Manganese in PDB 6dkt: Crystal Structure of Arginase From Bacillus Subtilis
Enzymatic activity of Crystal Structure of Arginase From Bacillus Subtilis
All present enzymatic activity of Crystal Structure of Arginase From Bacillus Subtilis:
3.5.3.1;
Protein crystallography data
The structure of Crystal Structure of Arginase From Bacillus Subtilis, PDB code: 6dkt
was solved by
M.C.Lewis,
S.A.Hollingsworth,
J.K.Holden,
T.L.Poulos,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.70 /
2.08
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
77.140,
128.550,
82.020,
90.00,
112.69,
90.00
|
|
R / Rfree (%)
|
20.4 /
23.1
|
Manganese Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Manganese atom in the Crystal Structure of Arginase From Bacillus Subtilis
(pdb code 6dkt). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the
Crystal Structure of Arginase From Bacillus Subtilis, PDB code: 6dkt:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Manganese binding site 1 out
of 12 in 6dkt
Go back to
Manganese Binding Sites List in 6dkt
Manganese binding site 1 out
of 12 in the Crystal Structure of Arginase From Bacillus Subtilis
 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 Arginase From Bacillus Subtilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn500
b:24.2
occ:1.00
|
OD2
|
A:ASP120
|
2.1
|
22.3
|
1.0
|
|
OD2
|
A:ASP124
|
2.1
|
29.0
|
1.0
|
|
ND1
|
A:HIS97
|
2.2
|
33.3
|
1.0
|
|
OD2
|
A:ASP223
|
2.3
|
21.0
|
1.0
|
|
O
|
A:HOH659
|
2.4
|
43.2
|
1.0
|
|
O
|
A:HOH643
|
2.6
|
30.8
|
1.0
|
|
CE1
|
A:HIS97
|
3.1
|
31.3
|
1.0
|
|
CG
|
A:ASP120
|
3.1
|
21.9
|
1.0
|
|
HB2
|
A:HIS97
|
3.1
|
36.0
|
1.0
|
|
CG
|
A:HIS97
|
3.2
|
30.0
|
1.0
|
|
MN
|
A:MN501
|
3.2
|
22.5
|
1.0
|
|
CG
|
A:ASP124
|
3.2
|
29.9
|
1.0
|
|
HB2
|
A:ASP223
|
3.2
|
26.9
|
1.0
|
|
HE1
|
A:HIS97
|
3.2
|
37.6
|
1.0
|
|
HZ3
|
A:TRP118
|
3.2
|
50.0
|
1.0
|
|
CG
|
A:ASP223
|
3.3
|
22.4
|
1.0
|
|
OD1
|
A:ASP120
|
3.5
|
22.3
|
1.0
|
|
CB
|
A:HIS97
|
3.5
|
30.0
|
1.0
|
|
OD1
|
A:ASP124
|
3.5
|
37.2
|
1.0
|
|
HH2
|
A:TRP118
|
3.6
|
52.4
|
1.0
|
|
HB3
|
A:HIS97
|
3.6
|
36.0
|
1.0
|
|
CB
|
A:ASP223
|
3.7
|
22.4
|
1.0
|
|
CZ3
|
A:TRP118
|
3.7
|
41.7
|
1.0
|
|
HB2
|
A:HIS122
|
3.9
|
28.5
|
1.0
|
|
CH2
|
A:TRP118
|
4.0
|
43.7
|
1.0
|
|
HB3
|
A:ASP223
|
4.1
|
26.9
|
1.0
|
|
HG3
|
A:GLU268
|
4.2
|
24.8
|
1.0
|
|
NE2
|
A:HIS97
|
4.2
|
28.4
|
1.0
|
|
CD2
|
A:HIS97
|
4.2
|
29.1
|
1.0
|
|
O
|
A:HIS137
|
4.4
|
31.4
|
1.0
|
|
OD1
|
A:ASP223
|
4.4
|
25.9
|
1.0
|
|
CB
|
A:ASP120
|
4.5
|
22.1
|
1.0
|
|
O
|
A:HOH622
|
4.5
|
57.2
|
1.0
|
|
HB2
|
A:ASP120
|
4.5
|
26.5
|
1.0
|
|
CB
|
A:ASP124
|
4.5
|
29.6
|
1.0
|
|
HB2
|
A:ASP124
|
4.5
|
35.5
|
1.0
|
|
HG21
|
A:VAL267
|
4.8
|
25.1
|
1.0
|
|
CE3
|
A:TRP118
|
4.8
|
33.5
|
1.0
|
|
OD2
|
A:ASP225
|
4.8
|
21.1
|
1.0
|
|
ND1
|
A:HIS122
|
4.8
|
22.3
|
1.0
|
|
CB
|
A:HIS122
|
4.8
|
23.7
|
1.0
|
|
HB3
|
A:ASP124
|
4.9
|
35.5
|
1.0
|
|
H
