Manganese in PDB 6q92: Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh
Enzymatic activity of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh
All present enzymatic activity of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh:
3.5.3.1;
Protein crystallography data
The structure of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh, PDB code: 6q92
was solved by
Y.Grobben,
J.C.M.Uitdehaag,
G.J.R.Zaman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.14 /
1.50
|
Space group
|
P 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.380,
90.380,
69.254,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
13.5 /
14.7
|
Other elements in 6q92:
The structure of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh
(pdb code 6q92). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh, PDB code: 6q92:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 6q92
Go back to
Manganese Binding Sites List in 6q92
Manganese binding site 1 out
of 4 in the Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn401
b:7.8
occ:1.00
|
OD2
|
A:ASP128
|
2.1
|
8.7
|
1.0
|
OD2
|
A:ASP232
|
2.2
|
7.2
|
1.0
|
O2
|
A:ABH403
|
2.2
|
11.0
|
1.0
|
OD2
|
A:ASP124
|
2.2
|
7.3
|
1.0
|
ND1
|
A:HIS101
|
2.2
|
7.6
|
1.0
|
O1
|
A:ABH403
|
2.3
|
9.7
|
1.0
|
B
|
A:ABH403
|
2.8
|
9.9
|
1.0
|
CG
|
A:ASP128
|
3.1
|
8.1
|
1.0
|
CG
|
A:ASP124
|
3.2
|
6.5
|
1.0
|
CG
|
A:HIS101
|
3.2
|
8.0
|
1.0
|
CG
|
A:ASP232
|
3.2
|
7.3
|
1.0
|
CE1
|
A:HIS101
|
3.3
|
8.1
|
1.0
|
OD1
|
A:ASP128
|
3.3
|
8.6
|
1.0
|
CB
|
A:HIS101
|
3.4
|
8.1
|
1.0
|
MN
|
A:MN402
|
3.4
|
6.2
|
1.0
|
OD1
|
A:ASP124
|
3.5
|
6.7
|
1.0
|
CB
|
A:ASP232
|
3.6
|
7.3
|
1.0
|
O3
|
A:ABH403
|
3.7
|
9.4
|
1.0
|
CE
|
A:ABH403
|
4.1
|
10.2
|
1.0
|
NA
|
A:NA404
|
4.2
|
12.2
|
1.0
|
CD2
|
A:HIS101
|
4.3
|
8.0
|
1.0
|
NE2
|
A:HIS101
|
4.3
|
8.0
|
1.0
|
OD1
|
A:ASP232
|
4.4
|
7.4
|
1.0
|
NE1
|
A:TRP122
|
4.4
|
6.8
|
1.0
|
O
|
A:HIS141
|
4.4
|
8.3
|
1.0
|
CB
|
A:ASP128
|
4.5
|
7.8
|
1.0
|
CB
|
A:ASP124
|
4.5
|
6.3
|
1.0
|
OD2
|
A:ASP234
|
4.6
|
8.7
|
1.0
|
CZ2
|
A:TRP122
|
4.6
|
6.8
|
1.0
|
CE2
|
A:TRP122
|
4.9
|
6.9
|
1.0
|
CG
|
A:GLU277
|
4.9
|
9.9
|
1.0
|
CA
|
A:HIS101
|
4.9
|
7.9
|
1.0
|
CA
|
A:ASP232
|
5.0
|
7.4
|
1.0
|
OE2
|
A:GLU277
|
5.0
|
11.0
|
1.0
|
|
Manganese binding site 2 out
of 4 in 6q92
Go back to
Manganese Binding Sites List in 6q92
Manganese binding site 2 out
of 4 in the Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn402
