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:
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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