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Fluorine in PDB 3ofs: Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography

Enzymatic activity of Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography

All present enzymatic activity of Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography:
3.2.2.5;

Protein crystallography data

The structure of Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography, PDB code: 3ofs was solved by 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) 48.73 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.655, 146.662, 191.086, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 25

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography (pdb code 3ofs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography, PDB code: 3ofs:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3ofs

Go back to Fluorine Binding Sites List in 3ofs
Fluorine binding site 1 out of 6 in the Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:42.1
occ:1.00
 F2R A:AVU301 0.0 42.1 1.0
C2R A:AVU301 1.4 39.3 1.0
C3R A:AVU301 2.4 38.7 1.0
C1R A:AVU301 2.4 36.5 1.0
O3R A:AVU301 3.1 35.0 1.0
OE2 A:GLU226 3.1 41.0 1.0
O A:HOH302 3.2 15.4 1.0
CD2 A:LEU145 3.3 39.8 1.0
CB A:LEU145 3.4 38.1 1.0
O4R A:AVU301 3.5 38.8 1.0
C4R A:AVU301 3.6 39.5 1.0
CD2 A:PHE196 3.9 34.1 1.0
CG A:LEU145 3.9 39.3 1.0
CD A:GLU226 4.0 39.6 1.0
OE1 A:GLU226 4.2 41.8 1.0
CE2 A:PHE196 4.3 34.4 1.0
CD2 A:LEU124 4.4 26.6 1.0
O A:HOH362 4.5 26.1 1.0
OG A:SER193 4.5 37.1 1.0
CA A:LEU145 4.7 39.4 1.0
C5R A:AVU301 4.7 40.2 1.0
CD1 A:LEU145 4.7 37.6 1.0
N A:LEU145 4.8 38.4 1.0
CG A:PHE196 4.9 35.4 1.0
O A:HOH347 4.9 22.5 1.0

Fluorine binding site 2 out of 6 in 3ofs

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Fluorine binding site 2 out of 6 in the Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:35.6
occ:1.00
 F2R B:AVU301 0.0 35.6 1.0
C2R B:AVU301 1.4 34.8 1.0
C3R B:AVU301 2.3 36.6 1.0
C1R B:AVU301 2.4 33.1 1.0
O3R B:AVU301 3.1 36.3 1.0
O B:HOH309 3.3 18.3 1.0
CD2 B:LEU145 3.3 43.6 1.0
CB B:LEU145 3.3 46.4 1.0
OE2 B:GLU226 3.4 42.4 1.0
O4R B:AVU301 3.5 35.2 1.0
C4R B:AVU301 3.5 37.9 1.0
CG B:LEU145 3.8 44.2 1.0
CD2 B:PHE196 3.9 36.4 1.0
CD B:GLU226 4.2 38.7 1.0
CD2 B:LEU124 4.3 32.2 1.0
CD1 B:LEU145 4.3 43.2 1.0
OE1 B:GLU226 4.3 39.5 1.0
CE2 B:PHE196 4.3 37.2 1.0
OG B:SER193 4.5 34.3 1.0
CA B:LEU145 4.5 48.1 1.0
C5R B:AVU301 4.6 39.3 1.0
N B:LEU145 4.7 51.1 1.0
N6 B:AVU301 4.7 66.8 1.0
CG B:PHE196 4.9 36.4 1.0

Fluorine binding site 3 out of 6 in 3ofs

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Fluorine binding site 3 out of 6 in the Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:37.6
occ:1.00
 F2R C:AVU301 0.0 37.6 1.0
C2R C:AVU301 1.4 35.1 1.0
C3R C:AVU301 2.4 35.7 1.0
C1R C:AVU301 2.4 33.9 1.0
O3R C:AVU301 3.0 35.8 1.0
OE2 C:GLU226 3.2 36.2 1.0
O C:HOH31 3.2 20.1 1.0
CB C:LEU145 3.3 28.6 1.0
CD2 C:LEU145 3.3 30.8 1.0
O4R C:AVU301 3.5 35.6 1.0
C4R C:AVU301 3.6 35.1 1.0
CD2 C:PHE196 3.7 32.4 1.0
CG C:LEU145 3.8 30.0 1.0
CD C:GLU226 4.1 33.8 1.0
CE2 C:PHE196 4.2 32.9 1.0
OE1 C:GLU226 4.3 34.8 1.0
CA C:LEU145 4.4 29.1 1.0
CD1 C:LEU145 4.4 29.1 1.0
OG C:SER193 4.4 33.3 1.0
CD2 C:LEU124 4.5 23.4 1.0
N C:LEU145 4.5 29.1 1.0
CG C:PHE196 4.8 31.7 1.0
C5R C:AVU301 4.8 34.9 1.0
NE1 C:TRP125 4.9 31.9 1.0