b:6.2
occ:1.00
|
O1
|
A:ABH403
|
1.9
|
9.7
|
1.0
|
OD1
|
A:ASP124
|
2.0
|
6.7
|
1.0
|
ND1
|
A:HIS126
|
2.0
|
8.2
|
1.0
|
OD2
|
A:ASP234
|
2.0
|
8.7
|
1.0
|
CG
|
A:ASP234
|
2.8
|
7.7
|
1.0
|
OD1
|
A:ASP234
|
2.8
|
7.4
|
1.0
|
CE1
|
A:HIS126
|
2.9
|
7.6
|
1.0
|
OD2
|
A:ASP232
|
3.0
|
7.2
|
1.0
|
CG
|
A:ASP124
|
3.0
|
6.5
|
1.0
|
CG
|
A:HIS126
|
3.0
|
7.6
|
1.0
|
B
|
A:ABH403
|
3.1
|
9.9
|
1.0
|
O3
|
A:ABH403
|
3.1
|
9.4
|
1.0
|
NA
|
A:NA404
|
3.4
|
12.2
|
1.0
|
CB
|
A:HIS126
|
3.4
|
7.4
|
1.0
|
MN
|
A:MN401
|
3.4
|
7.8
|
1.0
|
OD2
|
A:ASP124
|
3.4
|
7.3
|
1.0
|
CG
|
A:ASP232
|
3.7
|
7.3
|
1.0
|
N
|
A:HIS126
|
3.8
|
6.8
|
1.0
|
O2
|
A:ABH403
|
4.0
|
11.0
|
1.0
|
OG1
|
A:THR246
|
4.0
|
11.5
|
1.0
|
NE2
|
A:HIS126
|
4.1
|
8.0
|
1.0
|
CE
|
A:ABH403
|
4.1
|
10.2
|
1.0
|
OD1
|
A:ASP128
|
4.1
|
8.6
|
1.0
|
N
|
A:ALA125
|
4.1
|
6.3
|
1.0
|
CD2
|
A:HIS126
|
4.1
|
7.8
|
1.0
|
OD1
|
A:ASP232
|
4.2
|
7.4
|
1.0
|
CD
|
A:ABH403
|
4.2
|
10.3
|
1.0
|
CA
|
A:HIS126
|
4.2
|
7.1
|
1.0
|
CB
|
A:ASP234
|
4.2
|
7.6
|
1.0
|
CB
|
A:ASP124
|
4.4
|
6.3
|
1.0
|
CB
|
A:ASP232
|
4.5
|
7.3
|
1.0
|
CB
|
A:ALA125
|
4.5
|
6.6
|
1.0
|
C
|
A:ALA125
|
4.6
|
6.5
|
1.0
|
CA
|
A:ALA125
|
4.6
|
6.5
|
1.0
|
OD2
|
A:ASP128
|
4.7
|
8.7
|
1.0
|
CA
|
A:ASP124
|
4.8
|
6.4
|
1.0
|
CG
|
A:ASP128
|
4.8
|
8.1
|
1.0
|
O
|
A:HIS126
|
4.8
|
7.5
|
1.0
|
C
|
A:ASP124
|
4.9
|
6.3
|
1.0
|
C
|
A:HIS126
|
5.0
|
7.0
|
1.0
|
O
|
A:THR246
|
5.0
|
10.2
|
1.0
|
|
Manganese binding site 3 out
of 4 in 6q92
Go back to
Manganese Binding Sites List in 6q92
Manganese binding site 3 out
of 4 in the Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn401
b:9.6
occ:1.00
|
OD2
|
B:ASP124
|
2.1
|
7.4
|
1.0
|
OD2
|
B:ASP128
|
2.1
|
9.2
|
1.0
|
OD2
|
B:ASP232
|
2.2
|
8.7
|
1.0
|
ND1
|
B:HIS101
|
2.2
|
10.3
|
1.0
|
O1
|
B:ABH403
|
2.3
|
13.3
|
1.0
|
O2
|
B:ABH403
|
2.3
|
13.4
|
1.0
|
B
|
B:ABH403
|
2.8
|
12.3
|
1.0
|
CG
|
B:ASP124
|
3.1
|
7.3
|
1.0
|
CG
|
B:ASP128
|
3.1
|
8.9
|
1.0
|
CE1
|
B:HIS101
|
3.2
|
10.3
|
1.0
|
CG
|
B:HIS101
|
3.2
|
10.6
|
1.0
|
CG
|
B:ASP232
|
3.3
|
9.0
|
1.0
|
MN
|
B:MN402
|
3.4
|
7.8
|
1.0
|
OD1
|
B:ASP128
|
3.4
|
9.7
|
1.0
|
OD1
|
B:ASP124
|
3.5
|
7.7
|
1.0
|
CB
|
B:HIS101
|
3.5
|
11.0
|
1.0
|
CB
|
B:ASP232
|
3.6
|
9.2
|
1.0
|
O3
|
B:ABH403
|
3.7
|
11.8
|
1.0
|
CE
|
B:ABH403
|
4.0
|
12.9
|
1.0
|
NA
|
B:NA404
|
4.1
|
14.1
|
1.0
|
NE2
|
B:HIS101
|
4.3
|
10.1
|
1.0
|
CD2
|
