Magnesium in PDB 6nfp: 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
Enzymatic activity of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
All present enzymatic activity of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168:
3.5.3.1;
Protein crystallography data
The structure of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168, PDB code: 6nfp
was solved by
G.Minasov,
Z.Wawrzak,
E.Evdokimova,
S.Grimshaw,
K.Kwon,
A.Savchenko,
K.J.F.Satchell,
A.Joachimiak,
Center For Structural Genomics Ofinfectious Diseases (Csgid),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.99 /
1.70
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.414,
143.989,
85.515,
90.00,
109.35,
90.00
|
R / Rfree (%)
|
13.9 /
16.6
|
Other elements in 6nfp:
The structure of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Magnesium atom in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
(pdb code 6nfp). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the
1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168, PDB code: 6nfp:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 12 in 6nfp
Go back to
Magnesium Binding Sites List in 6nfp
Magnesium binding site 1 out
of 12 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg306
b:30.8
occ:0.50
|
O1
|
A:SO4318
|
2.1
|
48.3
|
1.0
|
OD2
|
A:ASP225
|
2.1
|
29.0
|
1.0
|
OD1
|
A:ASP120
|
2.1
|
25.8
|
1.0
|
ND1
|
A:HIS122
|
2.3
|
28.7
|
1.0
|
OD2
|
A:ASP223
|
2.6
|
28.4
|
1.0
|
CG
|
A:ASP225
|
2.8
|
22.7
|
1.0
|
OD1
|
A:ASP225
|
2.8
|
23.4
|
1.0
|
MG
|
A:MG307
|
2.9
|
34.2
|
0.5
|
CG
|
A:ASP120
|
3.1
|
26.3
|
1.0
|
S
|
A:SO4318
|
3.1
|
92.1
|
1.0
|
CG
|
A:HIS122
|
3.2
|
26.8
|
1.0
|
O3
|
A:SO4318
|
3.2
|
80.9
|
1.0
|
CE1
|
A:HIS122
|
3.3
|
29.1
|
1.0
|
OD2
|
A:ASP120
|
3.4
|
30.7
|
1.0
|
CB
|
A:HIS122
|
3.4
|
27.0
|
1.0
|
CG
|
A:ASP223
|
3.4
|
24.6
|
1.0
|
N
|
A:HIS122
|
3.8
|
23.3
|
1.0
|
OD1
|
A:ASP223
|
3.9
|
24.8
|
1.0
|
O2
|
A:SO4318
|
3.9
|
73.5
|
1.0
|
CA
|
A:HIS122
|
4.2
|
25.2
|
1.0
|
O4
|
A:SO4318
|
4.2
|
66.7
|
1.0
|
CB
|
A:ASP225
|
4.2
|
20.8
|
1.0
|
N
|
A:ALA121
|
4.3
|
22.1
|
1.0
|
CD2
|
A:HIS122
|
4.3
|
28.9
|
1.0
|
NE2
|
A:HIS122
|
4.4
|
28.6
|
1.0
|
CB
|
A:ASP223
|
4.4
|
24.0
|
1.0
|
O
|
A:HOH468
|
4.4
|
25.0
|
1.0
|
OD2
|
A:ASP124
|
4.4
|
34.0
|
1.0
|
CB
|
A:ASP120
|
4.5
|
22.8
|
1.0
|
CB
|
A:ALA121
|
4.7
|
22.2
|
1.0
|
OD1
|
A:ASP124
|
4.7
|
28.4
|
1.0
|
C
|
A:ALA121
|
4.7
|
23.1
|
1.0
|
CA
|
A:ALA121
|
4.8
|
21.8
|
1.0
|
O
|
A:HIS122
|
4.9
|
25.5
|
1.0
|
ND1
|
A:HIS97
|
4.9
|
28.4
|
1.0
|
CA
|
A:ASP120
|
4.9
|
22.1
|
1.0
|
CG
|
A:ASP124
|
5.0
