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Fluorine in PDB 3skk: Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure

Enzymatic activity of Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure

All present enzymatic activity of Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure, PDB code: 3skk was solved by K.J.Thorn, L.Di Costanzo, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.78 / 1.70
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 90.094, 90.094, 69.362, 90.00, 90.00, 120.00
R / Rfree (%) 13.6 / 17.8

Other elements in 3skk:

The structure of Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure (pdb code 3skk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure, PDB code: 3skk:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3skk

Go back to Fluorine Binding Sites List in 3skk
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure


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 Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F551

b:15.5
occ:1.00
 F1 A:4U7551 0.0 15.5 1.0
C9 A:4U7551 1.3 15.0 1.0
F2 A:4U7551 2.2 17.9 1.0
C1 A:4U7551 2.4 12.1 1.0
N1 A:4U7551 2.7 11.7 1.0
C2 A:4U7551 2.9 13.1 1.0
O A:HOH482 3.2 22.8 1.0
O1 A:4U7551 3.2 13.0 1.0
O A:HOH629 3.4 13.5 1.0
OD2 A:ASP183 3.5 13.5 1.0
O5 A:4U7551 3.6 11.2 1.0
C3 A:4U7551 3.6 11.1 1.0
O A:HOH517 3.7 25.3 1.0
O A:HOH622 3.7 13.2 1.0
OD1 A:ASP183 3.7 13.1 1.0
CG A:ASP183 4.1 12.7 1.0
O A:HOH738 4.2 20.0 1.0
C4 A:4U7551 4.3 12.7 1.0
O A:HOH725 4.7 23.9 1.0
CB A:SER137 4.9 13.6 1.0
OG A:SER137 5.0 13.1 1.0
O A:HOH562 5.0 13.6 1.0

Fluorine binding site 2 out of 4 in 3skk

Go back to Fluorine Binding Sites List in 3skk
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure


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 Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F551

b:17.9
occ:1.00
 F2 A:4U7551 0.0 17.9 1.0
C9 A:4U7551 1.3 15.0 1.0
F1 A:4U7551 2.2 15.5 1.0
C1 A:4U7551 2.3 12.1 1.0
C3 A:4U7551 2.7 11.1 1.0
N1 A:4U7551 2.9 11.7 1.0
O A:HOH629 2.9 13.5 1.0
C4 A:4U7551 3.2 12.7 1.0
O A:HOH738 3.4 20.0 1.0
O A:HOH431 3.5 14.1 1.0
C2 A:4U7551 3.6 13.1 1.0
CD2 A:HIS126 3.7 8.6 1.0
O A:HOH482 3.9 22.8 1.0
NE2 A:HIS126 4.0 9.1 1.0
O1 A:4U7551 4.0 13.0 1.0
C5 A:4U7551 4.3 9.7 1.0
CG2 A:THR246 4.4 12.7 1.0
O5 A:4U7551 4.6 11.2 1.0
OD1 A:ASP183 4.6 13.1 1.0
OD2 A:ASP181 4.7 16.7 1.0
O A:HOH725 4.7 23.9 1.0
CG A:HIS126 4.7 8.0 1.0
OD2 A:ASP183 4.8 13.5 1.0
CG A:ASP181 4.9 12.2 1.0
CE1 A:HIS126 4.9 9.2 1.0
OD1 A:ASP181 5.0 14.8 1.0

Fluorine binding site 3 out of 4 in 3skk

Go back to Fluorine Binding Sites List in 3skk
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure


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 Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F552

b:21.0
occ:1.00
 F1 B:4U7552 0.0 21.0 1.0
C9 B:4U7552 1.3 20.3 1.0
F2 B:4U7552 2.2 22.3 1.0
C1 B:4U7552 2.4 17.8 1.0
C3 B:4U7552 2.7 15.8 1.0
O B:HOH469 2.8 20.2 1.0
N1 B:4U7552 2.9 16.9 1.0
O B:HOH605 2.9 27.0 1.0
O B:HOH454 3.2 29.8 1.0
C4 B:4U7552 3.5 14.3 1.0
C2 B:4U7552 3.6 18.4 1.0
O B:HOH484 3.9 21.7 1.0
O1 B:4U7552 4.0 17.5 1.0
O B:HOH550 4.1 24.6 1.0
CD2 B:HIS126 4.3 12.5 1.0
NE2 B:HIS126 4.5 13.8 1.0
OD1 B:ASP183 4.5 21.5 1.0
C5 B:4U7552 4.6 12.6 1.0
CG2 B:THR246 4.6 14.5 1.0
O B:HOH685 4.7 24.7 1.0
O5 B:4U7552 4.7 18.0 1.0
OD2 B:ASP183 4.7 20.4 1.0
O B:HOH555 4.7 19.1 1.0
OD2 B:ASP181 5.0 21.8 1.0

Fluorine binding site 4 out of 4 in 3skk

Go back to Fluorine Binding Sites List in 3skk
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure


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 Arginase I in Complex with the Inhibitor Fabh, Resolution 1.70 A, Twinned Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F552

b:22.3
occ:1.00
 F2 B:4U7552 0.0 22.3 1.0
C9 B:4U7552 1.3 20.3 1.0
F1 B:4U7552 2.2 21.0 1.0
C1 B:4U7552 2.3 17.8 1.0
O B:HOH685 2.7 24.7 1.0
N1 B:4U7552 2.7 16.9 1.0
C2 B:4U7552 2.8 18.4 1.0
O B:HOH550 2.8 24.6 1.0
O1 B:4U7552 3.1 17.5 1.0
O B:HOH605 3.4 27.0 1.0
OD2 B:ASP183 3.6 20.4 1.0
C3 B:4U7552 3.6 15.8 1.0
O5 B:4U7552 3.7 18.0 1.0
O B:HOH667 3.7 19.6 1.0
O B:HOH469 3.8 20.2 1.0
OD1 B:ASP183 4.0 21.5 1.0
CG B:ASP183 4.2 19.4 1.0
C4 B:4U7552 4.4 14.3 1.0
CB B:SER137 4.5 18.4 1.0
O B:HOH454 4.5 29.8 1.0
OG B:SER137 4.6 18.1 1.0
OG1 B:THR136 4.7 27.9 1.0
O B:HOH395 4.9 14.9 1.0

Reference:

M.Ilies, L.Di Costanzo, D.P.Dowling, K.J.Thorn, D.W.Christianson. Binding of Alpha,Alpha-Disubstituted Amino Acids to Arginase Suggests New Avenues For Inhibitor Design J.Med.Chem. 2011.
ISSN: ISSN 0022-2623
PubMed: 21728378
DOI: 10.1021/JM200443B
Page generated: Wed Jul 31 22:33:41 2024

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