Manganese in PDB 6q39: Complex of Arginase 2 with Example 49
Enzymatic activity of Complex of Arginase 2 with Example 49
All present enzymatic activity of Complex of Arginase 2 with Example 49:
3.5.3.1;
Protein crystallography data
The structure of Complex of Arginase 2 with Example 49, PDB code: 6q39
was solved by
A.D.Podjarny,
M.C.Van Zandt,
A.Cousido-Siah,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.91 /
2.21
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
128.303,
128.303,
159.155,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.2 /
21
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Complex of Arginase 2 with Example 49
(pdb code 6q39). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the
Complex of Arginase 2 with Example 49, PDB code: 6q39:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
Manganese binding site 1 out
of 6 in 6q39
Go back to
Manganese Binding Sites List in 6q39
Manganese binding site 1 out
of 6 in the Complex of Arginase 2 with Example 49
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Complex of Arginase 2 with Example 49 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn401
b:22.9
occ:1.00
|
OD2
|
A:ASP143
|
2.1
|
24.9
|
1.0
|
OD2
|
A:ASP147
|
2.1
|
22.4
|
1.0
|
ND1
|
A:HIS120
|
2.2
|
21.5
|
1.0
|
O23
|
A:HDQ405
|
2.2
|
26.1
|
1.0
|
O7
|
A:HDQ405
|
2.2
|
20.0
|
1.0
|
OD2
|
A:ASP251
|
2.3
|
23.2
|
1.0
|
B6
|
A:HDQ405
|
2.9
|
25.1
|
1.0
|
CE1
|
A:HIS120
|
3.1
|
25.4
|
1.0
|
CG
|
A:ASP143
|
3.1
|
21.6
|
1.0
|
CG
|
A:ASP147
|
3.1
|
22.9
|
1.0
|
CG
|
A:HIS120
|
3.1
|
20.8
|
1.0
|
CG
|
A:ASP251
|
3.3
|
23.4
|
1.0
|
MN
|
A:MN402
|
3.3
|
25.0
|
1.0
|
OD1
|
A:ASP143
|
3.4
|
22.5
|
1.0
|
OD1
|
A:ASP147
|
3.4
|
24.6
|
1.0
|
CB
|
A:HIS120
|
3.5
|
22.1
|
1.0
|
CB
|
A:ASP251
|
3.6
|
20.2
|
1.0
|
O8
|
A:HDQ405
|
3.8
|
23.3
|
1.0
|
C5
|
A:HDQ405
|
4.2
|
21.6
|
1.0
|
NE2
|
A:HIS120
|
4.2
|
28.1
|
1.0
|
CD2
|
A:HIS120
|
4.2
|
21.6
|
1.0
|
NE1
|
A:TRP141
|
4.3
|
26.9
|
1.0
|
OD1
|
A:ASP251
|
4.4
|
19.1
|
1.0
|
CB
|
A:ASP143
|
4.5
|
22.1
|
1.0
|
CB
|
A:ASP147
|
4.5
|
20.6
|
1.0
|
O
|
A:HIS160
|
4.6
|
22.0
|
1.0
|
CZ2
|