B:HIS101
|
4.3
|
10.6
|
1.0
|
NE1
|
B:TRP122
|
4.3
|
9.3
|
1.0
|
OD1
|
B:ASP232
|
4.4
|
8.8
|
1.0
|
O
|
B:HIS141
|
4.4
|
11.6
|
1.0
|
CB
|
B:ASP124
|
4.5
|
7.7
|
1.0
|
CB
|
B:ASP128
|
4.5
|
8.9
|
1.0
|
CZ2
|
B:TRP122
|
4.6
|
9.5
|
1.0
|
OD2
|
B:ASP234
|
4.6
|
10.4
|
1.0
|
CE2
|
B:TRP122
|
4.8
|
9.2
|
1.0
|
CG
|
B:GLU277
|
4.9
|
13.0
|
1.0
|
CA
|
B:ASP232
|
5.0
|
9.4
|
1.0
|
OE2
|
B:GLU277
|
5.0
|
14.1
|
1.0
|
|
Manganese binding site 4 out
of 4 in 6q92
Go back to
Manganese Binding Sites List in 6q92
Manganese binding site 4 out
of 4 in the Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of Human Arginase-1 at pH 7.0 in Complex with Abh within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn402
b:7.8
occ:1.00
|
O1
|
B:ABH403
|
1.9
|
13.3
|
1.0
|
OD2
|
B:ASP234
|
2.0
|
10.4
|
1.0
|
OD1
|
B:ASP124
|
2.0
|
7.7
|
1.0
|
ND1
|
B:HIS126
|
2.0
|
9.2
|
1.0
|
CG
|
B:ASP234
|
2.7
|
9.2
|
1.0
|
OD1
|
B:ASP234
|
2.8
|
10.1
|
1.0
|
CE1
|
B:HIS126
|
2.9
|
9.0
|
1.0
|
CG
|
B:ASP124
|
3.0
|
7.3
|
1.0
|
OD2
|
B:ASP232
|
3.0
|
8.7
|
1.0
|
B
|
B:ABH403
|
3.0
|
12.3
|
1.0
|
CG
|
B:HIS126
|
3.1
|
9.1
|
1.0
|
O3
|
B:ABH403
|
3.1
|
11.8
|
1.0
|
NA
|
B:NA404
|
3.3
|
14.1
|
1.0
|
OD2
|
B:ASP124
|
3.4
|
7.4
|
1.0
|
CB
|
B:HIS126
|
3.4
|
8.8
|
1.0
|
MN
|
B:MN401
|
3.4
|
9.6
|
1.0
|
CG
|
B:ASP232
|
3.7
|
9.0
|
1.0
|
N
|
B:HIS126
|
3.9
|
8.1
|
1.0
|
O2
|
B:ABH403
|
4.0
|
13.4
|
1.0
|
CE
|
B:ABH403
|
4.0
|
12.9
|
1.0
|
OG1
|
B:THR246
|
4.1
|
13.3
|
1.0
|
NE2
|
B:HIS126
|
4.1
|
9.5
|
1.0
|
CD
|
B:ABH403
|
4.1
|
13.2
|
1.0
|
N
|
B:ALA125
|
4.1
|
7.6
|
1.0
|
CD2
|
B:HIS126
|
4.2
|
9.8
|
1.0
|
OD1
|
B:ASP232
|
4.2
|
8.8
|
1.0
|
OD1
|
B:ASP128
|
4.2
|
9.7
|
1.0
|
CB
|
B:ASP234
|
4.2
|
9.2
|
1.0
|
CA
|
B:HIS126
|
4.3
|
8.6
|
1.0
|
CB
|
B:ASP124
|
4.4
|
7.7
|
1.0
|
CB
|
B:ASP232
|
4.5
|
9.2
|
1.0
|
CB
|
B:ALA125
|
4.6
|
7.5
|
1.0
|
OD2
|
B:ASP128
|
4.6
|
9.2
|
1.0
|
C
|
B:ALA125
|
4.7
|
7.6
|
1.0
|
CA
|
B:ALA125
|
4.7
|
7.6
|
1.0
|
CA
|
B:ASP124
|
4.8
|
7.7
|
1.0
|
CG
|
B:ASP128
|
4.8
|
8.9
|
1.0
|
C
|
B:ASP124
|
4.9
|
7.6
|
1.0
|
O
|
B:THR246
|
4.9
|
12.8
|
1.0
|
O
|
B:HIS126
|
4.9
|
9.0
|
1.0
|
|
Reference:
Y.Grobben,
J.C.M.Uitdehaag,
G.J.R.Zaman.
Structural Insights Into Human Arginase-1 pH Dependence and Its Inhibition By the Small Molecule Inhibitor Cb-1158 J.Struct.Biol. 2019.
ISSN: ESSN 1095-8657
DOI: 10.1016/J.YJSBX.2019.100014
Page generated: Sun Oct 6 05:54:44 2024
|