|
A:HIS122
|
4.9
|
27.3
|
1.0
|
|
HB3
|
A:ASP120
|
4.9
|
26.5
|
1.0
|
|
OD1
|
A:ASP225
|
4.9
|
20.7
|
1.0
|
|
HE2
|
A:HIS97
|
4.9
|
34.1
|
1.0
|
|
CG
|
A:GLU268
|
4.9
|
20.6
|
1.0
|
|
HG2
|
A:GLU268
|
4.9
|
24.8
|
1.0
|
|
HG23
|
A:VAL267
|
5.0
|
25.1
|
1.0
|
|
OE2
|
A:GLU268
|
5.0
|
22.4
|
1.0
|
|
Manganese binding site 2 out
of 12 in 6dkt
Go back to
Manganese Binding Sites List in 6dkt
Manganese binding site 2 out
of 12 in the Crystal Structure of Arginase From Bacillus Subtilis
 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 Arginase From Bacillus Subtilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn501
b:22.5
occ:1.00
|
OD2
|
A:ASP225
|
2.1
|
21.1
|
1.0
|
|
OD1
|
A:ASP120
|
2.2
|
22.3
|
1.0
|
|
OD2
|
A:ASP223
|
2.2
|
21.0
|
1.0
|
|
OD1
|
A:ASP225
|
2.2
|
20.7
|
1.0
|
|
ND1
|
A:HIS122
|
2.3
|
22.3
|
1.0
|
|
CG
|
A:ASP225
|
2.5
|
22.3
|
1.0
|
|
O
|
A:HOH643
|
2.7
|
30.8
|
1.0
|
|
CG
|
A:ASP223
|
3.0
|
22.4
|
1.0
|
|
CG
|
A:ASP120
|
3.1
|
21.9
|
1.0
|
|
CE1
|
A:HIS122
|
3.1
|
22.3
|
1.0
|
|
HE1
|
A:HIS122
|
3.1
|
26.8
|
1.0
|
|
MN
|
A:MN500
|
3.2
|
24.2
|
1.0
|
|
HB2
|
A:HIS122
|
3.2
|
28.5
|
1.0
|
|
OD2
|
A:ASP120
|
3.3
|
22.3
|
1.0
|
|
H
|
A:HIS122
|
3.3
|
27.3
|
1.0
|
|
CG
|
A:HIS122
|
3.3
|
23.7
|
1.0
|
|
O
|
A:HOH622
|
3.5
|
57.2
|
1.0
|
|
OD1
|
A:ASP223
|
3.5
|
25.9
|
1.0
|
|
H
|
A:ALA121
|
3.6
|
31.4
|
1.0
|
|
HB3
|
A:ASP223
|
3.7
|
26.9
|
1.0
|
|
CB
|
A:HIS122
|
3.8
|
23.7
|
1.0
|
|
CB
|
A:ASP223
|
3.9
|
22.4
|
1.0
|
|
HB3
|
A:ALA121
|
3.9
|
29.9
|
1.0
|
|
N
|
A:HIS122
|
3.9
|
22.7
|
1.0
|
|
HG1
|
A:THR237
|
3.9
|
42.0
|
1.0
|
|
O
|
A:HOH659
|
4.0
|
43.2
|
1.0
|
|
CB
|
A:ASP225
|
4.1
|
19.5
|
1.0
|
|
HB2
|
A:ASP223
|
4.1
|
26.9
|
1.0
|
|
N
|
A:ALA121
|
4.2
|
26.2
|
1.0
|
|
NE2
|
A:HIS122
|
4.2
|
29.6
|
1.0
|
|
OG1
|
A:THR237
|
4.3
|
35.0
|
1.0
|
|
CD2
|
A:HIS122
|
4.4
|
27.8
|
1.0
|
|
HB3
|
A:ASP225
|
4.4
|
23.4
|
1.0
|
|
HA
|
A:ASP120
|
4.4
|
25.9
|
1.0
|
|
HB2
|
A:ASP225
|
4.4
|
23.4
|
1.0
|
|
CB
|
A:ASP120
|
4.5
|
22.1
|
1.0
|
|
CA
|
A:HIS122
|
4.5
|
24.6
|
1.0
|
|
HG3
|
A:GLU268
|
4.5
|
24.8
|
1.0
|
|
HB3
|
A:HIS122
|
4.6
|
28.5
|
1.0
|
|
H
|
A:ASP225
|
4.7
|
25.4
|
1.0
|
|
OD2
|
A:ASP124
|
4.7
|
29.0
|
1.0
|
|
C
|
A:ALA121
|
4.7
|
25.2
|
1.0
|
|
CB
|
A:ALA121
|
4.7
|
24.9
|
1.0
|
|
O
|
A:HOH624
|
4.7
|
32.4
|
1.0
|
|
CA
|
A:ALA121
|
4.8
|
25.8
|
1.0
|
|
CA
|
A:ASP120
|
4.8
|
21.6
|
1.0
|
|
OD1
|
A:ASP124
|
4.8
|
37.2
|
1.0
|
|
HB3
|
A:ASP120
|
4.9
|
26.5
|
1.0
|
|
CA
|
A:ASP225
|
5.0
|
20.0
|
1.0
|
|
C
|
A:ASP120
|
5.0
|
26.3
|
1.0
|
|
C
|
A:ASP225
|
5.0
|
22.5
|
1.0
|
|
HE2
|
A:HIS122
|
5.0
|
35.5
|
1.0
|
|
Manganese binding site 3 out
of 12 in 6dkt
Go back to
Manganese Binding Sites List in 6dkt
Manganese binding site 3 out
of 12 in the Crystal Structure of Arginase From Bacillus Subtilis
 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 Arginase From Bacillus Subtilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn500
