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Fluorine in PDB 3zwp: Crystal Structure of Adp Ribosyl Cyclase Complexed with Ara- 2'F-Adp-Ribose at 2.1 Angstrom

Enzymatic activity of Crystal Structure of Adp Ribosyl Cyclase Complexed with Ara- 2'F-Adp-Ribose at 2.1 Angstrom

All present enzymatic activity of Crystal Structure of Adp Ribosyl Cyclase Complexed with Ara- 2'F-Adp-Ribose at 2.1 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 2.1 Angstrom, PDB code: 3zwp 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 / 2.11
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 61.034, 77.610, 140.221, 87.91, 89.24, 88.16
R / Rfree (%) 18.543 / 24.109

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 2.1 Angstrom (pdb code 3zwp). 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 2.1 Angstrom, PDB code: 3zwp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3zwp

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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 2.1 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 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:58.4
occ:1.00
 F2R A:AVU301 0.0 58.4 1.0
C2R A:AVU301 1.4 52.3 1.0
C1R A:AVU301 2.3 51.8 1.0
C3R A:AVU301 2.3 49.9 1.0
O A:HOH2076 3.0 55.1 1.0
O4R A:AVU301 3.1 51.3 1.0
C4R A:AVU301 3.1 50.4 1.0
C5R A:AVU301 3.5 51.2 1.0
O3R A:AVU301 3.5 49.5 1.0
NE1 A:TRP77 3.6 43.3 1.0
OE2 A:GLU179 3.6 47.6 1.0
CZ2 A:TRP77 3.6 46.4 1.0
CE2 A:TRP77 3.7 42.6 1.0
O A:HOH2075 3.7 49.0 1.0
CD1 A:LEU97 3.9 39.7 1.0
N7 A:AVU301 4.1 86.0 1.0
C8 A:AVU301 4.3 86.2 1.0
CB A:LEU97 4.3 31.5 1.0
CD1 A:TRP77 4.5 41.7 1.0
CG A:LEU97 4.5 37.0 1.0
O5R A:AVU301 4.5 53.9 1.0
CD A:GLU179 4.6 42.8 1.0
CH2 A:TRP77 4.6 48.4 1.0
OG A:SER144 4.7 40.3 1.0
OE1 A:GLU179 4.8 37.5 1.0
CD2 A:TRP77 4.8 42.2 1.0
OE2 A:GLU98 4.8 40.9 1.0

Fluorine binding site 2 out of 8 in 3zwp

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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 2.1 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 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:36.5
occ:1.00
 F2R B:AVU301 0.0 36.5 1.0
C2R B:AVU301 1.4 37.1 1.0
C1R B:AVU301 2.2 33.5 1.0
C3R B:AVU301 2.4 34.6 1.0
O4R B:AVU301 2.8 35.7 1.0
C4R B:AVU301 3.1 34.6 1.0
O B:HOH2111 3.2 45.7 1.0
O3R B:AVU301 3.6 30.0 1.0
C5R B:AVU301 3.6 36.1 1.0
OE2 B:GLU179 3.6 27.3 1.0
CD2 B:LEU97 3.6 28.2 1.0
CB B:LEU97 3.8 22.5 1.0
NE1 B:TRP77 4.0 30.9 1.0
CE2 B:TRP77 4.2 30.5 1.0
CZ2 B:TRP77 4.2 37.0 1.0
CG B:LEU97 4.4 24.9 1.0
CD B:GLU179 4.6 27.0 1.0
OG B:SER144 4.7 23.9 1.0
OE1 B:GLU179 4.7 28.7 1.0
OE2 B:GLU98 4.7 31.7 1.0
CD1 B:TRP77 4.8 26.2 1.0
O B:HOH2137 4.9 75.7 1.0
O5R B:AVU301 4.9 40.9 1.0
CE2 B:TYR147 5.0 18.6 1.0

