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Fluorine in PDB 3b8z: High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)

Protein crystallography data

The structure of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2), PDB code: 3b8z was solved by H.-S.Shieh, J.M.Williams, K.J.Mathis, M.D.Tortorella, A.Tomasselli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.53 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.057, 44.487, 76.380, 90.00, 90.07, 90.00
R / Rfree (%) 18.5 / 21.4

Other elements in 3b8z:

The structure of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) also contains other interesting chemical elements:

Calcium (Ca) 6 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) (pdb code 3b8z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2), PDB code: 3b8z:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3b8z

Go back to Fluorine Binding Sites List in 3b8z
Fluorine binding site 1 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:23.0
occ:1.00
 F28 A:294801 0.0 23.0 1.0
C27 A:294801 1.4 21.9 1.0
F30 A:294801 2.1 24.0 1.0
F29 A:294801 2.2 24.0 1.0
C24 A:294801 2.4 21.4 1.0
C25 A:294801 2.9 21.1 1.0
CD1 A:PHE406 3.3 16.9 1.0
O A:HOH1091 3.4 39.0 1.0
C23 A:294801 3.5 21.6 1.0
ND1 A:HIS403 3.6 22.4 1.0
CE1 A:PHE406 3.7 18.4 1.0
CE1 A:HIS403 3.9 22.3 1.0
CG1 A:ILE446 4.0 22.1 1.0
O A:HOH1059 4.0 31.8 1.0
CA A:SER445 4.1 22.3 1.0
O A:HOH1062 4.2 44.5 1.0
C26 A:294801 4.2 20.5 1.0
CG A:PHE406 4.3 14.0 1.0
O A:THR444 4.4 23.9 1.0
C A:SER445 4.4 21.9 1.0
CD1 A:ILE446 4.5 22.2 1.0
N A:SER445 4.5 22.7 1.0
C A:THR444 4.6 23.3 1.0
N A:ILE446 4.6 21.9 1.0
CG A:HIS403 4.6 20.6 1.0
CB A:PHE406 4.7 12.4 1.0
C22 A:294801 4.7 21.5 1.0
O A:SER445 4.9 21.2 1.0
C21 A:294801 5.0 20.3 1.0
CZ A:PHE406 5.0 18.2 1.0
NE2 A:HIS403 5.0 22.7 1.0

Fluorine binding site 2 out of 6 in 3b8z

Go back to Fluorine Binding Sites List in 3b8z
Fluorine binding site 2 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:24.0
occ:1.00
 F29 A:294801 0.0 24.0 1.0
C27 A:294801 1.4 21.9 1.0
F30 A:294801 2.2 24.0 1.0
F28 A:294801 2.2 23.0 1.0
C24 A:294801 2.4 21.4 1.0
C23 A:294801 2.7 21.6 1.0
C A:SER445 3.2 21.9 1.0
N A:SER445 3.2 22.7 1.0
O A:HOH983 3.2 21.4 1.0
O A:SER445 3.2 21.2 1.0
CA A:SER445 3.3 22.3 1.0
CD1 A:ILE446 3.5 22.2 1.0
C A:THR444 3.6 23.3 1.0
CG1 A:ILE446 3.6 22.1 1.0
C25 A:294801 3.7 21.1 1.0
N A:THR444 3.8 23.9 1.0
N A:ILE446 3.8 21.9 1.0
O A:THR444 4.0 23.9 1.0
C22 A:294801 4.1 21.5 1.0
O A:HOH1107 4.2 34.8 1.0
CA A:THR444 4.3 24.0 1.0
OG1 A:THR444 4.4 25.2 1.0
CA A:ILE446 4.6 22.2 1.0
CB A:ILE446 4.7 22.4 1.0
C A:LEU443 4.7 24.4 1.0
O A:HOH1059 4.7 31.8 1.0
CB A:SER445 4.8 22.2 1.0
C26 A:294801 4.8 20.5 1.0
O A:ILE442 4.8 24.1 1.0
CA A:LEU443 4.8 24.2 1.0
C21 A:294801 4.9 20.3 1.0
CD1 A:PHE406 5.0 16.9 1.0

