Manganese in PDB 1p8r: Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.
Enzymatic activity of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.
All present enzymatic activity of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.:
3.5.3.1;
Protein crystallography data
The structure of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I., PDB code: 1p8r
was solved by
E.Cama,
F.A.Emig,
D.E.Ash,
D.W.Christianson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
500.00 /
2.50
|
Space group
|
P 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.000,
91.000,
69.300,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
14.4 /
20.1
|
Other elements in 1p8r:
The structure of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.
(pdb code 1p8r). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I., PDB code: 1p8r:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 1p8r
Go back to
Manganese Binding Sites List in 1p8r
Manganese binding site 1 out
of 4 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn500
b:18.2
occ:1.00
|
ND1
|
A:HIS126
|
2.1
|
6.7
|
1.0
|
O1
|
A:S2C551
|
2.2
|
40.5
|
1.0
|
OD2
|
A:ASP234
|
2.3
|
22.4
|
1.0
|
OD2
|
A:ASP124
|
2.4
|
11.9
|
1.0
|
OD1
|
A:ASP234
|
2.4
|
21.6
|
1.0
|
OD2
|
A:ASP232
|
2.6
|
17.6
|
1.0
|
CG
|
A:ASP234
|
2.7
|
19.6
|
1.0
|
CE1
|
A:HIS126
|
2.9
|
9.2
|
1.0
|
O3
|
A:S2C551
|
3.0
|
43.0
|
1.0
|
B
|
A:S2C551
|
3.1
|
42.3
|
1.0
|
CG
|
A:ASP124
|
3.2
|
10.3
|
1.0
|
OD1
|
A:ASP124
|
3.3
|
10.5
|
1.0
|
CG
|
A:HIS126
|
3.3
|
7.9
|
1.0
|
CG
|
A:ASP232
|
3.4
|
15.7
|
1.0
|
MN
|
A:MN501
|
3.6
|
23.2
|
1.0
|
CE
|
A:S2C551
|
3.7
|
43.6
|
1.0
|
CB
|
A:HIS126
|
3.9
|
7.8
|
1.0
|
OD1
|
A:ASP232
|
3.9
|
14.5
|
1.0
|
N
|
A:HIS126
|
4.0
|
9.1
|
1.0
|
NE2
|
A:HIS126
|
4.1
|
9.1
|
1.0
|
N
|
A:ALA125
|
4.1
|
8.9
|
1.0
|
CB
|
A:ASP234
|
4.2
|
16.8
|
1.0
|
O2
|
A:S2C551
|
4.3
|
40.8
|
1.0
|
CD2
|
A:HIS126
|
4.3
|
7.4
|
1.0
|
CB
|
A:ASP232
|
4.4
|
14.6
|
1.0
|
CD
|
A:S2C551
|
4.5
|
46.7
|
1.0
|
CA
|
A:HIS126
|
4.5
|
8.3
|
1.0
|
CB
|
A:ASP124
|
4.6
|
8.5
|
1.0
|
CB
|
A:ALA125
|
4.7
|
8.1
|
1.0
|
OD2
|
A:ASP128
|
4.7
|
10.8
|
1.0
|
O
|
A:THR246
|
4.8
|
16.9
|
1.0
|
C
|
A:ALA125
|
4.8
|
7.9
|
1.0
|
CA
|
A:ALA125
|
4.8
|
7.5
|
1.0
|
OD1
|
A:ASP128
|
4.9
|
8.6
|
1.0
|