|
28.7
|
1.0
|
C
|
A:ASP120
|
5.0
|
22.2
|
1.0
|
|
Magnesium binding site 2 out
of 12 in 6nfp
Go back to
Magnesium Binding Sites List in 6nfp
Magnesium binding site 2 out
of 12 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg307
b:34.2
occ:0.50
|
O1
|
A:SO4318
|
2.0
|
48.3
|
1.0
|
OD2
|
A:ASP120
|
2.1
|
30.7
|
1.0
|
OD2
|
A:ASP124
|
2.1
|
34.0
|
1.0
|
ND1
|
A:HIS97
|
2.3
|
28.4
|
1.0
|
OD2
|
A:ASP223
|
2.4
|
28.4
|
1.0
|
MG
|
A:MG306
|
2.9
|
30.8
|
0.5
|
CG
|
A:ASP120
|
3.0
|
26.3
|
1.0
|
CG
|
A:HIS97
|
3.2
|
24.7
|
1.0
|
CG
|
A:ASP124
|
3.2
|
28.7
|
1.0
|
OD1
|
A:ASP120
|
3.2
|
25.8
|
1.0
|
CE1
|
A:HIS97
|
3.3
|
26.6
|
1.0
|
S
|
A:SO4318
|
3.3
|
92.1
|
1.0
|
CB
|
A:HIS97
|
3.3
|
24.5
|
1.0
|
OD1
|
A:ASP124
|
3.6
|
28.4
|
1.0
|
CG
|
A:ASP223
|
3.6
|
24.6
|
1.0
|
O4
|
A:SO4318
|
3.7
|
66.7
|
1.0
|
O2
|
A:SO4318
|
4.0
|
73.5
|
1.0
|
CB
|
A:ASP223
|
4.1
|
24.0
|
1.0
|
CD2
|
A:HIS97
|
4.3
|
24.8
|
1.0
|
NE2
|
A:HIS97
|
4.4
|
24.6
|
1.0
|
O3
|
A:SO4318
|
4.4
|
80.9
|
1.0
|
CB
|
A:ASP120
|
4.4
|
22.8
|
1.0
|
CB
|
A:HIS122
|
4.5
|
27.0
|
1.0
|
CB
|
A:ASP124
|
4.5
|
27.1
|
1.0
|
OD2
|
A:ASP225
|
4.6
|
29.0
|
1.0
|
O
|
A:HIS137
|
4.6
|
22.4
|
1.0
|
OD1
|
A:ASP223
|
4.6
|
24.8
|
1.0
|
ND1
|
A:HIS122
|
4.7
|
28.7
|
1.0
|
NE1
|
A:TRP118
|
4.7
|
27.4
|
1.0
|
CZ2
|
A:TRP118
|
4.8
|
25.3
|
1.0
|
O
|
A:HIS122
|
4.8
|
25.5
|
1.0
|
CA
|
A:HIS97
|
4.8
|
22.4
|
1.0
|
CG
|
A:GLU268
|
4.9
|
22.6
|
1.0
|
OD1
|
A:ASP225
|
4.9
|
23.4
|
1.0
|
|
Magnesium binding site 3 out
of 12 in 6nfp
Go back to
Magnesium Binding Sites List in 6nfp
Magnesium binding site 3 out
of 12 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg303
b:30.2
occ:0.50
|
O2
|
B:SO4313
|
2.1
|
37.8
|
0.5
|
OD2
|
B:ASP225
|
2.1
|
32.3
|
1.0
|
OD1
|
B:ASP120
|
2.1
|
26.9
|
1.0
|
ND1
|
B:HIS122
|
2.3
|
34.3
|
1.0
|
OD2
|
B:ASP223
|
2.7
|
30.2
|
1.0
|
CG
|
B:ASP225
|
2.8
|
27.2
|
1.0
|
OD1
|
B:ASP225
|
2.9
|
26.7
|
1.0
|
MG
|
B:MG304
|
2.9
|
32.1
|
0.5
|
CG
|
B:ASP120
|
3.1
|
27.3
|
1.0
|
S
|
B:SO4313
|
3.1
|
56.3
|
0.5
|
O3
|
B:SO4313
|
3.1
|
49.3
|
0.5
|
CG
|
B:HIS122
|
3.2
|
30.3
|
1.0
|
CE1
|
B:HIS122
|
3.2
|
32.4
|
1.0
|
OD2
|
B:ASP120
|
3.4
|
30.4
|
1.0
|
CB
|
B:HIS122
|
3.4
|
28.1
|
1.0
|
CG
|
B:ASP223
|
3.5
|
27.1
|
1.0
|
O1
|
B:SO4313
|
3.9
|
45.9
|
0.5
|
N
|
B:HIS122
|
3.9
|
24.2
|
1.0
|
OD1
|
B:ASP223
|
4.0
|
25.6
|
1.0
|
O4
|
B:SO4313
|
4.2
|
44.9
|
0.5
|
CA
|
B:HIS122
|
4.3
|
26.2
|
1.0
|
CB
|
B:ASP225
|
4.3
|
23.8
|
1.0
|
CD2
|
B:HIS122
|
4.3
|
32.3
|
1.0
|
O
|
B:HOH456
|
4.3
|
29.0
|
1.0
|
NE2
|
B:HIS122
|
4.3
|
32.0
|
1.0
|
N
|
B:ALA121
|
4.4
|