Fluorine binding site 3 out of 6 in 3b8z

Go back to Fluorine Binding Sites List in 3b8z
Fluorine binding site 3 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:24.0
occ:1.00
 F30 A:294801 0.0 24.0 1.0
C27 A:294801 1.4 21.9 1.0
F28 A:294801 2.1 23.0 1.0
F29 A:294801 2.2 24.0 1.0
C24 A:294801 2.4 21.4 1.0
C25 A:294801 3.0 21.1 1.0
N A:THR444 3.2 23.9 1.0
C23 A:294801 3.4 21.6 1.0
CA A:LEU443 3.5 24.2 1.0
O A:THR444 3.5 23.9 1.0
C A:THR444 3.5 23.3 1.0
C A:LEU443 3.5 24.4 1.0
CE1 A:HIS403 3.6 22.3 1.0
CB A:LEU443 3.8 24.6 1.0
ND1 A:HIS403 3.8 22.4 1.0
N A:SER445 3.9 22.7 1.0
CA A:THR444 4.0 24.0 1.0
CD2 A:LEU443 4.1 25.4 1.0
CA A:SER445 4.3 22.3 1.0
NE2 A:HIS403 4.3 22.7 1.0
C26 A:294801 4.3 20.5 1.0
O A:HOH1062 4.5 44.5 1.0
O A:LEU443 4.5 24.8 1.0
C22 A:294801 4.5 21.5 1.0
CG A:LEU443 4.6 25.0 1.0
O A:ILE442 4.7 24.1 1.0
CG A:HIS403 4.7 20.6 1.0
N A:LEU443 4.8 23.9 1.0
O A:HOH1091 4.8 39.0 1.0
C A:SER445 4.9 21.9 1.0
C21 A:294801 4.9 20.3 1.0
O A:HOH1107 4.9 34.8 1.0
CD2 A:HIS403 4.9 21.9 1.0
O A:HOH983 5.0 21.4 1.0

Fluorine binding site 4 out of 6 in 3b8z

Go back to Fluorine Binding Sites List in 3b8z
Fluorine binding site 4 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:29.6
occ:1.00
 F28 B:294801 0.0 29.6 1.0
C27 B:294801 1.4 25.1 1.0
F29 B:294801 2.2 28.8 1.0
F30 B:294801 2.2 28.4 1.0
C24 B:294801 2.4 23.9 1.0
O B:HOH1142 2.6 40.9 1.0
ND1 B:HIS403 2.7 24.8 1.0
C25 B:294801 2.8 22.9 1.0
CE1 B:HIS403 3.4 25.9 1.0
CD1 B:PHE406 3.4 20.7 1.0
C23 B:294801 3.5 23.3 1.0
CG B:HIS403 3.7 23.4 1.0
CG B:PHE406 3.7 15.6 1.0
CB B:PHE406 3.8 12.5 1.0
CB B:HIS403 4.1 21.1 1.0
C26 B:294801 4.1 21.2 1.0
CE1 B:PHE406 4.1 22.0 1.0
O B:HOH1065 4.3 52.4 1.0
CA B:HIS403 4.4 20.7 1.0
NE2 B:HIS403 4.5 25.8 1.0
CD2 B:PHE406 4.6 17.7 1.0
CD2 B:HIS403 4.7 25.3 1.0
C22 B:294801 4.7 21.7 1.0
O B:HIS403 4.8 18.4 1.0
CG1 B:ILE446 4.9 27.5 1.0
C21 B:294801 4.9 20.7 1.0
O B:HOH1104 5.0 36.0 1.0
CZ B:PHE406 5.0 20.2 1.0