Fluorine binding site 3 out of 8 in 3zwp

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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 2.1 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 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:40.0
occ:1.00
 F2R C:AVU301 0.0 40.0 1.0
C2R C:AVU301 1.4 40.3 1.0
C1R C:AVU301 2.3 39.4 1.0
C3R C:AVU301 2.4 35.6 1.0
O4R C:AVU301 3.2 43.9 1.0
O3R C:AVU301 3.2 31.7 1.0
O C:HOH2072 3.2 50.0 1.0
OE2 C:GLU179 3.3 36.1 1.0
C4R C:AVU301 3.4 41.1 1.0
O C:HOH2071 3.5 47.4 1.0
CD2 C:LEU97 3.5 32.6 1.0
CB C:LEU97 3.8 26.6 1.0
NE1 C:TRP77 4.1 31.7 1.0
C5R C:AVU301 4.2 46.1 1.0
CD C:GLU179 4.2 32.6 1.0
CG C:LEU97 4.4 32.8 1.0
CE2 C:TYR147 4.4 26.1 1.0
CD2 C:TYR147 4.4 30.4 1.0
OG C:SER144 4.5 32.7 1.0
OE1 C:GLU179 4.5 36.9 1.0
CE2 C:TRP77 4.5 32.1 1.0
CZ2 C:TRP77 4.6 39.2 1.0
CD1 C:TRP77 4.8 29.6 1.0
N7 C:AVU301 4.8 82.4 1.0

Fluorine binding site 4 out of 8 in 3zwp

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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 2.1 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 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:43.2
occ:1.00
 F2R D:AVU301 0.0 43.2 1.0
C2R D:AVU301 1.4 40.6 1.0
C1R D:AVU301 2.2 38.4 1.0
C3R D:AVU301 2.4 38.8 1.0
O4R D:AVU301 2.8 39.5 1.0
C4R D:AVU301 3.0 38.1 1.0
O D:HOH2085 3.3 49.0 1.0
C5R D:AVU301 3.4 37.7 1.0
O D:HOH2177 3.5 58.8 1.0
O3R D:AVU301 3.6 36.1 1.0
CD2 D:LEU97 3.6 27.3 1.0
OE2 D:GLU179 3.7 36.9 1.0
NE1 D:TRP77 3.9 35.0 1.0
CZ2 D:TRP77 4.0 38.3 1.0
CB D:LEU97 4.1 24.4 1.0
CE2 D:TRP77 4.1 34.2 1.0
CG D:LEU97 4.4 28.0 1.0
OG D:SER144 4.5 26.0 1.0
CD D:GLU179 4.6 32.9 1.0
O5R D:AVU301 4.6 43.1 1.0
OE1 D:GLU179 4.6 32.9 1.0
OE2 D:GLU98 4.7 32.5 1.0
CD1 D:TRP77 4.9 30.9 1.0
CH2 D:TRP77 4.9 45.6 1.0

Fluorine binding site 5 out of 8 in 3zwp

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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 2.1 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 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F301

b:46.0
occ:1.00
 F2R E:AVU301 0.0 46.0 1.0
C2R E:AVU301 1.3 41.2 1.0
C1R E:AVU301 2.2 37.5 1.0
C3R E:AVU301 2.3 34.2 1.0
O E:HOH2063 3.0 49.3 1.0
O4R E:AVU301 3.2 32.6 1.0
C4R E:AVU301 3.2 38.3 1.0
OE2 E:GLU179 3.4 32.6 1.0
O3R E:AVU301 3.4 34.6 1.0
CD2 E:LEU97 3.5 30.0 1.0
CB E:LEU97 3.7 28.0 1.0
C5R E:AVU301 3.9 34.9 1.0
NE1 E:TRP77 4.1 31.7 1.0
CG E:LEU97 4.2 30.8 1.0
CD E:GLU179 4.3 29.8 1.0
CE2 E:TRP77 4.4 29.6 1.0
CZ2 E:TRP77 4.4 36.7 1.0
OE1 E:GLU179 4.5 35.2 1.0
CD2 E:TYR147 4.7 25.0 1.0
CE2 E:TYR147 4.7 27.7 1.0
OG E:SER144 4.8 30.1 1.0
CD1 E:TRP77 4.9 27.0 1.0
N E:LEU97 4.9 28.1 1.0
CA E:LEU97 4.9 28.8 1.0