b:28.2
occ:1.00
|
OD2
|
B:ASP120
|
2.1
|
21.5
|
1.0
|
|
OD2
|
B:ASP124
|
2.2
|
39.1
|
1.0
|
|
ND1
|
B:HIS97
|
2.2
|
30.7
|
1.0
|
|
OD2
|
B:ASP223
|
2.2
|
18.3
|
1.0
|
|
HH2
|
B:TRP118
|
3.1
|
47.5
|
1.0
|
|
HB2
|
B:HIS97
|
3.1
|
31.1
|
1.0
|
|
HB2
|
B:ASP223
|
3.1
|
22.9
|
1.0
|
|
CE1
|
B:HIS97
|
3.2
|
29.0
|
1.0
|
|
CG
|
B:HIS97
|
3.2
|
25.9
|
1.0
|
|
CG
|
B:ASP120
|
3.2
|
23.1
|
1.0
|
|
MN
|
B:MN501
|
3.2
|
24.1
|
1.0
|
|
CG
|
B:ASP223
|
3.2
|
20.7
|
1.0
|
|
CG
|
B:ASP124
|
3.3
|
35.6
|
1.0
|
|
HE1
|
B:HIS97
|
3.3
|
34.9
|
1.0
|
|
O
|
B:HOH680
|
3.4
|
54.4
|
1.0
|
|
CB
|
B:HIS97
|
3.5
|
25.9
|
1.0
|
|
OD1
|
B:ASP120
|
3.6
|
21.9
|
1.0
|
|
HB3
|
B:HIS97
|
3.6
|
31.1
|
1.0
|
|
HZ3
|
B:TRP118
|
3.6
|
42.0
|
1.0
|
|
CB
|
B:ASP223
|
3.6
|
19.1
|
1.0
|
|
CH2
|
B:TRP118
|
3.6
|
39.6
|
1.0
|
|
OD1
|
B:ASP124
|
3.8
|
36.5
|
1.0
|
|
CZ3
|
B:TRP118
|
3.9
|
35.0
|
1.0
|
|
HB3
|
B:ASP223
|
3.9
|
22.9
|
1.0
|
|
HB2
|
B:HIS122
|
4.0
|
29.7
|
1.0
|
|
HG3
|
B:GLU268
|
4.1
|
29.6
|
1.0
|
|
NE2
|
B:HIS97
|
4.2
|
29.0
|
1.0
|
|
CD2
|
B:HIS97
|
4.3
|
28.6
|
1.0
|
|
OD1
|
B:ASP223
|
4.3
|
23.2
|
1.0
|
|
O
|
B:HIS137
|
4.4
|
33.3
|
1.0
|
|
CB
|
B:ASP120
|
4.5
|
21.2
|
1.0
|
|
HB2
|
B:ASP120
|
4.5
|
25.4
|
1.0
|
|
HB2
|
B:ASP124
|
4.5
|
43.1
|
1.0
|
|
CB
|
B:ASP124
|
4.5
|
35.9
|
1.0
|
|
CZ2
|
B:TRP118
|
4.7
|
38.7
|
1.0
|
|
OD2
|
B:ASP225
|
4.7
|
28.4
|
1.0
|
|
HG21
|
B:VAL267
|
4.7
|
22.1
|
1.0
|
|
OE2
|
B:GLU268
|
4.8
|
22.5
|
1.0
|
|
HG2
|
B:GLU268
|
4.8
|
29.6
|
1.0
|
|
HG23
|
B:VAL267
|
4.8
|
22.1
|
1.0
|
|
HB3
|
B:ASP124
|
4.8
|
43.1
|
1.0
|
|
CG
|
B:GLU268
|
4.8
|
24.6
|
1.0
|
|
ND1
|
B:HIS122
|
4.9
|
25.6
|
1.0
|
|
HZ2
|
B:TRP118
|
4.9
|
46.4
|
1.0
|
|
HB3
|
B:ASP120
|
4.9
|
25.4
|
1.0
|
|
CB
|
B:HIS122
|
4.9
|
24.8
|
1.0
|
|
OD1
|
B:ASP225
|
5.0
|
22.4
|
1.0
|
|
CA
|
B:HIS97
|
5.0
|
26.3
|
1.0
|
|
CA
|
B:ASP223
|
5.0
|
17.1
|
1.0
|
|
Manganese binding site 4 out
of 12 in 6dkt
Go back to
Manganese Binding Sites List in 6dkt
Manganese binding site 4 out
of 12 in the Crystal Structure of Arginase From Bacillus Subtilis
 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 Arginase From Bacillus Subtilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn501
b:24.1
occ:1.00
|
OD2
|
B:ASP225
|
2.1
|
28.4
|
1.0
|
|
OD1
|
B:ASP120
|
2.1
|
21.9
|
1.0
|
|
OD2
|
B:ASP223
|
2.2
|
18.3
|
1.0
|
|
ND1
|
B:HIS122
|
2.2
|
25.6
|
1.0
|
|
OD1
|
B:ASP225
|
2.2
|
22.4
|
1.0
|
|
CG
|
B:ASP225
|
2.5
|
25.1
|
1.0
|
|
CE1
|
B:HIS122
|
3.0
|
28.8
|
1.0
|
|
CG
|
B:ASP223
|
3.0
|
20.7
|
1.0
|
|
CG
|
B:ASP120
|
3.0
|
23.1
|
1.0
|
|
HE1
|
B:HIS122
|
3.1
|
34.5
|
1.0
|
|
O
|
B:HOH680
|
3.1
|
54.4
|
1.0
|
|
HB2
|
B:HIS122
|
3.2
|
29.7
|
1.0
|
|
MN
|
B:MN500
|
3.2
|
28.2
|
1.0
|
|
OD2
|
B:ASP120
|
3.2
|
21.5
|
1.0
|
|
CG
|
B:HIS122
|
3.3
|
29.1
|
1.0
|
|
H
|
B:HIS122
|
3.4
|
33.0
|
1.0
|
|
OD1
|
B:ASP223
|
3.6
|
23.2
|
1.0
|
|
H
|
B:ALA121