Fluorine binding site 5 out of 6 in 3b8z

Go back to Fluorine Binding Sites List in 3b8z
Fluorine binding site 5 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:28.8
occ:1.00
 F29 B:294801 0.0 28.8 1.0
C27 B:294801 1.4 25.1 1.0
F28 B:294801 2.2 29.6 1.0
F30 B:294801 2.2 28.4 1.0
C24 B:294801 2.4 23.9 1.0
O B:HOH1065 2.7 52.4 1.0
C23 B:294801 2.8 23.3 1.0
CG1 B:ILE446 3.1 27.5 1.0
CD1 B:ILE446 3.5 27.9 1.0
C25 B:294801 3.6 22.9 1.0
N B:ILE446 3.9 27.8 1.0
C B:SER445 3.9 28.5 1.0
O B:HOH1104 4.0 36.0 1.0
CA B:SER445 4.0 28.9 1.0
CG B:PHE406 4.1 15.6 1.0
C22 B:294801 4.2 21.7 1.0
CB B:ILE446 4.2 27.3 1.0
O B:HOH1142 4.3 40.9 1.0
CB B:PHE406 4.3 12.5 1.0
CD1 B:PHE406 4.4 20.7 1.0
N B:SER445 4.4 29.2 1.0
CD2 B:PHE406 4.5 17.7 1.0
O B:SER445 4.5 28.7 1.0
CA B:ILE446 4.6 27.4 1.0
O B:THR444 4.6 29.5 1.0
C B:THR444 4.6 29.4 1.0
ND1 B:HIS403 4.7 24.8 1.0
C26 B:294801 4.8 21.2 1.0
O B:HOH1025 4.8 33.0 1.0
CE1 B:PHE406 4.9 22.0 1.0
C21 B:294801 5.0 20.7 1.0
CE2 B:PHE406 5.0 19.4 1.0

Fluorine binding site 6 out of 6 in 3b8z

Go back to Fluorine Binding Sites List in 3b8z
Fluorine binding site 6 out of 6 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:28.4
occ:1.00
 F30 B:294801 0.0 28.4 1.0
C27 B:294801 1.4 25.1 1.0
F29 B:294801 2.2 28.8 1.0
F28 B:294801 2.2 29.6 1.0
C24 B:294801 2.4 23.9 1.0
O B:HOH1065 2.7 52.4 1.0
C25 B:294801 3.1 22.9 1.0
C23 B:294801 3.3 23.3 1.0
CE1 B:HIS403 3.5 25.9 1.0
ND1 B:HIS403 3.5 24.8 1.0
O B:THR444 3.6 29.5 1.0
N B:THR444 3.8 29.0 1.0
C B:THR444 3.9 29.4 1.0
CA B:LEU443 4.1 28.2 1.0
CB B:LEU443 4.2 28.4 1.0
O B:HOH1142 4.2 40.9 1.0
C26 B:294801 4.3 21.2 1.0
N B:SER445 4.3 29.2 1.0
C B:LEU443 4.3 28.7 1.0
O B:HOH1052 4.4 56.0 1.0
CD2 B:LEU443 4.4 28.9 1.0
NE2 B:HIS403 4.4 25.8 1.0
CG B:HIS403 4.5 23.4 1.0
C22 B:294801 4.5 21.7 1.0
CA B:SER445 4.5 28.9 1.0
CA B:THR444 4.5 29.7 1.0
C21 B:294801 4.9 20.7 1.0
CG B:LEU443 4.9 28.7 1.0
CD2 B:HIS403 4.9 25.3 1.0
C B:SER445 5.0 28.5 1.0

Reference:

H.S.Shieh, K.J.Mathis, J.M.Williams, R.L.Hills, J.F.Wiese, T.E.Benson, J.R.Kiefer, M.H.Marino, J.N.Carroll, J.W.Leone, A.M.Malfait, E.C.Arner, M.D.Tortorella, A.Tomasselli. High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2). J.Biol.Chem. V. 283 1501 2008.
ISSN: ISSN 0021-9258
PubMed: 17991750
DOI: 10.1074/JBC.M705879200
Page generated: Wed Jul 31 17:14:05 2024

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