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Fluorine in PDB 3gn0: Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)

Enzymatic activity of Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)

All present enzymatic activity of Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo):
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo), PDB code: 3gn0 was solved by 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) 33.82 / 1.70
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 89.587, 89.587, 69.020, 90.00, 90.00, 120.00
R / Rfree (%) 16.1 / 20.2

Other elements in 3gn0:

The structure of Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo) 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 Difluoromethylornithine (Dfmo) (pdb code 3gn0). 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 Difluoromethylornithine (Dfmo), PDB code: 3gn0:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3gn0

Go back to Fluorine Binding Sites List in 3gn0
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)


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 Difluoromethylornithine (Dfmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F551

b:35.6
occ:1.00
 F1 A:DMO551 0.0 35.6 1.0
CO A:DMO551 1.5 31.5 1.0
F2 A:DMO551 2.3 36.7 1.0
CAO A:DMO551 2.5 29.5 1.0
C A:DMO551 2.9 29.5 1.0
OD2 A:ASP183 2.9 20.4 1.0
O A:HOH428 3.0 26.8 1.0
NO A:DMO551 3.0 28.1 1.0
OD1 A:ASP183 3.3 22.6 1.0
O A:DMO551 3.4 28.6 1.0
CG A:ASP183 3.5 21.0 1.0
OH A:DMO551 3.5 27.5 1.0
CBO A:DMO551 3.8 27.3 1.0
O A:HOH434 3.8 28.5 1.0
OG1 A:THR136 4.3 25.8 1.0
O A:HOH534 4.3 27.1 1.0
CB A:SER137 4.5 18.5 1.0
OG A:SER137 4.6 16.5 1.0
ND2 A:ASN130 4.9 13.2 1.0
CB A:ASP183 5.0 19.1 1.0

Fluorine binding site 2 out of 4 in 3gn0

Go back to Fluorine Binding Sites List in 3gn0
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)


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 Difluoromethylornithine (Dfmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F551

b:36.7
occ:1.00
 F2 A:DMO551 0.0 36.7 1.0
CO A:DMO551 1.4 31.5 1.0
F1 A:DMO551 2.3 35.6 1.0
CAO A:DMO551 2.5 29.5 1.0
O A:DMO551 2.8 28.6 1.0
CBO A:DMO551 2.8 27.3 1.0
O A:HOH534 2.9 27.1 1.0
C A:DMO551 2.9 29.5 1.0
O A:HOH535 3.3 31.4 1.0
O A:HOH436 3.5 21.7 1.0
NO A:DMO551 3.8 28.1 1.0
OH A:DMO551 4.1 27.5 1.0
CB A:SER137 4.1 18.5 1.0
OG A:SER137 4.3 16.5 1.0
CGO A:DMO551 4.3 24.4 1.0
O A:HOH434 4.5 28.5 1.0
O A:HOH428 4.7 26.8 1.0
CDO A:DMO551 4.8 25.3 1.0
OD2 A:ASP183 5.0 20.4 1.0

Fluorine binding site 3 out of 4 in 3gn0

Go back to Fluorine Binding Sites List in 3gn0
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)


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 Difluoromethylornithine (Dfmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F552

b:42.9
occ:1.00
 F1 B:DMO552 0.0 42.9 1.0
CO B:DMO552 1.5 39.5 1.0
F2 B:DMO552 2.4 42.0 1.0
CAO B:DMO552 2.5 37.2 1.0
C B:DMO552 2.9 37.0 1.0
OD2 B:ASP183 3.0 25.6 1.0
NO B:DMO552 3.0 37.2 1.0
OD1 B:ASP183 3.2 26.0 1.0
O B:DMO552 3.4 36.5 1.0
O B:HOH409 3.5 41.8 1.0
CG B:ASP183 3.5 24.8 1.0
OH B:DMO552 3.5 36.1 1.0
O B:HOH431 3.6 22.1 1.0
CBO B:DMO552 3.8 34.4 1.0
OG1 B:THR136 4.3 29.0 1.0
O B:HOH389 4.5 36.4 1.0
CB B:SER137 4.5 27.9 1.0
OG B:SER137 4.5 24.8 1.0
ND2 B:ASN130 4.8 22.6 1.0
O B:HOH539 4.8 30.4 1.0
CB B:ASP183 5.0 22.1 1.0

Fluorine binding site 4 out of 4 in 3gn0

Go back to Fluorine Binding Sites List in 3gn0
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Arginase I in Complex with Difluoromethylornithine (Dfmo)


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 Difluoromethylornithine (Dfmo) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F552

b:42.0
occ:1.00
 F2 B:DMO552 0.0 42.0 1.0
CO B:DMO552 1.4 39.5 1.0
F1 B:DMO552 2.4 42.9 1.0
CAO B:DMO552 2.5 37.2 1.0
O B:DMO552 2.8 36.5 1.0
CBO B:DMO552 2.8 34.4 1.0
C B:DMO552 3.0 37.0 1.0
O B:HOH539 3.1 30.4 1.0
O B:HOH380 3.5 23.3 1.0
O B:HOH562 3.8 36.8 1.0
NO B:DMO552 3.8 37.2 1.0
CB B:SER137 4.1 27.9 1.0
OH B:DMO552 4.1 36.1 1.0
OG B:SER137 4.2 24.8 1.0
CGO B:DMO552 4.3 33.0 1.0
O B:HOH431 4.5 22.1 1.0
CDO B:DMO552 4.8 32.5 1.0
O B:HOH389 4.9 36.4 1.0
O B:HOH409 5.0 41.8 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. V. 54 5432 2011.
ISSN: ISSN 0022-2623
PubMed: 21728378
DOI: 10.1021/JM200443B
Page generated: Wed Jul 31 18:56:00 2024

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