|
3.7
|
34.5
|
1.0
|
|
CB
|
B:HIS122
|
3.7
|
24.8
|
1.0
|
|
HB3
|
B:ASP223
|
3.7
|
22.9
|
1.0
|
|
HB3
|
B:ALA121
|
3.9
|
31.9
|
1.0
|
|
CB
|
B:ASP223
|
3.9
|
19.1
|
1.0
|
|
HG1
|
B:THR237
|
3.9
|
43.9
|
1.0
|
|
N
|
B:HIS122
|
3.9
|
27.5
|
1.0
|
|
CB
|
B:ASP225
|
4.0
|
23.8
|
1.0
|
|
NE2
|
B:HIS122
|
4.1
|
25.7
|
1.0
|
|
HB2
|
B:ASP223
|
4.2
|
22.9
|
1.0
|
|
N
|
B:ALA121
|
4.2
|
28.7
|
1.0
|
|
OG1
|
B:THR237
|
4.3
|
36.6
|
1.0
|
|
CD2
|
B:HIS122
|
4.3
|
28.8
|
1.0
|
|
O
|
B:HOH617
|
4.4
|
31.6
|
1.0
|
|
HB2
|
B:ASP225
|
4.4
|
28.5
|
1.0
|
|
HB3
|
B:ASP225
|
4.4
|
28.5
|
1.0
|
|
CB
|
B:ASP120
|
4.4
|
21.2
|
1.0
|
|
HA
|
B:ASP120
|
4.4
|
26.7
|
1.0
|
|
CA
|
B:HIS122
|
4.5
|
24.2
|
1.0
|
|
HG3
|
B:GLU268
|
4.5
|
29.6
|
1.0
|
|
HB3
|
B:HIS122
|
4.5
|
29.7
|
1.0
|
|
OD2
|
B:ASP124
|
4.6
|
39.1
|
1.0
|
|
H
|
B:ASP225
|
4.6
|
18.8
|
1.0
|
|
CB
|
B:ALA121
|
4.7
|
26.6
|
1.0
|
|
C
|
B:ALA121
|
4.7
|
26.6
|
1.0
|
|
OD1
|
B:ASP124
|
4.8
|
36.5
|
1.0
|
|
CA
|
B:ALA121
|
4.8
|
27.0
|
1.0
|
|
CA
|
B:ASP120
|
4.8
|
22.2
|
1.0
|
|
HB3
|
B:ASP120
|
4.9
|
25.4
|
1.0
|
|
HE2
|
B:HIS122
|
4.9
|
30.8
|
1.0
|
|
CA
|
B:ASP225
|
4.9
|
19.8
|
1.0
|
|
C
|
B:ASP120
|
4.9
|
24.6
|
1.0
|
|
C
|
B:ASP225
|
5.0
|
23.3
|
1.0
|
|
HZ3
|
B:TRP118
|
5.0
|
42.0
|
1.0
|
|
HB2
|
B:ASP120
|
5.0
|
25.4
|
1.0
|
|
Manganese binding site 5 out
of 12 in 6dkt
Go back to
Manganese Binding Sites List in 6dkt
Manganese binding site 5 out
of 12 in the Crystal Structure of Arginase From Bacillus Subtilis
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Crystal Structure of Arginase From Bacillus Subtilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn500
b:28.2
occ:1.00
|
ND1
|
C:HIS97
|
2.1
|
28.2
|
1.0
|
|
OD2
|
C:ASP120
|
2.1
|
28.9
|
1.0
|
|
OD2
|
C:ASP124
|
2.2
|
38.0
|
1.0
|
|
OD2
|
C:ASP223
|
2.2
|
31.2
|
1.0
|
|
CE1
|
C:HIS97
|
3.0
|
31.2
|
1.0
|
|
HE1
|
C:HIS97
|
3.1
|
37.5
|
1.0
|
|
HB2
|
C:ASP223
|
3.1
|
32.7
|
1.0
|
|
CG
|
C:ASP124
|
3.1
|
41.2
|
1.0
|
|
HB2
|
C:HIS97
|
3.1
|
36.0
|
1.0
|
|
CG
|
C:ASP120
|
3.1
|
28.9
|
1.0
|
|
CG
|
C:HIS97
|
3.1
|
29.8
|
1.0
|
|
MN
|
C:MN501
|
3.2
|
33.6
|
1.0
|
|
CG
|
C:ASP223
|
3.2
|
28.6
|
1.0
|
|
OD1
|
C:ASP124
|
3.4
|
46.0
|
1.0
|
|
OD1
|
C:ASP120
|
3.5
|
33.6
|
1.0
|
|
CB
|
C:HIS97
|
3.5
|
30.0
|
1.0
|
|
CB
|
C:ASP223
|
3.6
|
27.2
|
1.0
|
|
HB3
|
C:HIS97
|
3.7
|
36.0
|
1.0
|
|
HE1
|
C:TRP118
|
3.9
|
44.0
|
1.0
|
|
HB2
|
C:HIS122
|
3.9
|
34.2
|
1.0
|
|
HB3
|
C:ASP223
|
3.9
|
32.7
|
1.0
|
|
HG3
|
C:GLU268
|
4.0
|
35.4
|
1.0
|
|
NE2
|
C:HIS97
|
4.1
|
30.9
|
1.0
|
|
CD2
|
C:HIS97
|
4.2
|
28.1
|
1.0
|
|
OD1
|
C:ASP223
|
4.3
|
24.2
|
1.0
|
|
HZ2
|
C:TRP118
|
4.3
|
46.5
|
1.0
|
|
HB2
|
C:ASP120
|
4.4
|
29.8
|
1.0
|
|
CB
|
C:ASP120
|
4.4
|
24.8
|
1.0
|
|
NE1
|
C:TRP118
|
4.5
|
36.7
|
1.0
|
|
CB
|
C:ASP124
|
4.5
|
40.7
|
1.0
|
|
O
|
C:HIS137
|
4.5
|
37.6
|
1.0
|
|
OD2
|
C:ASP225
|
4.6
|
35.8
|
1.0
|
|
HB2
|
C:ASP124
|
4.6
