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Fluorine in PDB 3dzf: Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate

Enzymatic activity of Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate

All present enzymatic activity of Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate:
3.2.2.5;

Protein crystallography data

The structure of Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate, PDB code: 3dzf was solved by Q.Liu, I.A.Kriksunov, H.Jiang, R.Graeff, H.Lin, H.C.Lee, Q.Hao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.01
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 41.746, 96.156, 103.605, 79.48, 82.72, 86.78
R / Rfree (%) 20.1 / 27.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate (pdb code 3dzf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate, PDB code: 3dzf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3dzf

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Fluorine binding site 1 out of 6 in the Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate


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 Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:38.9
occ:1.00
 F2 A:RF5301 0.0 38.9 1.0
C2 A:RF5301 1.4 33.6 1.0
C1 A:RF5301 2.3 28.6 1.0
C3 A:RF5301 2.4 32.7 1.0
CB A:SER193 3.0 38.2 1.0
OG A:SER193 3.1 42.2 1.0
O3 A:RF5301 3.1 41.4 1.0
O4 A:RF5301 3.3 29.6 1.0
O A:TRP189 3.3 33.7 1.0
OE2 A:GLU226 3.4 41.2 1.0
C4 A:RF5301 3.5 32.4 1.0
CB A:TRP189 3.6 32.9 1.0
CG2 A:THR221 3.6 40.7 1.0
C A:TRP189 3.8 34.5 1.0
CA A:TRP189 4.1 34.4 1.0
CE3 A:TRP189 4.1 36.5 1.0
CD A:GLU226 4.3 44.9 1.0
CB A:THR221 4.3 39.6 1.0
CA A:SER193 4.4 37.6 1.0
CG A:TRP189 4.4 34.4 1.0
OE1 A:GLU226 4.4 52.9 1.0
O A:HOH394 4.5 32.2 1.0
CD2 A:TRP189 4.6 35.9 1.0
CD2 A:LEU145 4.6 37.2 1.0
N A:LYS190 4.7 34.5 1.0
OG1 A:THR221 4.8 42.2 1.0
C5 A:RF5301 4.8 24.8 1.0
N A:SER193 4.8 37.5 1.0
O5 A:RF5301 4.8 24.9 1.0
O A:HOH363 4.9 50.7 1.0

Fluorine binding site 2 out of 6 in 3dzf

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Fluorine binding site 2 out of 6 in the Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate


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 Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:36.6
occ:1.00
 F2 B:RF5301 0.0 36.6 1.0
C2 B:RF5301 1.4 35.7 1.0
C3 B:RF5301 2.4 30.9 1.0
C1 B:RF5301 2.4 31.1 1.0
CB B:SER193 2.9 37.2 1.0
OG B:SER193 3.0 45.1 1.0
O3 B:RF5301 3.1 35.2 1.0
O4 B:RF5301 3.2 28.2 1.0
O B:TRP189 3.3 31.5 1.0
OE2 B:GLU226 3.4 45.3 1.0
C4 B:RF5301 3.4 30.0 1.0
CG2 B:THR221 3.6 42.5 1.0
CB B:TRP189 3.8 33.0 1.0
C B:TRP189 3.8 32.5 1.0
CE3 B:TRP189 4.2 35.4 1.0
CA B:TRP189 4.2 33.1 1.0
CA B:SER193 4.2 38.6 1.0
CD2 B:LEU145 4.3 32.7 1.0
CB B:THR221 4.4 40.6 1.0
CD B:GLU226 4.6 50.0 1.0
CG B:TRP189 4.6 33.5 1.0
N B:SER193 4.7 36.5 1.0
N B:LYS190 4.7 32.8 1.0
CD2 B:TRP189 4.7 34.7 1.0
C5 B:RF5301 4.8 19.4 1.0
O5 B:RF5301 4.9 21.8 1.0
OG1 B:THR221 4.9 41.4 1.0

Fluorine binding site 3 out of 6 in 3dzf

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Fluorine binding site 3 out of 6 in the Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate


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 Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:49.6
occ:1.00
 F2 C:RF5301 0.0 49.6 1.0
C2 C:RF5301 1.4 51.7 1.0
C1 C:RF5301 2.3 48.1 1.0
C3 C:RF5301 2.4 51.8 1.0
OG C:SER193 2.7 42.7 1.0
OE2 C:GLU226 3.3 42.6 1.0
O4 C:RF5301 3.3 44.6 1.0
C4 C:RF5301 3.4 48.5 1.0
O3 C:RF5301 3.4 55.2 1.0
CG2 C:THR221 3.6 44.8 1.0
CB C:TRP189 3.7 34.4 1.0
CE3 C:TRP189 3.9 31.5 1.0
CB C:SER193 4.0 35.4 1.0
O C:TRP189 4.0 37.3 1.0
CB C:THR221 4.1 44.5 1.0
CD2 C:LEU145 4.2 35.8 1.0
C5 C:RF5301 4.3 45.8 1.0
CG C:TRP189 4.3 34.3 1.0
CD2 C:TRP189 4.3 33.1 1.0
C C:TRP189 4.4 36.4 1.0
O5 C:RF5301 4.4 45.4 1.0
CD C:GLU226 4.5 47.7 1.0
OG1 C:THR221 4.5 48.3 1.0
CA C:TRP189 4.5 34.5 1.0
CZ3 C:TRP189 4.9 30.7 1.0
CA C:SER193 4.9 36.6 1.0

Fluorine binding site 4 out of 6 in 3dzf

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Fluorine binding site 4 out of 6 in the Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate


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 Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:57.5
occ:1.00
 F2 D:RF5301 0.0 57.5 1.0
C2 D:RF5301 1.4 54.6 1.0
C1 D:RF5301 2.3 51.2 1.0
C3 D:RF5301 2.4 54.3 1.0
OG D:SER193 2.6 43.8 1.0
O3 D:RF5301 3.2 59.4 1.0
OE2 D:GLU226 3.3 51.1 1.0
CB D:TRP189 3.3 34.3 1.0
O4 D:RF5301 3.5 48.7 1.0
C4 D:RF5301 3.6 51.2 1.0
O D:TRP189 3.6 34.6 1.0
CE3 D:TRP189 3.7 36.8 1.0
CG2 D:THR221 3.8 46.9 1.0
CB D:SER193 3.9 36.7 1.0
CG D:TRP189 3.9 37.3 1.0
C D:TRP189 4.0 35.4 1.0
CD2 D:TRP189 4.0 36.4 1.0
CA D:TRP189 4.1 34.9 1.0
CB D:THR221 4.4 46.9 1.0
CD2 D:LEU145 4.5 35.9 1.0
CA D:SER193 4.5 38.0 1.0
CD D:GLU226 4.5 51.6 1.0
OG1 D:THR221 4.7 50.5 1.0
C5 D:RF5301 4.7 51.3 1.0
N D:SER193 4.8 38.3 1.0
CZ3 D:TRP189 4.8 33.9 1.0
O5 D:RF5301 4.9 52.4 1.0
N D:LYS190 5.0 37.0 1.0

Fluorine binding site 5 out of 6 in 3dzf

Go back to Fluorine Binding Sites List in 3dzf
Fluorine binding site 5 out of 6 in the Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate


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 Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F301

b:44.0
occ:1.00
 F2 E:RF5301 0.0 44.0 1.0
C2 E:RF5301 1.4 37.1 1.0
C1 E:RF5301 2.4 33.3 1.0
C3 E:RF5301 2.5 32.3 1.0
CB E:SER193 2.9 36.7 1.0
OG E:SER193 2.9 40.5 1.0
O3 E:RF5301 3.1 37.2 1.0
O E:TRP189 3.2 34.0 1.0
OE2 E:GLU226 3.4 40.5 1.0
CG2 E:THR221 3.5 39.1 1.0
O4 E:RF5301 3.5 31.6 1.0
C4 E:RF5301 3.6 31.2 1.0
CB E:TRP189 3.7 31.8 1.0
C E:TRP189 3.8 33.0 1.0
CE3 E:TRP189 4.2 35.1 1.0
CA E:TRP189 4.2 32.7 1.0
CB E:THR221 4.3 38.9 1.0
CA E:SER193 4.3 36.9 1.0
CD2 E:LEU145 4.4 29.8 1.0
CG E:TRP189 4.5 32.4 1.0
O E:HOH447 4.5 34.9 1.0
CD2 E:TRP189 4.6 35.1 1.0
N E:LYS190 4.6 32.5 1.0
CD E:GLU226 4.7 48.5 1.0
N E:SER193 4.7 36.8 1.0
OG1 E:THR221 4.8 39.5 1.0
O5 E:RF5301 4.9 26.0 1.0
C5 E:RF5301 4.9 23.8 1.0

Fluorine binding site 6 out of 6 in 3dzf

Go back to Fluorine Binding Sites List in 3dzf
Fluorine binding site 6 out of 6 in the Crystal Structure of Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate


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 Human CD38 Extracellular Domain Complexed with A Covalent Intermediate, Ara-F-Ribose-5'-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F301

b:54.0
occ:1.00
 F2 F:RF5301 0.0 54.0 1.0
C2 F:RF5301 1.3 52.0 1.0
C3 F:RF5301 2.2 53.3 1.0
OG F:SER193 2.4 42.2 1.0
C1 F:RF5301 2.4 54.2 1.0
O3 F:RF5301 2.9 54.4 1.0
CB F:TRP189 3.4 33.8 1.0
C4 F:RF5301 3.5 52.5 1.0
O4 F:RF5301 3.5 51.0 1.0
OE2 F:GLU226 3.6 44.0 1.0
CG2 F:THR221 3.6 43.1 1.0
CB F:SER193 3.7 36.0 1.0
O F:TRP189 3.8 35.8 1.0
CE3 F:TRP189 3.9 34.8 1.0
CD2 F:LEU145 4.0 21.6 1.0
CG F:TRP189 4.0 35.6 1.0
C F:TRP189 4.1 35.6 1.0
CA F:TRP189 4.2 34.0 1.0
CD2 F:TRP189 4.2 35.8 1.0
CB F:THR221 4.3 41.7 1.0
OG1 F:THR221 4.4 41.5 1.0
C5 F:RF5301 4.5 51.4 1.0
CD F:GLU226 4.7 52.9 1.0
O5 F:RF5301 4.7 47.7 1.0
CA F:SER193 4.7 37.5 1.0
N F:LYS190 4.9 36.5 1.0

Reference:

Q.Liu, I.A.Kriksunov, H.Jiang, R.Graeff, H.Lin, H.C.Lee, Q.Hao. Covalent and Noncovalent Intermediates of An Nad Utilizing Enzyme, Human CD38. Chem.Biol. V. 15 1068 2008.
ISSN: ISSN 1074-5521
PubMed: 18940667
DOI: 10.1016/J.CHEMBIOL.2008.08.007
Page generated: Mon Jul 14 16:01:44 2025

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