Fluorine binding site 4 out of 6 in 3ofs

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Fluorine binding site 4 out of 6 in the Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:39.5
occ:1.00
 F2R D:AVU301 0.0 39.5 1.0
C2R D:AVU301 1.4 37.2 1.0
C1R D:AVU301 2.4 35.6 1.0
C3R D:AVU301 2.4 36.6 1.0
CB D:LEU145 3.0 29.6 1.0
O3R D:AVU301 3.1 35.2 1.0
O D:HOH33 3.3 11.8 1.0
CD2 D:LEU145 3.3 31.4 1.0
O4R D:AVU301 3.5 37.1 1.0
C4R D:AVU301 3.5 37.2 1.0
OE2 D:GLU226 3.5 43.4 1.0
CG D:LEU145 3.6 30.8 1.0
CD2 D:PHE196 4.0 29.8 1.0
CD1 D:LEU145 4.2 29.4 1.0
CA D:LEU145 4.2 30.5 1.0
CD D:GLU226 4.3 39.3 1.0
N D:LEU145 4.4 30.6 1.0
CE2 D:PHE196 4.4 30.0 1.0
OE1 D:GLU226 4.5 37.2 1.0
OG D:SER193 4.6 35.7 1.0
CD2 D:LEU124 4.6 27.5 1.0
NE1 D:TRP125 4.8 35.1 1.0
C5R D:AVU301 4.8 38.8 1.0
CG D:PHE196 5.0 30.5 1.0

Fluorine binding site 5 out of 6 in 3ofs

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Fluorine binding site 5 out of 6 in the Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F301

b:44.6
occ:1.00
 F2R E:AVU301 0.0 44.6 1.0
C2R E:AVU301 1.4 42.8 1.0
C1R E:AVU301 2.4 39.1 1.0
C3R E:AVU301 2.4 42.4 1.0
OE2 E:GLU226 2.9 47.6 1.0
O3R E:AVU301 3.1 42.6 1.0
CD2 E:LEU145 3.5 39.8 1.0
O E:HOH307 3.5 14.9 1.0
O4R E:AVU301 3.5 42.0 1.0
CB E:LEU145 3.5 44.2 1.0
C4R E:AVU301 3.5 41.7 1.0
CD2 E:PHE196 3.6 47.3 1.0
CD E:GLU226 3.9 43.0 1.0
N6 E:AVU301 3.9 55.0 1.0
N1 E:AVU301 3.9 52.4 1.0
CG E:LEU145 4.0 43.0 1.0
CE2 E:PHE196 4.0 47.8 1.0
OE1 E:GLU226 4.0 42.1 1.0
C6 E:AVU301 4.3 53.6 1.0
CD2 E:LEU124 4.4 38.4 1.0
OG E:SER193 4.4 42.1 1.0
CD1 E:LEU145 4.6 46.0 1.0
CG E:PHE196 4.7 50.8 1.0
CA E:LEU145 4.8 47.3 1.0
C5R E:AVU301 4.8 39.0 1.0
N E:LEU145 4.9 50.8 1.0
C2 E:AVU301 4.9 52.8 1.0
CB E:SER193 5.0 44.1 1.0

Fluorine binding site 6 out of 6 in 3ofs

Go back to Fluorine Binding Sites List in 3ofs
Fluorine binding site 6 out of 6 in the Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured Using Multi-Copy Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F301

b:39.4
occ:1.00
 F2R F:AVU301 0.0 39.4 1.0
C2R F:AVU301 1.4 36.5 1.0
C3R F:AVU301 2.3 36.2 1.0
C1R F:AVU301 2.4 34.7 1.0
O3R F:AVU301 3.0 33.7 1.0
CB F:LEU145 3.3 55.6 1.0
OE2 F:GLU226 3.3 39.4 1.0
CD2 F:LEU145 3.3 50.6 1.0
O4R F:AVU301 3.5 37.9 1.0
C4R F:AVU301 3.5 36.8 1.0
CD2 F:PHE196 3.7 41.8 1.0
N6 F:AVU301 3.8 57.6 1.0
CG F:LEU145 3.8 54.0 1.0
N1 F:AVU301 4.0 55.8 1.0
CE2 F:PHE196 4.1 43.1 1.0
CD F:GLU226 4.1 36.4 1.0
OE1 F:GLU226 4.2 37.1 1.0
C6 F:AVU301 4.3 56.2 1.0
CD2 F:LEU124 4.4 48.5 1.0
CD1 F:LEU145 4.4 55.9 1.0
OG F:SER193 4.5 34.4 1.0
CA F:LEU145 4.5 60.0 1.0
N F:LEU145 4.6 61.5 1.0
CG F:PHE196 4.7 45.5 1.0
C5R F:AVU301 4.7 37.9 1.0

Reference:

H.Zhang, R.Graeff, Z.Chen, L.R.Zhang, L.H.Zhang, H.C.Lee, Q.Hao. Dynamic Conformations of the CD38-Mediated Nad Cyclization Captured in A Single Crystal J.Mol.Biol. V. 405 1070 2011.
ISSN: ISSN 0022-2836
PubMed: 21134381
DOI: 10.1016/J.JMB.2010.11.044
Page generated: Wed Jul 31 21:12:09 2024

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