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Manganese 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:

Fluorine (F) 6 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 6 in 1t5g

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:26.8
occ:1.00
 OD2 A:ASP234 2.1 24.8 1.0
OD2 A:ASP232 2.2 22.6 1.0
F A:F602 2.2 30.8 1.0
OD1 A:ASP124 2.3 27.8 1.0
ND1 A:HIS126 2.3 32.4 1.0
OD1 A:ASP234 2.4 20.7 1.0
CG A:ASP234 2.5 22.6 1.0
NH2 A:ARG1000 2.8 44.3 1.0
CE1 A:HIS126 2.8 33.6 1.0
CG A:ASP232 3.2 23.6 1.0
CG A:ASP124 3.3 27.2 1.0
MN A:MN501 3.3 29.5 1.0
CG A:HIS126 3.5 33.0 1.0
OD2 A:ASP124 3.5 27.4 1.0
OD1 A:ASP232 3.8 24.7 1.0
F A:F603 3.8 64.9 1.0
CZ A:ARG1000 4.0 45.7 1.0
NE2 A:HIS126 4.0 34.3 1.0
CB A:ASP234 4.1 20.5 1.0
CB A:HIS126 4.2 32.6 1.0
N A:HIS126 4.2 29.7 1.0
N A:ALA125 4.2 31.6 1.0
CB A:ASP232 4.3 23.7 1.0
CD A:ARG1000 4.3 44.6 1.0
CD2 A:HIS126 4.4 34.1 1.0
OD1 A:ASP128 4.5 34.0 1.0
NE A:ARG1000 4.5 45.3 1.0
CB A:ASP124 4.6 28.8 1.0
CB A:ALA125 4.7 31.6 1.0
OD2 A:ASP128 4.7 35.0 1.0
CA A:HIS126 4.8 31.1 1.0
CA A:ALA125 4.9 30.7 1.0
C A:ALA125 4.9 30.2 1.0
O A:ASP234 4.9 20.4 1.0
NH1 A:ARG1000 5.0 47.5 1.0
CA A:ASP234 5.0 20.7 1.0

Manganese binding site 2 out of 6 in 1t5g

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:29.5
occ:1.00
 OD2 A:ASP124 2.0 27.4 1.0
ND1 A:HIS101 2.3 29.7 1.0
OD2 A:ASP232 2.3 22.6 1.0
OD2 A:ASP128 2.3 35.0 1.0
F A:F603 2.3 64.9 1.0
F A:F602 2.4 30.8 1.0
NH2 A:ARG1000 2.9 44.3 1.0
CG A:ASP124 3.0 27.2 1.0
CG A:ASP232 3.2 23.6 1.0
CG A:HIS101 3.2 29.1 1.0
CE1 A:HIS101 3.3 28.0 1.0
MN A:MN500 3.3 26.8 1.0
CG A:ASP128 3.3 35.6 1.0
OD1 A:ASP124 3.4 27.8 1.0
CB A:HIS101 3.4 28.7 1.0
CB A:ASP232 3.5 23.7 1.0
OD1 A:ASP128 3.7 34.0 1.0
CZ A:ARG1000 4.1 45.7 1.0
OD1 A:ASP232 4.3 24.7 1.0
CD2 A:HIS101 4.3 27.7 1.0
NE2 A:HIS101 4.3 26.3 1.0
CB A:ASP124 4.3 28.8 1.0
NE1 A:TRP122 4.5 29.9 1.0
NH1 A:ARG1000 4.5 47.5 1.0
CG A:GLU277 4.6 32.4 1.0
CB A:ASP128 4.7 36.0 1.0
O A:ALA141 4.7 37.7 1.0
CZ2 A:TRP122 4.8 31.9 1.0
OD2 A:ASP234 4.8 24.8 1.0
CA A:ASP232 4.8 23.1 1.0
CA A:HIS101 4.9 30.0 1.0
OE2 A:GLU277 4.9 33.6 1.0
OD1 A:ASP234 4.9 20.7 1.0
CE2 A:TRP122 5.0 31.0 1.0