|
48.8
|
1.0
|
|
HG21
|
C:VAL267
|
4.7
|
35.9
|
1.0
|
|
HG2
|
C:GLU268
|
4.7
|
35.4
|
1.0
|
|
CG
|
C:GLU268
|
4.8
|
29.5
|
1.0
|
|
ND1
|
C:HIS122
|
4.8
|
28.8
|
1.0
|
|
CB
|
C:HIS122
|
4.8
|
28.5
|
1.0
|
|
HG23
|
C:VAL267
|
4.9
|
35.9
|
1.0
|
|
HB3
|
C:ASP124
|
4.9
|
48.8
|
1.0
|
|
H
|
C:HIS122
|
4.9
|
35.7
|
1.0
|
|
HB3
|
C:ASP120
|
4.9
|
29.8
|
1.0
|
|
HE2
|
C:HIS97
|
4.9
|
37.1
|
1.0
|
|
OE2
|
C:GLU268
|
4.9
|
31.4
|
1.0
|
|
OD1
|
C:ASP225
|
4.9
|
23.7
|
1.0
|
|
CZ2
|
C:TRP118
|
4.9
|
38.8
|
1.0
|
|
Manganese binding site 6 out
of 12 in 6dkt
Go back to
Manganese Binding Sites List in 6dkt
Manganese binding site 6 out
of 12 in the Crystal Structure of Arginase From Bacillus Subtilis
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Crystal Structure of Arginase From Bacillus Subtilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn501
b:33.6
occ:1.00
|
OD2
|
C:ASP225
|
2.2
|
35.8
|
1.0
|
|
OD1
|
C:ASP120
|
2.2
|
33.6
|
1.0
|
|
OD2
|
C:ASP223
|
2.2
|
31.2
|
1.0
|
|
OD1
|
C:ASP225
|
2.2
|
23.7
|
1.0
|
|
ND1
|
C:HIS122
|
2.3
|
28.8
|
1.0
|
|
CG
|
C:ASP225
|
2.5
|
26.1
|
1.0
|
|
CG
|
C:ASP223
|
3.0
|
28.6
|
1.0
|
|
CG
|
C:ASP120
|
3.0
|
28.9
|
1.0
|
|
CE1
|
C:HIS122
|
3.1
|
30.8
|
1.0
|
|
HE1
|
C:HIS122
|
3.2
|
37.0
|
1.0
|
|
MN
|
C:MN500
|
3.2
|
28.2
|
1.0
|
|
HB2
|
C:HIS122
|
3.2
|
34.2
|
1.0
|
|
OD2
|
C:ASP120
|
3.3
|
28.9
|
1.0
|
|
H
|
C:HIS122
|
3.3
|
35.7
|
1.0
|
|
CG
|
C:HIS122
|
3.4
|
29.4
|
1.0
|
|
OD1
|
C:ASP223
|
3.6
|
24.2
|
1.0
|
|
H
|
C:ALA121
|
3.7
|
31.5
|
1.0
|
|
HB3
|
C:ASP223
|
3.7
|
32.7
|
1.0
|
|
CB
|
C:HIS122
|
3.8
|
28.5
|
1.0
|
|
CB
|
C:ASP223
|
3.9
|
27.2
|
1.0
|
|
HB3
|
C:ALA121
|
3.9
|
31.1
|
1.0
|
|
N
|
C:HIS122
|
3.9
|
29.7
|
1.0
|
|
HG1
|
C:THR237
|
4.0
|
45.3
|
1.0
|
|
CB
|
C:ASP225
|
4.0
|
23.1
|
1.0
|
|
HB2
|
C:ASP223
|
4.2
|
32.7
|
1.0
|
|
N
|
C:ALA121
|
4.2
|
26.2
|
1.0
|
|
NE2
|
C:HIS122
|
4.3
|
32.6
|
1.0
|
|
HB2
|
C:ASP225
|
4.3
|
27.7
|
1.0
|
|
HG3
|
C:GLU268
|
4.4
|
35.4
|
1.0
|
|
OG1
|
C:THR237
|
4.4
|
37.8
|
1.0
|
|
HB3
|
C:ASP225
|
4.4
|
27.7
|
1.0
|
|
HA
|
C:ASP120
|
4.4
|
30.2
|
1.0
|
|
CD2
|
C:HIS122
|
4.4
|
30.7
|
1.0
|
|
CB
|
C:ASP120
|
4.4
|
24.8
|
1.0
|
|
CA
|
C:HIS122
|
4.5
|
29.1
|
1.0
|
|
HB3
|
C:HIS122
|
4.6
|
34.2
|
1.0
|
|
H
|
C:ASP225
|
4.6
|
31.1
|
1.0
|
|
CB
|
C:ALA121
|
4.7
|
25.9
|
1.0
|
|
C
|
C:ALA121
|
4.7
|
27.7
|
1.0
|
|
CA
|
C:ALA121
|
4.8
|
24.8
|
1.0
|
|
OD2
|
C:ASP124
|
4.8
|
38.0
|
1.0
|
|
CA
|
C:ASP120
|
4.8
|
25.1
|
1.0
|
|
OD1
|
C:ASP124
|
4.9
|
46.0
|
1.0
|
|
CA
|
C:ASP225
|
4.9
|
27.1
|
1.0
|
|
C
|
C:ASP120
|
4.9
|
25.8
|
1.0
|
|
HB3
|
C:ASP120
|
4.9
|
29.8
|
1.0
|
|
HB2
|
C:ASP120
|
5.0
|
29.8
|
1.0
|
|
C
|
C:ASP225
|
5.0
|
27.5
|
1.0
|
|
Manganese binding site 7 out
of 12 in 6dkt
Go back to
Manganese Binding Sites List in 6dkt
Manganese binding site 7 out
of 12 in the Crystal Structure of Arginase From Bacillus Subtilis
