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Fluorine in PDB 1t5g: Arginase-F2-L-Arginine Complex

Enzymatic activity of Arginase-F2-L-Arginine Complex

All present enzymatic activity of Arginase-F2-L-Arginine Complex:
3.5.3.1;

Protein crystallography data

The structure of Arginase-F2-L-Arginine Complex, PDB code: 1t5g was solved by E.Cama, S.Pethe, J.-L.Boucher, S.Han, F.A.Emig, D.E.Ash, R.E.Viola, D.Mansuy, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.69 / 2.40
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 87.720, 87.720, 104.520, 90.00, 90.00, 120.00
R / Rfree (%) 22.8 / 25.4

Other elements in 1t5g:

The structure of Arginase-F2-L-Arginine Complex also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Arginase-F2-L-Arginine Complex (pdb code 1t5g). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Arginase-F2-L-Arginine Complex, PDB code: 1t5g:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 1t5g

Go back to Fluorine Binding Sites List in 1t5g
Fluorine binding site 1 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:30.8
occ:1.00
 MN A:MN500 2.2 26.8 1.0
MN A:MN501 2.4 29.5 1.0
OD1 A:ASP128 2.4 34.0 1.0
OD1 A:ASP124 2.4 27.8 1.0
OD2 A:ASP124 2.5 27.4 1.0
NH2 A:ARG1000 2.5 44.3 1.0
CG A:ASP124 2.7 27.2 1.0
OD2 A:ASP128 2.8 35.0 1.0
CG A:ASP128 2.9 35.6 1.0
ND1 A:HIS126 2.9 32.4 1.0
OD2 A:ASP232 3.1 22.6 1.0
CB A:HIS126 3.1 32.6 1.0
CG A:HIS126 3.4 33.0 1.0
O A:HIS126 3.6 31.5 1.0
CZ A:ARG1000 3.7 45.7 1.0
N A:HIS126 3.8 29.7 1.0
F A:F603 3.8 64.9 1.0
CA A:HIS126 3.8 31.1 1.0
CD A:ARG1000 3.8 44.6 1.0
C A:HIS126 3.9 31.5 1.0
CB A:ASP124 4.0 28.8 1.0
CE1 A:HIS126 4.0 33.6 1.0
CG A:ASP232 4.2 23.6 1.0
NE A:ARG1000 4.2 45.3 1.0
OD1 A:ASP234 4.3 20.7 1.0
OD2 A:ASP234 4.3 24.8 1.0
CB A:ASP128 4.3 36.0 1.0
ND1 A:HIS101 4.5 29.7 1.0
CD2 A:HIS126 4.6 34.1 1.0
N A:ALA125 4.7 31.6 1.0
CG A:ASP234 4.7 22.6 1.0
CG A:ARG1000 4.7 46.4 1.0
NH1 A:ARG1000 4.7 47.5 1.0
CB A:ASP232 4.7 23.7 1.0
N A:ASP128 4.8 35.5 1.0
NE2 A:HIS126 4.9 34.3 1.0
NE1 A:TRP122 4.9 29.9 1.0
C A:ALA125 4.9 30.2 1.0
N A:THR127 4.9 32.8 1.0
CA A:ASP128 5.0 36.2 1.0
CA A:ASP124 5.0 29.5 1.0

Fluorine binding site 2 out of 6 in 1t5g

Go back to Fluorine Binding Sites List in 1t5g
Fluorine binding site 2 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:64.9
occ:1.00
 MN A:MN501 2.3 29.5 1.0
NH2 A:ARG1000 2.4 44.3 1.0
OE2 A:GLU277 2.8 33.6 1.0
NH1 A:ARG1000 2.8 47.5 1.0
CB A:HIS101 3.0 28.7 1.0
CZ A:ARG1000 3.0 45.7 1.0
OD2 A:ASP232 3.0 22.6 1.0
CG A:GLU277 3.0 32.4 1.0
CD A:GLU277 3.2 33.0 1.0
ND1 A:HIS101 3.6 29.7 1.0
OD2 A:ASP128 3.7 35.0 1.0
CG A:HIS101 3.7 29.1 1.0
F A:F602 3.8 30.8 1.0
MN A:MN500 3.8 26.8 1.0
CG A:ASP232 3.9 23.6 1.0
N A:HIS101 3.9 31.7 1.0
CA A:HIS101 4.1 30.0 1.0
O A:ALA141 4.1 37.7 1.0
OE1 A:GLU277 4.3 32.8 1.0
NE A:ARG1000 4.3 45.3 1.0
OD2 A:ASP124 4.3 27.4 1.0
OD1 A:ASP232 4.5 24.7 1.0
CB A:GLU277 4.5 31.1 1.0
OD2 A:ASP234 4.6 24.8 1.0
CG A:ASP128 4.6 35.6 1.0
CB A:ASP232 4.8 23.7 1.0
OD1 A:ASP128 4.8 34.0 1.0
CE1 A:HIS101 4.9 28.0 1.0
CB A:ALA141 4.9 37.3 1.0
CD2 A:HIS101 5.0 27.7 1.0
C A:ALA141 5.0 37.5 1.0