A:TRP141
|
4.6
|
22.1
|
1.0
|
CE2
|
A:TRP141
|
4.8
|
20.6
|
1.0
|
CG
|
A:GLU296
|
4.8
|
22.1
|
1.0
|
CA
|
A:ASP251
|
4.9
|
21.9
|
1.0
|
CG2
|
A:VAL295
|
4.9
|
19.2
|
1.0
|
OE1
|
A:GLU296
|
4.9
|
26.1
|
1.0
|
CA
|
A:HIS120
|
5.0
|
22.2
|
1.0
|
|
Manganese binding site 2 out
of 6 in 6q39
Go back to
Manganese Binding Sites List in 6q39
Manganese binding site 2 out
of 6 in the Complex of Arginase 2 with Example 49
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Complex of Arginase 2 with Example 49 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn402
b:25.0
occ:1.00
|
ND1
|
A:HIS145
|
2.2
|
23.9
|
1.0
|
OD1
|
A:ASP143
|
2.2
|
22.5
|
1.0
|
OD2
|
A:ASP253
|
2.2
|
23.4
|
1.0
|
O7
|
A:HDQ405
|
2.2
|
20.0
|
1.0
|
OD2
|
A:ASP251
|
2.3
|
23.2
|
1.0
|
OD1
|
A:ASP253
|
2.6
|
21.4
|
1.0
|
CG
|
A:ASP253
|
2.8
|
30.0
|
1.0
|
O8
|
A:HDQ405
|
2.9
|
23.3
|
1.0
|
CE1
|
A:HIS145
|
3.0
|
24.7
|
1.0
|
CG
|
A:ASP143
|
3.1
|
21.6
|
1.0
|
CG
|
A:ASP251
|
3.2
|
23.4
|
1.0
|
B6
|
A:HDQ405
|
3.2
|
25.1
|
1.0
|
CG
|
A:HIS145
|
3.3
|
22.9
|
1.0
|
MN
|
A:MN401
|
3.3
|
22.9
|
1.0
|
OD2
|
A:ASP143
|
3.4
|
24.9
|
1.0
|
CB
|
A:HIS145
|
3.7
|
22.9
|
1.0
|
OD1
|
A:ASP251
|
3.8
|
19.1
|
1.0
|
O23
|
A:HDQ405
|
3.9
|
26.1
|
1.0
|
N
|
A:HIS145
|
4.0
|
19.8
|
1.0
|
CB
|
A:ASP251
|
4.1
|
20.2
|
1.0
|
NE2
|
A:HIS145
|
4.2
|
25.0
|
1.0
|
N
|
A:ALA144
|
4.2
|
21.7
|
1.0
|
CB
|
A:ASP253
|
4.3
|
19.7
|
1.0
|
CD2
|
A:HIS145
|
4.3
|
18.6
|
1.0
|
C4
|
A:HDQ405
|
4.3
|
22.2
|
1.0
|
OG1
|
A:THR265
|
4.3
|
27.4
|
0.4
|
C5
|
A:HDQ405
|
4.3
|
21.6
|
1.0
|
CA
|
A:HIS145
|
4.4
|
21.3
|
1.0
|
OD1
|
A:ASP147
|
4.5
|
24.6
|
1.0
|
CB
|
A:ASP143
|
4.5
|
22.1
|
1.0
|
OD2
|
A:ASP147
|
4.7
|
22.4
|
1.0
|
CB
|
A:ALA144
|
4.8
|
22.1
|
1.0
|
C
|
A:ALA144
|
4.8
|
25.7
|
1.0
|
O
|
A:HOH562
|
4.8
|
25.4
|
1.0
|
CA
|
A:ALA144
|
4.8
|
24.5
|
1.0
|
CA
|
A:ASP143
|
4.9
|
20.0
|
1.0
|
|
Manganese binding site 3 out
of 6 in 6q39
Go back to
Manganese Binding Sites List in 6q39
Manganese binding site 3 out
of 6 in the Complex of Arginase 2 with Example 49
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Complex of Arginase 2 with Example 49 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn401