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Crystal Structure of Arginase From Bacillus Subtilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn500
b:24.1
occ:1.00
|
OD2
|
D:ASP120
|
2.1
|
27.7
|
1.0
|
|
OD2
|
D:ASP124
|
2.1
|
24.5
|
1.0
|
|
OD2
|
D:ASP223
|
2.2
|
19.4
|
1.0
|
|
ND1
|
D:HIS97
|
2.2
|
24.2
|
1.0
|
|
O
|
D:HOH688
|
2.7
|
53.6
|
1.0
|
|
CE1
|
D:HIS97
|
3.1
|
26.5
|
1.0
|
|
HZ3
|
D:TRP118
|
3.1
|
45.1
|
1.0
|
|
CG
|
D:ASP120
|
3.1
|
24.2
|
1.0
|
|
HB2
|
D:ASP223
|
3.1
|
25.1
|
1.0
|
|
HB2
|
D:HIS97
|
3.2
|
31.0
|
1.0
|
|
CG
|
D:HIS97
|
3.2
|
22.2
|
1.0
|
|
MN
|
D:MN501
|
3.2
|
24.4
|
1.0
|
|
HE1
|
D:HIS97
|
3.2
|
31.8
|
1.0
|
|
CG
|
D:ASP223
|
3.2
|
22.0
|
1.0
|
|
CG
|
D:ASP124
|
3.3
|
33.1
|
1.0
|
|
HH2
|
D:TRP118
|
3.3
|
51.0
|
1.0
|
|
OD1
|
D:ASP120
|
3.4
|
22.7
|
1.0
|
|
CB
|
D:HIS97
|
3.6
|
25.9
|
1.0
|
|
CZ3
|
D:TRP118
|
3.6
|
37.6
|
1.0
|
|
CB
|
D:ASP223
|
3.6
|
20.9
|
1.0
|
|
HB3
|
D:HIS97
|
3.7
|
31.0
|
1.0
|
|
CH2
|
D:TRP118
|
3.7
|
42.5
|
1.0
|
|
OD1
|
D:ASP124
|
3.8
|
41.6
|
1.0
|
|
HB2
|
D:HIS122
|
3.9
|
28.3
|
1.0
|
|
HB3
|
D:ASP223
|
3.9
|
25.1
|
1.0
|
|
NE2
|
D:HIS97
|
4.2
|
29.5
|
1.0
|
|
HG3
|
D:GLU268
|
4.2
|
34.1
|
1.0
|
|
CD2
|
D:HIS97
|
4.2
|
22.8
|
1.0
|
|
OD1
|
D:ASP223
|
4.3
|
20.5
|
1.0
|
|
CB
|
D:ASP120
|
4.4
|
24.1
|
1.0
|
|
O
|
D:HIS137
|
4.4
|
33.5
|
1.0
|
|
HB2
|
D:ASP120
|
4.5
|
28.9
|
1.0
|
|
HB2
|
D:ASP124
|
4.5
|
42.2
|
1.0
|
|
CB
|
D:ASP124
|
4.5
|
35.1
|
1.0
|
|
CE3
|
D:TRP118
|
4.7
|
33.7
|
1.0
|
|
OD2
|
D:ASP225
|
4.8
|
28.0
|
1.0
|
|
ND1
|
D:HIS122
|
4.8
|
26.3
|
1.0
|
|
HG21
|
D:VAL267
|
4.8
|
24.2
|
1.0
|
|
CB
|
D:HIS122
|
4.8
|
23.6
|
1.0
|
|
HB3
|
D:ASP120
|
4.8
|
28.9
|
1.0
|
|
H
|
D:HIS122
|
4.8
|
27.4
|
1.0
|
|
HB3
|
D:ASP124
|
4.8
|
42.2
|
1.0
|
|
CZ2
|
D:TRP118
|
4.9
|
39.7
|
1.0
|
|
OD1
|
D:ASP225
|
4.9
|
25.6
|
1.0
|
|
HE2
|
D:HIS97
|
4.9
|
35.4
|
1.0
|
|
HG2
|
D:GLU268
|
4.9
|
34.1
|
1.0
|
|
CG
|
D:GLU268
|
4.9
|
28.4
|
1.0
|
|
HG23
|
D:VAL267
|
4.9
|
24.2
|
1.0
|
|
HE3
|
D:TRP118
|
5.0
|
40.4
|
1.0
|
|
Manganese binding site 8 out
of 12 in 6dkt
Go back to
Manganese Binding Sites List in 6dkt
Manganese binding site 8 out
of 12 in the Crystal Structure of Arginase From Bacillus Subtilis
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Crystal Structure of Arginase From Bacillus Subtilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn501
b:24.4
occ:1.00
|
OD2
|
D:ASP225
|
2.1
|
28.0
|
1.0
|
|
OD1
|
D:ASP120
|
2.1
|
22.7
|
1.0
|
|
OD2
|
D:ASP223
|
2.2
|
19.4
|
1.0
|
|
ND1
|
D:HIS122
|
2.2
|
26.3
|
1.0
|
|
OD1
|
D:ASP225
|
2.2
|
25.6
|
1.0
|
|
CG
|
D:ASP225
|
2.5
|
25.0
|
1.0
|
|
CE1
|
D:HIS122
|
3.0
|
26.2
|
1.0
|
|
CG
|
D:ASP223
|
3.0
|
22.0
|
1.0
|
|
HE1
|
D:HIS122
|
3.0
|
31.5
|
1.0
|
|
CG
|
D:ASP120
|
3.1
|
24.2
|
1.0
|
|
MN
|
D:MN500
|
3.2
|
24.1
|
1.0
|
|
HB2
|
D:HIS122
|
3.3
|
28.3
|
1.0
|
|
O
|
D:HOH688
|
3.3
|
53.6
|
1.0
|
|
CG
|
D:HIS122
|
3.3
|
23.4
|
1.0
|
|