CA
|
A:ASP124
|
4.9
|
8.9
|
1.0
|
|
Manganese binding site 2 out
of 4 in 1p8r
Go back to
Manganese Binding Sites List in 1p8r
Manganese binding site 2 out
of 4 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:23.2
occ:1.00
|
OD1
|
A:ASP128
|
2.1
|
8.6
|
1.0
|
O1
|
A:S2C551
|
2.1
|
40.5
|
1.0
|
OD1
|
A:ASP124
|
2.3
|
10.5
|
1.0
|
OE1
|
A:GLU101
|
2.3
|
18.3
|
1.0
|
OD2
|
A:ASP232
|
2.4
|
17.6
|
1.0
|
O2
|
A:S2C551
|
2.5
|
40.8
|
1.0
|
B
|
A:S2C551
|
2.7
|
42.3
|
1.0
|
CG
|
A:ASP128
|
3.1
|
7.5
|
1.0
|
O3
|
A:S2C551
|
3.2
|
43.0
|
1.0
|
CG
|
A:ASP124
|
3.4
|
10.3
|
1.0
|
OD2
|
A:ASP128
|
3.4
|
10.8
|
1.0
|
CD
|
A:GLU101
|
3.4
|
18.6
|
1.0
|
CG
|
A:ASP232
|
3.5
|
15.7
|
1.0
|
MN
|
A:MN500
|
3.6
|
18.2
|
1.0
|
CB
|
A:GLU101
|
3.8
|
18.0
|
1.0
|
OD2
|
A:ASP124
|
3.9
|
11.9
|
1.0
|
CB
|
A:ASP232
|
3.9
|
14.6
|
1.0
|
CG
|
A:GLU101
|
4.0
|
16.6
|
1.0
|
O
|
A:HIS141
|
4.1
|
19.6
|
1.0
|
CE
|
A:S2C551
|
4.2
|
43.6
|
1.0
|
CZ2
|
A:TRP122
|
4.2
|
12.9
|
1.0
|
NE1
|
A:TRP122
|
4.2
|
12.3
|
1.0
|
CB
|
A:ASP128
|
4.4
|
8.2
|
1.0
|
OE2
|
A:GLU101
|
4.4
|
17.7
|
1.0
|
OD1
|
A:ASP232
|
4.5
|
14.5
|
1.0
|
CE2
|
A:TRP122
|
4.6
|
12.4
|
1.0
|
CD
|
A:S2C551
|
4.6
|
46.7
|
1.0
|
CB
|
A:ASP124
|
4.6
|
8.5
|
1.0
|
CG
|
A:GLU277
|
4.7
|
17.1
|
1.0
|
OD2
|
A:ASP234
|
5.0
|
22.4
|
1.0
|
|
Manganese binding site 3 out
of 4 in 1p8r
Go back to
Manganese Binding Sites List in 1p8r
Manganese binding site 3 out
of 4 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn502
b:15.6
occ:1.00
|
O1
|
B:S2C552
|
2.2
|
29.1
|
1.0
|
ND1
|
B:HIS126
|
2.2
|
12.5
|
1.0
|
OD1
|
B:ASP234
|
2.3
|
8.9
|
1.0
|
OD2
|
B:ASP234
|
2.3
|
9.7
|
1.0
|
OD2
|
B:ASP124
|
2.3
|
18.2
|
1.0
|
OD2
|
B:ASP232
|
2.5
|
16.0
|
1.0
|
CG
|
B:ASP234
|
2.6
|
7.1
|
1.0
|
CE1
|
B:HIS126
|
2.9
|
13.1
|
1.0
|
CG
|
B:ASP124
|
3.1
|
16.6
|
1.0
|
B
|
B:S2C552
|
3.2
|
29.4
|
1.0
|
O3
|
B:S2C552
|
3.2
|
30.6
|
1.0
|
OD1
|
B:ASP124
|
3.2
|
15.9
|
1.0
|
CG
|
B:ASP232
|
3.3
|
15.1
|
1.0
|
CG
|
B:HIS126
|
3.4
|
14.3
|
1.0
|
MN
|
B:MN503
|
3.7
|
22.7
|
1.0
|
OD1
|
B:ASP232
|
3.8
|
16.9
|
1.0
|
CE
|
B:S2C552
|
3.9
|
29.1
|
1.0
|
CB
|
B:HIS126
|
4.0
|
13.8
|
1.0
|
N
|
B:HIS126
|
4.0
|
13.8
|
1.0
|
N
|
B:ALA125
|
4.0
|
12.3
|
1.0
|
CB
|
B:ASP234
|
4.1
|
6.4
|
1.0
|
NE2
|
B:HIS126