Fluorine binding site 3 out of 6 in 1t5g

Go back to Fluorine Binding Sites List in 1t5g
Fluorine binding site 3 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F604

b:30.8
occ:1.00
 MN B:MN502 2.2 26.8 1.0
OD1 B:ASP128 2.4 38.3 1.0
MN B:MN503 2.4 29.5 1.0
OD2 B:ASP124 2.4 30.3 1.0
OD1 B:ASP124 2.4 28.9 1.0
NH2 B:ARG1001 2.5 44.3 1.0
CG B:ASP124 2.7 28.3 1.0
OD2 B:ASP128 2.8 39.6 1.0
CG B:ASP128 2.9 38.2 1.0
ND1 B:HIS126 2.9 31.6 1.0
OD2 B:ASP232 3.1 23.4 1.0
CB B:HIS126 3.1 31.2 1.0
CG B:HIS126 3.3 33.2 1.0
O B:HIS126 3.6 32.0 1.0
CZ B:ARG1001 3.7 45.7 1.0
N B:HIS126 3.7 29.0 1.0
CA B:HIS126 3.8 30.8 1.0
F B:F605 3.8 64.9 1.0
CD B:ARG1001 3.8 44.6 1.0
C B:HIS126 3.9 31.7 1.0
CB B:ASP124 4.0 28.5 1.0
CE1 B:HIS126 4.0 33.1 1.0
OD1 B:ASP234 4.1 24.2 1.0
OD2 B:ASP234 4.2 21.2 1.0
NE B:ARG1001 4.2 45.3 1.0
CG B:ASP232 4.2 25.4 1.0
CB B:ASP128 4.3 36.5 1.0
ND1 B:HIS101 4.5 28.9 1.0
CD2 B:HIS126 4.6 34.2 1.0
CG B:ASP234 4.6 21.2 1.0
N B:ALA125 4.7 30.6 1.0
CG B:ARG1001 4.7 46.4 1.0
NH1 B:ARG1001 4.7 47.5 1.0
CB B:ASP232 4.7 24.8 1.0
N B:ASP128 4.8 35.5 1.0
NE2 B:HIS126 4.9 33.1 1.0
NE1 B:TRP122 4.9 31.1 1.0
C B:ALA125 4.9 29.3 1.0
N B:THR127 4.9 33.0 1.0
CA B:ASP128 5.0 35.8 1.0
CA B:ASP124 5.0 29.3 1.0

Fluorine binding site 4 out of 6 in 1t5g

Go back to Fluorine Binding Sites List in 1t5g
Fluorine binding site 4 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F605

b:64.9
occ:1.00
 MN B:MN503 2.3 29.5 1.0
NH2 B:ARG1001 2.4 44.3 1.0
OE2 B:GLU277 2.8 33.6 1.0
NH1 B:ARG1001 2.8 47.5 1.0
CB B:HIS101 3.0 28.7 1.0
CZ B:ARG1001 3.0 45.7 1.0
OD2 B:ASP232 3.0 23.4 1.0
CG B:GLU277 3.0 33.2 1.0
CD B:GLU277 3.2 34.3 1.0
ND1 B:HIS101 3.6 28.9 1.0
OD2 B:ASP128 3.6 39.6 1.0
CG B:HIS101 3.7 30.0 1.0
F B:F604 3.8 30.8 1.0
MN B:MN502 3.8 26.8 1.0
CG B:ASP232 3.9 25.4 1.0
N B:HIS101 3.9 31.8 1.0
CA B:HIS101 4.1 30.3 1.0
O B:ALA141 4.1 37.3 1.0
OE1 B:GLU277 4.3 35.0 1.0
NE B:ARG1001 4.3 45.3 1.0
OD2 B:ASP124 4.4 30.3 1.0
OD1 B:ASP232 4.5 25.4 1.0
CB B:GLU277 4.5 30.5 1.0
CG B:ASP128 4.6 38.2 1.0
CB B:ASP232 4.8 24.8 1.0
OD1 B:ASP128 4.8 38.3 1.0
CB B:ALA141 4.8 38.5 1.0
CE1 B:HIS101 4.9 28.5 1.0
OD2 B:ASP234 4.9 21.2 1.0
CD2 B:HIS101 4.9 27.9 1.0
C B:ALA141 5.0 37.6 1.0