b:25.7
occ:1.00
|
OD2
|
B:ASP147
|
2.1
|
25.8
|
1.0
|
OD2
|
B:ASP143
|
2.1
|
22.4
|
1.0
|
O23
|
B:HDQ405
|
2.3
|
21.8
|
1.0
|
O7
|
B:HDQ405
|
2.3
|
24.0
|
1.0
|
OD2
|
B:ASP251
|
2.3
|
23.6
|
1.0
|
ND1
|
B:HIS120
|
2.3
|
23.9
|
1.0
|
B6
|
B:HDQ405
|
2.9
|
26.4
|
1.0
|
CG
|
B:ASP147
|
3.1
|
28.2
|
1.0
|
CG
|
B:ASP143
|
3.2
|
22.2
|
1.0
|
CG
|
B:HIS120
|
3.2
|
25.4
|
1.0
|
MN
|
B:MN402
|
3.3
|
27.0
|
1.0
|
CE1
|
B:HIS120
|
3.3
|
20.8
|
1.0
|
CG
|
B:ASP251
|
3.3
|
23.6
|
1.0
|
OD1
|
B:ASP147
|
3.4
|
22.9
|
1.0
|
CB
|
B:HIS120
|
3.4
|
19.4
|
1.0
|
OD1
|
B:ASP143
|
3.5
|
22.8
|
1.0
|
O8
|
B:HDQ405
|
3.6
|
24.5
|
1.0
|
CB
|
B:ASP251
|
3.6
|
20.4
|
1.0
|
C5
|
B:HDQ405
|
4.2
|
24.9
|
1.0
|
NE1
|
B:TRP141
|
4.3
|
23.4
|
1.0
|
CD2
|
B:HIS120
|
4.4
|
24.8
|
1.0
|
NE2
|
B:HIS120
|
4.4
|
25.3
|
1.0
|
CB
|
B:ASP147
|
4.5
|
21.3
|
1.0
|
OD1
|
B:ASP251
|
4.5
|
21.3
|
1.0
|
CB
|
B:ASP143
|
4.5
|
19.7
|
1.0
|
O
|
B:HIS160
|
4.6
|
22.9
|
1.0
|
CZ2
|
B:TRP141
|
4.7
|
22.7
|
1.0
|
CG
|
B:GLU296
|
4.8
|
21.0
|
1.0
|
CE2
|
B:TRP141
|
4.9
|
19.6
|
1.0
|
CA
|
B:HIS120
|
5.0
|
20.4
|
1.0
|
CA
|
B:ASP251
|
5.0
|
17.6
|
1.0
|
OE2
|
B:GLU296
|
5.0
|
26.4
|
1.0
|
|
Manganese binding site 4 out
of 6 in 6q39
Go back to
Manganese Binding Sites List in 6q39
Manganese binding site 4 out
of 6 in the Complex of Arginase 2 with Example 49
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Complex of Arginase 2 with Example 49 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn402
b:27.0
occ:1.00
|
OD1
|
B:ASP143
|
2.2
|
22.8
|
1.0
|
OD2
|
B:ASP253
|
2.2
|
23.1
|
1.0
|
ND1
|
B:HIS145
|
2.3
|
25.2
|
1.0
|
O7
|
B:HDQ405
|
2.3
|
24.0
|
1.0
|
OD2
|
B:ASP251
|
2.5
|
23.6
|
1.0
|
OD1
|
B:ASP253
|
2.6
|
24.5
|
1.0
|
O8
|
B:HDQ405
|
2.7
|
24.5
|
1.0
|
CG
|
B:ASP253
|
2.7
|
23.0
|
1.0
|
CE1
|
B:HIS145
|
3.0
|
22.2
|
1.0
|
CG
|
B:ASP143
|
3.1
|
22.2
|
1.0
|
B6
|
B:HDQ405
|
3.2
|
26.4
|
1.0
|
CG
|
B:ASP251
|
3.3
|
23.6
|
1.0
|
MN
|
B:MN401
|
3.3
|
25.7
|
1.0
|
CG
|
B:HIS145
|
3.4
|
25.7
|
1.0
|
OD2
|
B:ASP143
|
3.4
|
22.4
|
1.0
|
CB
|
B:HIS145
|
3.8