OD2
|
D:ASP120
|
3.3
|
27.7
|
1.0
|
|
H
|
D:HIS122
|
3.3
|
27.4
|
1.0
|
|
OD1
|
D:ASP223
|
3.6
|
20.5
|
1.0
|
|
H
|
D:ALA121
|
3.6
|
29.4
|
1.0
|
|
HB3
|
D:ASP223
|
3.8
|
25.1
|
1.0
|
|
CB
|
D:HIS122
|
3.8
|
23.6
|
1.0
|
|
HB3
|
D:ALA121
|
3.8
|
32.4
|
1.0
|
|
N
|
D:HIS122
|
3.9
|
22.8
|
1.0
|
|
CB
|
D:ASP223
|
3.9
|
20.9
|
1.0
|
|
HG1
|
D:THR237
|
4.0
|
48.2
|
1.0
|
|
CB
|
D:ASP225
|
4.0
|
21.2
|
1.0
|
|
NE2
|
D:HIS122
|
4.2
|
24.6
|
1.0
|
|
N
|
D:ALA121
|
4.2
|
24.5
|
1.0
|
|
HB2
|
D:ASP223
|
4.2
|
25.1
|
1.0
|
|
CD2
|
D:HIS122
|
4.3
|
23.3
|
1.0
|
|
HB2
|
D:ASP225
|
4.4
|
25.4
|
1.0
|
|
OG1
|
D:THR237
|
4.4
|
40.2
|
1.0
|
|
HB3
|
D:ASP225
|
4.4
|
25.4
|
1.0
|
|
HA
|
D:ASP120
|
4.4
|
23.8
|
1.0
|
|
CB
|
D:ASP120
|
4.4
|
24.1
|
1.0
|
|
CA
|
D:HIS122
|
4.5
|
25.1
|
1.0
|
|
OD2
|
D:ASP124
|
4.5
|
24.5
|
1.0
|
|
HG3
|
D:GLU268
|
4.5
|
34.1
|
1.0
|
|
HB3
|
D:HIS122
|
4.6
|
28.3
|
1.0
|
|
H
|
D:ASP225
|
4.6
|
25.6
|
1.0
|
|
CB
|
D:ALA121
|
4.7
|
27.0
|
1.0
|
|
C
|
D:ALA121
|
4.7
|
28.8
|
1.0
|
|
CA
|
D:ALA121
|
4.7
|
30.8
|
1.0
|
|
O
|
D:HOH650
|
4.7
|
37.6
|
1.0
|
|
CA
|
D:ASP120
|
4.8
|
19.8
|
1.0
|
|
HB3
|
D:ASP120
|
4.9
|
28.9
|
1.0
|
|
HE2
|
D:HIS122
|
4.9
|
29.5
|
1.0
|
|
OD1
|
D:ASP124
|
4.9
|
41.6
|
1.0
|
|
C
|
D:ASP120
|
5.0
|
21.0
|
1.0
|
|
CA
|
D:ASP225
|
5.0
|
20.9
|
1.0
|
|
Manganese binding site 9 out
of 12 in 6dkt
Go back to
Manganese Binding Sites List in 6dkt
Manganese binding site 9 out
of 12 in the Crystal Structure of Arginase From Bacillus Subtilis
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 9 of Crystal Structure of Arginase From Bacillus Subtilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn500
b:23.0
occ:1.00
|
OD2
|
E:ASP120
|
2.1
|
21.4
|
1.0
|
|
OD2
|
E:ASP124
|
2.2
|
44.6
|
1.0
|
|
ND1
|
E:HIS97
|
2.2
|
28.2
|
1.0
|
|
OD2
|
E:ASP223
|
2.2
|
20.7
|
1.0
|
|
O
|
E:HOH633
|
2.4
|
35.2
|
1.0
|
|
HH2
|
E:TRP118
|
3.1
|
53.3
|
1.0
|
|
CE1
|
E:HIS97
|
3.1
|
26.0
|
1.0
|
|
CG
|
E:ASP120
|
3.1
|
23.9
|
1.0
|
|
HB2
|
E:HIS97
|
3.2
|
28.3
|
1.0
|
|
HZ3
|
E:TRP118
|
3.2
|
48.2
|
1.0
|
|
MN
|
E:MN501
|
3.2
|
22.5
|
1.0
|
|
CG
|
E:HIS97
|
3.2
|
24.6
|
1.0
|
|
HB2
|
E:ASP223
|
3.3
|
28.2
|
1.0
|
|
HE1
|
E:HIS97
|
3.3
|
31.2
|
1.0
|
|
CG
|
E:ASP223
|
3.3
|
24.2
|
1.0
|
|
CG
|
E:ASP124
|
3.4
|
47.0
|
1.0
|
|
OD1
|
E:ASP120
|
3.5
|
20.7
|
1.0
|
|
CH2
|
E:TRP118
|
3.5
|
44.4
|
1.0
|
|
CB
|
E:HIS97
|
3.6
|
23.6
|
1.0
|
|
CZ3
|
E:TRP118
|
3.6
|
40.1
|
1.0
|
|
HB3
|
E:HIS97
|
3.6
|
28.3
|
1.0
|
|
CB
|
E:ASP223
|
3.8
|
23.5
|
1.0
|
|
HB2
|
E:HIS122
|
3.8
|
33.0
|
1.0
|
|
OD1
|
E:ASP124
|
4.0
|
54.3
|
1.0
|
|
HB3
|
E:ASP223
|
4.1
|
28.2
|
1.0
|
|
NE2
|
E:HIS97
|
4.2
|
22.5
|
1.0
|
|
HG3
|
E:GLU268
|
4.3
|
25.3
|
1.0
|
|
CD2
|
E:HIS97
|
4.3
|
24.9
|
1.0
|
|
HB2
|
E:ASP124
|
4.3
|
50.6
|
1.0
|
|
OD1
|
E:ASP223
|
4.4
|
26.4
|
1.0
|
|
CB
|
E:ASP120
|
4.4
|
23.8
|
1.0
|
|
HB2
|
E:ASP120
|
4.5
|
28.6
|
1.0
|
|
CB
|