Fluorine binding site 6 out of 8 in 3zwp

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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 2.1 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 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F301

b:59.3
occ:1.00
 F2R F:AVU301 0.0 59.3 1.0
C2R F:AVU301 1.3 53.6 1.0
C1R F:AVU301 2.3 53.4 1.0
C3R F:AVU301 2.3 52.2 1.0
C4R F:AVU301 3.2 52.3 1.0
O4R F:AVU301 3.3 52.1 1.0
CD1 F:LEU97 3.3 46.8 1.0
O3R F:AVU301 3.4 51.4 1.0
OE2 F:GLU179 3.5 54.9 1.0
NE1 F:TRP77 3.5 39.0 1.0
O F:HOH2023 3.6 53.1 1.0
C5R F:AVU301 3.7 47.8 1.0
CB F:LEU97 3.9 43.9 1.0
CE2 F:TRP77 3.9 36.7 1.0
N7 F:AVU301 4.0 70.1 1.0
CZ2 F:TRP77 4.1 37.6 1.0
CG F:LEU97 4.2 48.3 1.0
CD1 F:TRP77 4.3 33.4 1.0
C8 F:AVU301 4.4 71.7 1.0
OG F:SER144 4.5 51.0 1.0
CD F:GLU179 4.5 52.3 1.0
OE1 F:GLU179 4.7 52.3 1.0
OE2 F:GLU98 4.7 57.0 1.0
O5R F:AVU301 4.8 50.3 1.0
CD2 F:TRP77 4.8 32.7 1.0

Fluorine binding site 7 out of 8 in 3zwp

Go back to Fluorine Binding Sites List in 3zwp
Fluorine binding site 7 out of 8 in the Crystal Structure of Adp Ribosyl Cyclase Complexed with Ara- 2'F-Adp-Ribose at 2.1 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 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F301

b:40.6
occ:1.00
 F2R G:AVU301 0.0 40.6 1.0
C2R G:AVU301 1.4 36.5 1.0
C1R G:AVU301 2.3 32.9 1.0
C3R G:AVU301 2.3 32.9 1.0
O4R G:AVU301 2.9 32.9 1.0
O G:HOH2064 3.2 53.4 1.0
C4R G:AVU301 3.2 34.6 1.0
CD2 G:LEU97 3.4 27.8 1.0
O3R G:AVU301 3.4 30.1 1.0
OE2 G:GLU179 3.5 33.6 1.0
N1 G:AVU301 3.7 97.7 1.0
C2 G:AVU301 3.8 96.6 1.0
C5R G:AVU301 3.8 35.7 1.0
CB G:LEU97 3.9 27.4 1.0
NE1 G:TRP77 4.0 30.0 1.0
CZ2 G:TRP77 4.2 36.2 1.0
CE2 G:TRP77 4.3 29.4 1.0
CG G:LEU97 4.4 29.2 1.0
CD G:GLU179 4.5 27.6 1.0
OE1 G:GLU179 4.6 25.6 1.0
C6 G:AVU301 4.7 97.7 1.0
OG G:SER144 4.7 22.4 1.0
N3 G:AVU301 4.8 97.7 1.0
O5R G:AVU301 4.9 38.9 1.0
CD1 G:TRP77 4.9 22.6 1.0
CE2 G:TYR147 4.9 28.2 1.0
CD2 G:TYR147 4.9 23.5 1.0

Fluorine binding site 8 out of 8 in 3zwp

Go back to Fluorine Binding Sites List in 3zwp
Fluorine binding site 8 out of 8 in the Crystal Structure of Adp Ribosyl Cyclase Complexed with Ara- 2'F-Adp-Ribose at 2.1 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 2.1 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F301

b:71.0
occ:1.00
 F2R H:AVU301 0.0 71.0 1.0
C2R H:AVU301 1.3 68.9 1.0
C1R H:AVU301 2.2 69.8 1.0
C3R H:AVU301 2.3 67.5 1.0
O4R H:AVU301 2.8 72.4 1.0
C4R H:AVU301 3.0 70.1 1.0
OE2 H:GLU179 3.4 68.0 1.0
O3R H:AVU301 3.4 67.5 1.0
C5R H:AVU301 3.6 68.1 1.0
CD1 H:LEU97 3.7 62.7 1.0
N7 H:AVU301 3.7 90.6 1.0
NE1 H:TRP77 3.8 47.7 1.0
C8 H:AVU301 4.0 89.9 1.0
CE2 H:TRP77 4.1 50.4 1.0
CZ2 H:TRP77 4.1 53.0 1.0
CB H:LEU97 4.1 60.1 1.0
CG H:LEU97 4.3 61.8 1.0
OE2 H:GLU98 4.5 60.7 1.0
OG H:SER144 4.5 73.7 1.0
CD1 H:TRP77 4.6 49.9 1.0
CD H:GLU179 4.6 66.1 1.0
O5R H:AVU301 4.6 70.9 1.0
CB H:SER144 4.8 69.5 1.0
CD2 H:TRP77 4.9 48.4 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: Wed Jul 31 23:50:51 2024

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