|
22.6
|
1.0
|
OD1
|
B:ASP251
|
3.8
|
21.3
|
1.0
|
N
|
B:HIS145
|
4.0
|
23.3
|
1.0
|
O23
|
B:HDQ405
|
4.0
|
21.8
|
1.0
|
CB
|
B:ASP251
|
4.2
|
20.4
|
1.0
|
N
|
B:ALA144
|
4.2
|
23.4
|
1.0
|
NE2
|
B:HIS145
|
4.2
|
26.5
|
1.0
|
OG1
|
B:THR265
|
4.3
|
24.8
|
0.5
|
CB
|
B:ASP253
|
4.3
|
21.3
|
1.0
|
C5
|
B:HDQ405
|
4.3
|
24.9
|
1.0
|
C4
|
B:HDQ405
|
4.3
|
19.6
|
1.0
|
CD2
|
B:HIS145
|
4.4
|
25.1
|
1.0
|
OD1
|
B:ASP147
|
4.4
|
22.9
|
1.0
|
CA
|
B:HIS145
|
4.5
|
23.8
|
1.0
|
CB
|
B:ASP143
|
4.5
|
19.7
|
1.0
|
CB
|
B:ALA144
|
4.7
|
25.7
|
1.0
|
O
|
B:HOH538
|
4.7
|
30.3
|
1.0
|
OD2
|
B:ASP147
|
4.7
|
25.8
|
1.0
|
C
|
B:ALA144
|
4.8
|
31.7
|
1.0
|
CA
|
B:ALA144
|
4.8
|
24.3
|
1.0
|
CA
|
B:ASP143
|
4.9
|
18.4
|
1.0
|
C
|
B:ASP143
|
5.0
|
23.1
|
1.0
|
|
Manganese binding site 5 out
of 6 in 6q39
Go back to
Manganese Binding Sites List in 6q39
Manganese binding site 5 out
of 6 in the Complex of Arginase 2 with Example 49
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Complex of Arginase 2 with Example 49 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn401
b:27.6
occ:1.00
|
OD2
|
C:ASP253
|
2.2
|
26.1
|
1.0
|
OD2
|
C:ASP251
|
2.2
|
24.1
|
1.0
|
OD1
|
C:ASP143
|
2.2
|
24.6
|
1.0
|
O7
|
C:HDQ405
|
2.3
|
23.9
|
1.0
|
ND1
|
C:HIS145
|
2.3
|
22.7
|
1.0
|
OD1
|
C:ASP253
|
2.6
|
22.6
|
1.0
|
CG
|
C:ASP253
|
2.7
|
30.1
|
1.0
|
O8
|
C:HDQ405
|
2.8
|
28.0
|
1.0
|
CG
|
C:ASP251
|
3.2
|
25.1
|
1.0
|
CE1
|
C:HIS145
|
3.2
|
28.8
|
1.0
|
B6
|
C:HDQ405
|
3.2
|
32.3
|
1.0
|
CG
|
C:ASP143
|
3.2
|
21.3
|
1.0
|
CG
|
C:HIS145
|
3.4
|
29.5
|
1.0
|
MN
|
C:MN402
|
3.4
|
26.0
|
1.0
|
OD2
|
C:ASP143
|
3.5
|
24.8
|
1.0
|
CB
|
C:HIS145
|
3.7
|
27.1
|
1.0
|
OD1
|
C:ASP251
|
3.8
|
24.1
|
1.0
|
O23
|
C:HDQ405
|
4.0
|
25.8
|
1.0
|
N
|
C:HIS145
|
4.0
|
22.4
|
1.0
|
CB
|
C:ASP251
|
4.1
|
19.8
|
1.0
|
CB
|
C:ASP253
|
4.2
|
23.9
|
1.0
|
N
|
C:ALA144
|
4.3
|
22.1
|
1.0
|
C4
|
C:HDQ405
|
4.3
|
20.4
|
1.0
|
C5
|
C:HDQ405
|
4.3
|
28.2
|
1.0
|
NE2
|
C:HIS145
|
4.3
|
24.7
|
1.0
|
OG1
|
C:THR265
|
4.3
|
28.6
|
0.5
|
OD2
|
C:ASP147
|
4.4
|
26.1
|
1.0
|
CD2
|
C:HIS145
|
4.4
|
26.1
|
1.0
|
CA
|
C:HIS145
|
4.5
|
