1 F:TRP77 3.6 50.5 1.0
OE2 F:GLU179 3.7 69.6 1.0
CE2 F:TRP77 3.8 50.2 1.0
CZ2 F:TRP77 3.8 53.3 1.0
CD2 F:LEU97 3.8 54.8 1.0
N7 F:AVU301 3.9 84.8 1.0
C8 F:AVU301 3.9 85.9 1.0
O5R F:AVU301 4.3 61.8 1.0
CD1 F:TRP77 4.5 48.8 1.0
OG F:SER144 4.5 60.9 1.0
CB F:LEU97 4.6 54.5 1.0
CH2 F:TRP77 4.7 51.6 1.0
CG F:LEU97 4.7 54.3 1.0
CD2 F:TRP77 4.7 49.3 1.0
OE2 F:GLU98 4.7 60.9 1.0
CD F:GLU179 4.9 69.3 1.0

Fluorine binding site 7 out of 8 in 3zwv

Go back to Fluorine Binding Sites List in 3zwv
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:45.2
occ:1.00
 F2R G:AVU301 0.0 45.2 1.0
C2R G:AVU301 1.4 42.0 1.0
C1R G:AVU301 2.3 39.5 1.0
C3R G:AVU301 2.3 42.4 1.0
O4R G:AVU301 3.2 41.4 1.0
C4R G:AVU301 3.3 40.6 1.0
O3R G:AVU301 3.4 41.5 1.0
CD2 G:LEU97 3.4 33.8 1.0
OE2 G:GLU179 3.4 37.3 1.0
CB G:LEU97 3.8 33.4 1.0
C5R G:AVU301 3.9 42.6 1.0
NE1 G:TRP77 4.1 38.2 1.0
N6 G:AVU301 4.2 1.0 1.0
CG G:LEU97 4.3 33.7 1.0
CZ2 G:TRP77 4.4 39.7 1.0
CE2 G:TRP77 4.4 36.7 1.0
CD G:GLU179 4.4 38.1 1.0
OE2 G:GLU98 4.6 47.3 1.0
OE1 G:GLU179 4.7 40.8 1.0
CE2 G:TYR147 4.7 33.9 1.0
CD2 G:TYR147 4.8 33.1 1.0
OG G:SER144 4.8 30.1 1.0
N7 G:AVU301 4.9 0.5 1.0
CD1 G:TRP77 5.0 33.1 1.0
N G:LEU97 5.0 31.2 1.0

Fluorine binding site 8 out of 8 in 3zwv

Go back to Fluorine Binding Sites List in 3zwv
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:64.8
occ:1.00
 F2R H:AVU301 0.0 64.8 1.0
C2R H:AVU301 1.4 62.1 1.0
C3R H:AVU301 2.3 60.6 1.0
C1R H:AVU301 2.4 64.1 1.0
O4R H:AVU301 3.1 62.9 1.0
C4R H:AVU301 3.2 60.7 1.0
O3R H:AVU301 3.3 60.4 1.0
CD2 H:LEU97 3.5 48.7 1.0
OE2 H:GLU179 3.5 64.3 1.0
NE1 H:TRP77 3.7 46.3 1.0
C5R H:AVU301 3.8 60.4 1.0
CB H:LEU97 3.9 47.8 1.0
CE2 H:TRP77 4.1 44.3 1.0
CZ2 H:TRP77 4.3 48.0 1.0
CG H:LEU97 4.3 49.0 1.0
CD1 H:TRP77 4.5 43.7 1.0
OG H:SER144 4.5 50.8 1.0
CD H:GLU179 4.5 63.0 1.0
N7 H:AVU301 4.5 77.0 1.0
C8 H:AVU301 4.6 76.0 1.0
OE1 H:GLU179 4.7 64.6 1.0
O5R H:AVU301 4.9 57.9 1.0
CD2 H:TRP77 5.0 42.7 1.0
OE1 H:GLU98 5.0 58.0 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: ESSN 1089-8638
PubMed: 22138343
DOI: 10.1016/J.JMB.2011.11.022
Page generated: Wed Jul 31 23:50:57 2024

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