E:ASP124
|
4.5
|
42.1
|
1.0
|
|
CZ2
|
E:TRP118
|
4.6
|
41.5
|
1.0
|
|
CE3
|
E:TRP118
|
4.7
|
31.9
|
1.0
|
|
ND1
|
E:HIS122
|
4.8
|
26.2
|
1.0
|
|
CB
|
E:HIS122
|
4.8
|
27.5
|
1.0
|
|
OD2
|
E:ASP225
|
4.8
|
23.9
|
1.0
|
|
HB3
|
E:ASP120
|
4.8
|
28.6
|
1.0
|
|
H
|
E:HIS122
|
4.9
|
26.5
|
1.0
|
|
HG21
|
E:VAL267
|
4.9
|
25.5
|
1.0
|
|
HZ2
|
E:TRP118
|
4.9
|
49.8
|
1.0
|
|
HB3
|
E:ASP124
|
5.0
|
50.6
|
1.0
|
|
HE2
|
E:HIS97
|
5.0
|
27.1
|
1.0
|
|
Manganese binding site 10 out
of 12 in 6dkt
Go back to
Manganese Binding Sites List in 6dkt
Manganese binding site 10 out
of 12 in the Crystal Structure of Arginase From Bacillus Subtilis
 Mono view
 Stereo pair view
|
|
A full contact list of Manganese with other atoms in the Mn binding
site number 10 of Crystal Structure of Arginase From Bacillus Subtilis within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn501
b:22.5
occ:1.00
|
OD1
|
E:ASP120
|
2.1
|
20.7
|
1.0
|
|
OD2
|
E:ASP225
|
2.2
|
23.9
|
1.0
|
|
OD2
|
E:ASP223
|
2.2
|
20.7
|
1.0
|
|
OD1
|
E:ASP225
|
2.2
|
19.7
|
1.0
|
|
ND1
|
E:HIS122
|
2.2
|
26.2
|
1.0
|
|
CG
|
E:ASP225
|
2.5
|
19.8
|
1.0
|
|
O
|
E:HOH633
|
2.6
|
35.2
|
1.0
|
|
CG
|
E:ASP223
|
2.9
|
24.2
|
1.0
|
|
CG
|
E:ASP120
|
3.0
|
23.9
|
1.0
|
|
CE1
|
E:HIS122
|
3.1
|
25.0
|
1.0
|
|
HE1
|
E:HIS122
|
3.1
|
30.0
|
1.0
|
|
MN
|
E:MN500
|
3.2
|
23.0
|
1.0
|
|
HB2
|
E:HIS122
|
3.3
|
33.0
|
1.0
|
|
OD2
|
E:ASP120
|
3.3
|
21.4
|
1.0
|
|
CG
|
E:HIS122
|
3.4
|
28.6
|
1.0
|
|
H
|
E:HIS122
|
3.4
|
26.5
|
1.0
|
|
OD1
|
E:ASP223
|
3.5
|
26.4
|
1.0
|
|
H
|
E:ALA121
|
3.6
|
26.8
|
1.0
|
|
HB3
|
E:ASP223
|
3.7
|
28.2
|
1.0
|
|
CB
|
E:HIS122
|
3.8
|
27.5
|
1.0
|
|
CB
|
E:ASP223
|
3.9
|
23.5
|
1.0
|
|
HB3
|
E:ALA121
|
3.9
|
25.8
|
1.0
|
|
N
|
E:HIS122
|
4.0
|
22.1
|
1.0
|
|
HG1
|
E:THR237
|
4.0
|
52.3
|
1.0
|
|
CB
|
E:ASP225
|
4.1
|
19.3
|
1.0
|
|
HB2
|
E:ASP223
|
4.1
|
28.2
|
1.0
|
|
N
|
E:ALA121
|
4.2
|
22.3
|
1.0
|
|
NE2
|
E:HIS122
|
4.2
|
24.9
|
1.0
|
|
HA
|
E:ASP120
|
4.4
|
24.9
|
1.0
|
|
CD2
|
E:HIS122
|
4.4
|
30.6
|
1.0
|
|
CB
|
E:ASP120
|
4.4
|
23.8
|
1.0
|
|
HB2
|
E:ASP225
|
4.4
|
23.2
|
1.0
|
|
HB3
|
E:ASP225
|
4.4
|
23.2
|
1.0
|
|
OG1
|
E:THR237
|
4.5
|
43.6
|
1.0
|
|
HG3
|
E:GLU268
|
4.5
|
25.3
|
1.0
|
|
CA
|
E:HIS122
|
4.5
|
27.6
|
1.0
|
|
HB3
|
E:HIS122
|
4.6
|
33.0
|
1.0
|
|
H
|
E:ASP225
|
4.6
|
25.7
|
1.0
|
|
OD2
|
E:ASP124
|
4.6
|
44.6
|
1.0
|
|
CB
|
E:ALA121
|
4.7
|
21.5
|
1.0
|
|
O
|
E:HOH639
|
4.7
|
29.8
|
1.0
|
|
C
|
E:ALA121
|
4.8
|
21.7
|
1.0
|
|
CA
|
E:ASP120
|
4.8
|
20.7
|
1.0
|
|
CA
|
E:ALA121
|
4.8
|
20.3
|
1.0
|
|
HB3
|
E:ASP120
|
4.9
|
28.6
|
1.0
|
|
C
|
E:ASP120
|
4.9
|
25.1
|
1.0
|
|
HE2
|
E:HIS122
|
5.0
|
29.8
|
1.0
|
|
CA
|
E:ASP225
|
5.0
|
18.9
|
1.0
|
|
Reference:
M.C.Lewis,
S.A.Hollingsworth,
J.K.Holden,
T.L.Poulos.
Structure of Arginase From Bacillus Subtilis at 2.08 Angstroms Resolution To Be Published.
Page generated: Tue Dec 15 04:51:48 2020
|