Manganese binding site 3 out of 6 in 1t5g

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:26.8
occ:1.00
 OD2 B:ASP234 2.0 21.2 1.0
OD2 B:ASP232 2.2 23.4 1.0
F B:F604 2.2 30.8 1.0
OD1 B:ASP124 2.3 28.9 1.0
ND1 B:HIS126 2.3 31.6 1.0
OD1 B:ASP234 2.4 24.2 1.0
CG B:ASP234 2.5 21.2 1.0
NH2 B:ARG1001 2.8 44.3 1.0
CE1 B:HIS126 2.8 33.1 1.0
CG B:ASP232 3.2 25.4 1.0
CG B:ASP124 3.3 28.3 1.0
MN B:MN503 3.3 29.5 1.0
CG B:HIS126 3.5 33.2 1.0
OD2 B:ASP124 3.6 30.3 1.0
OD1 B:ASP232 3.8 25.4 1.0
F B:F605 3.8 64.9 1.0
CB B:ASP234 3.9 20.1 1.0
CZ B:ARG1001 4.0 45.7 1.0
NE2 B:HIS126 4.1 33.1 1.0
CB B:HIS126 4.1 31.2 1.0
N B:HIS126 4.2 29.0 1.0
N B:ALA125 4.2 30.6 1.0
CB B:ASP232 4.3 24.8 1.0
CD B:ARG1001 4.3 44.6 1.0
CD2 B:HIS126 4.4 34.2 1.0
OD1 B:ASP128 4.5 38.3 1.0
NE B:ARG1001 4.5 45.3 1.0
CB B:ASP124 4.6 28.5 1.0
OD2 B:ASP128 4.7 39.6 1.0
CB B:ALA125 4.7 30.4 1.0
O B:ASP234 4.7 19.5 1.0
CA B:HIS126 4.8 30.8 1.0
CA B:ALA125 4.9 29.9 1.0
C B:ALA125 4.9 29.3 1.0
CA B:ASP234 4.9 19.5 1.0
NH1 B:ARG1001 5.0 47.5 1.0

Manganese binding site 4 out of 6 in 1t5g

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn503

b:29.5
occ:1.00
 OD2 B:ASP124 2.1 30.3 1.0
ND1 B:HIS101 2.3 28.9 1.0
OD2 B:ASP232 2.3 23.4 1.0
OD2 B:ASP128 2.3 39.6 1.0
F B:F605 2.3 64.9 1.0
F B:F604 2.4 30.8 1.0
NH2 B:ARG1001 2.9 44.3 1.0
CG B:ASP124 3.0 28.3 1.0
CG B:HIS101 3.2 30.0 1.0
CG B:ASP232 3.2 25.4 1.0
CE1 B:HIS101 3.3 28.5 1.0
MN B:MN502 3.3 26.8 1.0
OD1 B:ASP124 3.3 28.9 1.0
CG B:ASP128 3.3 38.2 1.0
CB B:HIS101 3.4 28.7 1.0
CB B:ASP232 3.5 24.8 1.0
OD1 B:ASP128 3.7 38.3 1.0
CZ B:ARG1001 4.1 45.7 1.0
OD1 B:ASP232 4.3 25.4 1.0
CD2 B:HIS101 4.3 27.9 1.0
NE2 B:HIS101 4.3 26.5 1.0
CB B:ASP124 4.4 28.5 1.0
NE1 B:TRP122 4.5 31.1 1.0
NH1 B:ARG1001 4.5 47.5 1.0
CG B:GLU277 4.5 33.2 1.0
CB B:ASP128 4.6 36.5 1.0
OD1 B:ASP234 4.7 24.2 1.0
O B:ALA141 4.7 37.3 1.0
CZ2 B:TRP122 4.8 33.3 1.0
CA B:ASP232 4.9 25.4 1.0
CA B:HIS101 4.9 30.3 1.0
OE2 B:GLU277 4.9 33.6 1.0
OD2 B:ASP234 4.9 21.2 1.0
CE2 B:TRP122 5.0 32.7 1.0