|
4.2
|
14.8
|
1.0
|
CB
|
B:ASP232
|
4.2
|
12.7
|
1.0
|
O2
|
B:S2C552
|
4.4
|
29.5
|
1.0
|
CD2
|
B:HIS126
|
4.4
|
14.6
|
1.0
|
CB
|
B:ASP124
|
4.5
|
13.2
|
1.0
|
CB
|
B:ALA125
|
4.6
|
10.0
|
1.0
|
CA
|
B:HIS126
|
4.6
|
13.3
|
1.0
|
CD
|
B:S2C552
|
4.6
|
29.7
|
1.0
|
CA
|
B:ALA125
|
4.7
|
11.6
|
1.0
|
C
|
B:ALA125
|
4.7
|
13.1
|
1.0
|
O
|
B:THR246
|
4.8
|
18.4
|
1.0
|
CA
|
B:ASP124
|
4.8
|
12.8
|
1.0
|
OD2
|
B:ASP128
|
4.8
|
11.2
|
1.0
|
C
|
B:ASP234
|
4.9
|
8.8
|
1.0
|
C
|
B:ASP124
|
4.9
|
12.9
|
1.0
|
CA
|
B:ASP234
|
4.9
|
9.0
|
1.0
|
O
|
B:ASP234
|
4.9
|
10.1
|
1.0
|
OD1
|
B:ASP128
|
5.0
|
8.3
|
1.0
|
|
Manganese binding site 4 out
of 4 in 1p8r
Go back to
Manganese Binding Sites List in 1p8r
Manganese binding site 4 out
of 4 in the Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I.
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn503
b:22.7
occ:1.00
|
OD1
|
B:ASP128
|
2.2
|
8.3
|
1.0
|
O1
|
B:S2C552
|
2.2
|
29.1
|
1.0
|
OE1
|
B:GLU101
|
2.2
|
18.9
|
1.0
|
OD1
|
B:ASP124
|
2.3
|
15.9
|
1.0
|
OD2
|
B:ASP232
|
2.4
|
16.0
|
1.0
|
O2
|
B:S2C552
|
2.5
|
29.5
|
1.0
|
B
|
B:S2C552
|
2.8
|
29.4
|
1.0
|
CG
|
B:ASP128
|
3.2
|
10.4
|
1.0
|
CD
|
B:GLU101
|
3.4
|
19.6
|
1.0
|
CG
|
B:ASP232
|
3.4
|
15.1
|
1.0
|
O3
|
B:S2C552
|
3.4
|
30.6
|
1.0
|
CG
|
B:ASP124
|
3.4
|
16.6
|
1.0
|
OD2
|
B:ASP128
|
3.5
|
11.2
|
1.0
|
MN
|
B:MN502
|
3.7
|
15.6
|
1.0
|
CB
|
B:GLU101
|
3.8
|
18.9
|
1.0
|
CB
|
B:ASP232
|
3.9
|
12.7
|
1.0
|
OD2
|
B:ASP124
|
3.9
|
18.2
|
1.0
|
CG
|
B:GLU101
|
3.9
|
18.6
|
1.0
|
O
|
B:HIS141
|
4.1
|
4.2
|
1.0
|
CZ2
|
B:TRP122
|
4.2
|
11.2
|
1.0
|
NE1
|
B:TRP122
|
4.2
|
11.7
|
1.0
|
CE
|
B:S2C552
|
4.3
|
29.1
|
1.0
|
OE2
|
B:GLU101
|
4.4
|
19.3
|
1.0
|
OD1
|
B:ASP232
|
4.4
|
16.9
|
1.0
|
CB
|
B:ASP128
|
4.5
|
13.7
|
1.0
|
CE2
|
B:TRP122
|
4.6
|
10.3
|
1.0
|
CG
|
B:GLU277
|
4.6
|
20.7
|
1.0
|
CB
|
B:ASP124
|
4.6
|
13.2
|
1.0
|
CD
|
B:S2C552
|
4.7
|
29.7
|
1.0
|
OD2
|
B:ASP234
|
5.0
|
9.7
|
1.0
|
|
Reference:
E.Cama,
F.A.Emig,
D.E.Ash,
D.W.Christianson.
Structural and Functional Importance of First-Shell Metal Ligands in the Binuclear Manganese Cluster of Arginase I Biochemistry V. 42 7748 2003.
ISSN: ISSN 0006-2960
PubMed: 12820884
DOI: 10.1021/BI030074Y
Page generated: Sat Oct 5 12:03:39 2024
|