24.1
|
1.0
|
CB
|
C:ASP143
|
4.6
|
23.3
|
1.0
|
CB
|
C:ALA144
|
4.7
|
21.1
|
1.0
|
C
|
C:ALA144
|
4.8
|
23.3
|
1.0
|
O
|
C:HOH559
|
4.8
|
28.1
|
1.0
|
CA
|
C:ALA144
|
4.8
|
22.8
|
1.0
|
CA
|
C:ASP143
|
4.9
|
23.8
|
1.0
|
|
Manganese binding site 6 out
of 6 in 6q39
Go back to
Manganese Binding Sites List in 6q39
Manganese binding site 6 out
of 6 in the Complex of Arginase 2 with Example 49
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Complex of Arginase 2 with Example 49 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn402
b:26.0
occ:1.00
|
OD1
|
C:ASP147
|
2.1
|
29.8
|
1.0
|
OD2
|
C:ASP143
|
2.2
|
24.8
|
1.0
|
O23
|
C:HDQ405
|
2.2
|
25.8
|
1.0
|
ND1
|
C:HIS120
|
2.3
|
24.4
|
1.0
|
O7
|
C:HDQ405
|
2.3
|
23.9
|
1.0
|
OD2
|
C:ASP251
|
2.4
|
24.1
|
1.0
|
B6
|
C:HDQ405
|
2.9
|
32.3
|
1.0
|
CG
|
C:ASP147
|
3.0
|
24.7
|
1.0
|
OD2
|
C:ASP147
|
3.1
|
26.1
|
1.0
|
CG
|
C:HIS120
|
3.2
|
27.4
|
1.0
|
CG
|
C:ASP143
|
3.2
|
21.3
|
1.0
|
CE1
|
C:HIS120
|
3.2
|
34.3
|
1.0
|
CG
|
C:ASP251
|
3.4
|
25.1
|
1.0
|
MN
|
C:MN401
|
3.4
|
27.6
|
1.0
|
CB
|
C:HIS120
|
3.4
|
23.9
|
1.0
|
OD1
|
C:ASP143
|
3.5
|
24.6
|
1.0
|
CB
|
C:ASP251
|
3.7
|
19.8
|
1.0
|
O8
|
C:HDQ405
|
3.7
|
28.0
|
1.0
|
C5
|
C:HDQ405
|
4.1
|
28.2
|
1.0
|
NE1
|
C:TRP141
|
4.3
|
25.6
|
1.0
|
CD2
|
C:HIS120
|
4.3
|
26.1
|
1.0
|
NE2
|
C:HIS120
|
4.3
|
36.0
|
1.0
|
CB
|
C:ASP147
|
4.4
|
25.8
|
1.0
|
O
|
C:HIS160
|
4.4
|
26.0
|
1.0
|
OD1
|
C:ASP251
|
4.5
|
24.1
|
1.0
|
CB
|
C:ASP143
|
4.6
|
23.3
|
1.0
|
CZ2
|
C:TRP141
|
4.6
|
21.3
|
1.0
|
CE2
|
C:TRP141
|
4.8
|
30.0
|
1.0
|
CG
|
C:GLU296
|
4.9
|
29.1
|
1.0
|
OE2
|
C:GLU296
|
4.9
|
28.7
|
1.0
|
CA
|
C:HIS120
|
4.9
|
25.3
|
1.0
|
|
Reference:
M.C.Van Zandt,
G.E.Jagdmann,
D.L.Whitehouse,
M.Ji,
J.Savoy,
O.Potapova,
A.Cousido-Siah,
A.Mitschler,
E.I.Howard,
A.M.Pyle,
A.D.Podjarny.
Discovery Ofn-Substituted 3-Amino-4-(3-Boronopropyl)Pyrrolidine-3-Carboxylic Acids As Highly Potent Third-Generation Inhibitors of Human Arginase I and II. J.Med.Chem. V. 62 8164 2019.
ISSN: ISSN 0022-2623
PubMed: 31408339
DOI: 10.1021/ACS.JMEDCHEM.9B00931
Page generated: Sun Oct 6 05:53:11 2024
|