Manganese binding site 5 out of 6 in 1t5g

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn504

b:26.8
occ:1.00
 OD2 C:ASP234 2.1 25.4 1.0
OD2 C:ASP232 2.2 19.0 1.0
F C:F600 2.2 30.8 1.0
ND1 C:HIS126 2.3 30.2 1.0
OD1 C:ASP124 2.3 32.8 1.0
OD1 C:ASP234 2.5 26.3 1.0
CG C:ASP234 2.6 23.8 1.0
NH2 C:ARG1002 2.8 44.3 1.0
CE1 C:HIS126 2.8 30.5 1.0
CG C:ASP232 3.2 22.3 1.0
CG C:ASP124 3.2 30.8 1.0
MN C:MN505 3.3 29.5 1.0
OD2 C:ASP124 3.5 31.5 1.0
CG C:HIS126 3.5 31.0 1.0
OD1 C:ASP232 3.8 22.8 1.0
F C:F601 3.8 64.9 1.0
CZ C:ARG1002 4.0 45.7 1.0
NE2 C:HIS126 4.1 30.1 1.0
CB C:ASP234 4.1 22.3 1.0
CB C:HIS126 4.2 31.6 1.0
N C:HIS126 4.2 30.7 1.0
N C:ALA125 4.2 30.0 1.0
CB C:ASP232 4.3 22.5 1.0
CD C:ARG1002 4.3 44.6 1.0
CD2 C:HIS126 4.4 30.6 1.0
OD1 C:ASP128 4.5 36.1 1.0
NE C:ARG1002 4.5 45.3 1.0
CB C:ASP124 4.6 29.5 1.0
CB C:ALA125 4.7 28.4 1.0
OD2 C:ASP128 4.7 36.8 1.0
CA C:HIS126 4.8 31.9 1.0
CA C:ALA125 4.9 30.0 1.0
NH1 C:ARG1002 4.9 47.5 1.0
C C:ALA125 4.9 30.0 1.0
O C:ASP234 5.0 21.9 1.0

Manganese binding site 6 out of 6 in 1t5g

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Arginase-F2-L-Arginine Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn505

b:29.5
occ:1.00
 OD2 C:ASP124 2.0 31.5 1.0
ND1 C:HIS101 2.3 29.0 1.0
OD2 C:ASP232 2.3 19.0 1.0
F C:F601 2.3 64.9 1.0
OD2 C:ASP128 2.3 36.8 1.0
F C:F600 2.4 30.8 1.0
NH2 C:ARG1002 2.9 44.3 1.0
CG C:ASP124 3.0 30.8 1.0
CG C:HIS101 3.2 29.7 1.0
CG C:ASP232 3.2 22.3 1.0
CE1 C:HIS101 3.3 28.1 1.0
MN C:MN504 3.3 26.8 1.0
CG C:ASP128 3.4 35.5 1.0
CB C:HIS101 3.4 29.9 1.0
OD1 C:ASP124 3.4 32.8 1.0
CB C:ASP232 3.5 22.5 1.0
OD1 C:ASP128 3.7 36.1 1.0
CZ C:ARG1002 4.1 45.7 1.0
CD2 C:HIS101 4.3 27.8 1.0
OD1 C:ASP232 4.3 22.8 1.0
NE2 C:HIS101 4.3 27.6 1.0
CB C:ASP124 4.3 29.5 1.0
NH1 C:ARG1002 4.5 47.5 1.0
NE1 C:TRP122 4.5 30.6 1.0
CG C:GLU277 4.6 30.9 1.0
CB C:ASP128 4.7 34.6 1.0
O C:ALA141 4.7 37.1 1.0
CZ2 C:TRP122 4.8 30.6 1.0
CA C:ASP232 4.8 22.9 1.0
CA C:HIS101 4.9 32.2 1.0
OE2 C:GLU277 4.9 31.1 1.0
OD1 C:ASP234 4.9 26.3 1.0
OD2 C:ASP234 5.0 25.4 1.0
CE2 C:TRP122 5.0 31.1 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: Sat Oct 5 12:31:04 2024

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