Fluorine binding site 5 out of 6 in 1t5g

Go back to Fluorine Binding Sites List in 1t5g
Fluorine binding site 5 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F600

b:30.8
occ:1.00
 MN C:MN504 2.2 26.8 1.0
OD1 C:ASP124 2.3 32.8 1.0
OD1 C:ASP128 2.4 36.1 1.0
MN C:MN505 2.4 29.5 1.0
NH2 C:ARG1002 2.5 44.3 1.0
OD2 C:ASP124 2.5 31.5 1.0
CG C:ASP124 2.6 30.8 1.0
OD2 C:ASP128 2.8 36.8 1.0
ND1 C:HIS126 2.9 30.2 1.0
CG C:ASP128 2.9 35.5 1.0
OD2 C:ASP232 3.1 19.0 1.0
CB C:HIS126 3.1 31.6 1.0
CG C:HIS126 3.4 31.0 1.0
O C:HIS126 3.7 32.1 1.0
CZ C:ARG1002 3.7 45.7 1.0
N C:HIS126 3.8 30.7 1.0
CD C:ARG1002 3.8 44.6 1.0
F C:F601 3.8 64.9 1.0
CA C:HIS126 3.8 31.9 1.0
C C:HIS126 3.9 32.4 1.0
CB C:ASP124 4.0 29.5 1.0
CE1 C:HIS126 4.0 30.5 1.0
NE C:ARG1002 4.2 45.3 1.0
CG C:ASP232 4.2 22.3 1.0
OD1 C:ASP234 4.3 26.3 1.0
OD2 C:ASP234 4.3 25.4 1.0
CB C:ASP128 4.3 34.6 1.0
ND1 C:HIS101 4.5 29.0 1.0
CD2 C:HIS126 4.6 30.6 1.0
N C:ALA125 4.7 30.0 1.0
CG C:ARG1002 4.7 46.4 1.0
NH1 C:ARG1002 4.7 47.5 1.0
CG C:ASP234 4.7 23.8 1.0
CB C:ASP232 4.7 22.5 1.0
N C:ASP128 4.8 33.4 1.0
NE2 C:HIS126 4.9 30.1 1.0
NE1 C:TRP122 4.9 30.6 1.0
N C:THR127 4.9 33.3 1.0
C C:ALA125 4.9 30.0 1.0
CA C:ASP128 5.0 34.3 1.0
CA C:ASP124 5.0 28.3 1.0

Fluorine binding site 6 out of 6 in 1t5g

Go back to Fluorine Binding Sites List in 1t5g
Fluorine binding site 6 out of 6 in the Arginase-F2-L-Arginine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F601

b:64.9
occ:1.00
 MN C:MN505 2.3 29.5 1.0
NH2 C:ARG1002 2.4 44.3 1.0
NH1 C:ARG1002 2.8 47.5 1.0
OE2 C:GLU277 2.8 31.1 1.0
CB C:HIS101 3.0 29.9 1.0
CZ C:ARG1002 3.0 45.7 1.0
OD2 C:ASP232 3.0 19.0 1.0
CG C:GLU277 3.0 30.9 1.0
CD C:GLU277 3.2 31.0 1.0
ND1 C:HIS101 3.6 29.0 1.0
OD2 C:ASP128 3.7 36.8 1.0
CG C:HIS101 3.7 29.7 1.0
F C:F600 3.8 30.8 1.0
MN C:MN504 3.8 26.8 1.0
CG C:ASP232 3.9 22.3 1.0
N C:HIS101 3.9 32.9 1.0
CA C:HIS101 4.0 32.2 1.0
O C:ALA141 4.1 37.1 1.0
OD2 C:ASP124 4.3 31.5 1.0
OE1 C:GLU277 4.3 30.1 1.0
NE C:ARG1002 4.3 45.3 1.0
CB C:GLU277 4.5 30.3 1.0
OD1 C:ASP232 4.5 22.8 1.0
CG C:ASP128 4.6 35.5 1.0
O C:HOH775 4.7 30.7 1.0
CB C:ASP232 4.7 22.5 1.0
OD1 C:ASP128 4.8 36.1 1.0
CE1 C:HIS101 4.9 28.1 1.0
CB C:ALA141 4.9 36.0 1.0
OD2 C:ASP234 4.9 25.4 1.0
CD2 C:HIS101 4.9 27.8 1.0
C C:ALA141 5.0 36.5 1.0

Reference:

E.Cama, S.Pethe, J.-L.Boucher, S.Han, F.A.Emig, D.E.Ash, R.E.Viola, D.Mansuy, D.W.Christianson. Inhibitor Coordination Interactions in the Binuclear Manganese Cluster of Arginase Biochemistry V. 43 8987 2004.
ISSN: ISSN 0006-2960
PubMed: 15248756
DOI: 10.1021/BI0491705
Page generated: Wed Jul 31 12:55:14 2024

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