22.8
|
1.0
|
CB
|
B:ASP223
|
4.4
|
25.4
|
1.0
|
OD2
|
B:ASP124
|
4.5
|
33.8
|
1.0
|
CB
|
B:ASP120
|
4.5
|
23.7
|
1.0
|
OD1
|
B:ASP124
|
4.6
|
31.1
|
1.0
|
C
|
B:ALA121
|
4.8
|
24.5
|
1.0
|
CB
|
B:ALA121
|
4.8
|
23.3
|
1.0
|
ND1
|
B:HIS97
|
4.9
|
27.1
|
1.0
|
O
|
B:HIS122
|
4.9
|
27.2
|
1.0
|
CG
|
B:ASP124
|
4.9
|
28.9
|
1.0
|
CA
|
B:ALA121
|
5.0
|
22.9
|
1.0
|
CA
|
B:ASP120
|
5.0
|
22.6
|
1.0
|
|
Magnesium binding site 4 out
of 12 in 6nfp
Go back to
Magnesium Binding Sites List in 6nfp
Magnesium binding site 4 out
of 12 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg304
b:32.1
occ:0.50
|
O2
|
B:SO4313
|
2.0
|
37.8
|
0.5
|
OD2
|
B:ASP120
|
2.1
|
30.4
|
1.0
|
OD2
|
B:ASP124
|
2.2
|
33.8
|
1.0
|
ND1
|
B:HIS97
|
2.3
|
27.1
|
1.0
|
OD2
|
B:ASP223
|
2.5
|
30.2
|
1.0
|
MG
|
B:MG303
|
2.9
|
30.2
|
0.5
|
CG
|
B:ASP120
|
3.1
|
27.3
|
1.0
|
CG
|
B:HIS97
|
3.1
|
25.6
|
1.0
|
CG
|
B:ASP124
|
3.2
|
28.9
|
1.0
|
CB
|
B:HIS97
|
3.2
|
24.3
|
1.0
|
OD1
|
B:ASP120
|
3.3
|
26.9
|
1.0
|
S
|
B:SO4313
|
3.3
|
56.3
|
0.5
|
CE1
|
B:HIS97
|
3.3
|
26.1
|
1.0
|
O4
|
B:SO4313
|
3.6
|
44.9
|
0.5
|
OD1
|
B:ASP124
|
3.6
|
31.1
|
1.0
|
CG
|
B:ASP223
|
3.7
|
27.1
|
1.0
|
O1
|
B:SO4313
|
4.1
|
45.9
|
0.5
|
CB
|
B:ASP223
|
4.1
|
25.4
|
1.0
|
CD2
|
B:HIS97
|
4.3
|
23.6
|
1.0
|
O3
|
B:SO4313
|
4.3
|
49.3
|
0.5
|
NE2
|
B:HIS97
|
4.4
|
23.6
|
1.0
|
CB
|
B:ASP120
|
4.4
|
23.7
|
1.0
|
O
|
B:HIS137
|
4.5
|
25.1
|
1.0
|
CB
|
B:ASP124
|
4.5
|
28.4
|
1.0
|
CB
|
B:HIS122
|
4.6
|
28.1
|
1.0
|
NE1
|
B:TRP118
|
4.6
|
25.7
|
1.0
|
CZ2
|
B:TRP118
|
4.6
|
23.8
|
1.0
|
OD2
|
B:ASP225
|
4.7
|
32.3
|
1.0
|
CA
|
B:HIS97
|
4.7
|
24.0
|
1.0
|
OD1
|
B:ASP223
|
4.7
|
25.6
|
1.0
|
ND1
|
B:HIS122
|
4.8
|
34.3
|
1.0
|
O
|
B:HIS122
|
4.9
|
27.2
|
1.0
|
CG
|
B:GLU268
|
4.9
|
24.2
|
1.0
|
CE2
|
B:TRP118
|
4.9
|
24.4
|
1.0
|
OE2
|
B:GLU268
|
5.0
|
27.8
|
1.0
|
|
Magnesium binding site 5 out
of 12 in 6nfp
Go back to
Magnesium Binding Sites List in 6nfp
Magnesium binding site 5 out
of 12 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg304
b:29.2
occ:0.50
|
O4
|
C:SO4318
|
2.1
|
40.3
|
0.5
|
OD2
|
C:ASP225
|
2.1
|
29.7
|
1.0
|
OD1
|
C:ASP120
|
2.1
|
27.0
|
1.0
|
ND1
|
C:HIS122
|
2.3
|
30.5
|
1.0
|
OD2
|
C:ASP223
|
2.6
|
30.7
|
1.0
|
CG
|
C:ASP225
|
2.8
|
25.4
|
1.0
|
MG
|
C:MG305
|
2.8
|
34.0
|
0.5
|
OD1
|
C:ASP225
|
2.8
|
25.6
|
1.0
|
CG
|
C:ASP120
|
3.1
|
26.0
|
1.0
|
S
|
C:SO4318
|
3.2
|
59.9
|
0.5
|
CG
|
C:HIS122
|
3.2
|
28.5
|
1.0
|
CE1
|
C:HIS122
|
3.2
|
30.1
|
1.0
|
O2
|
C:SO4318
|
3.3
|
55.2
|
0.5
|
OD2
|
C:ASP120
|
3.4
|
30.5
|
1.0
|
CG
|
C:ASP223
|
3.4
|
26.2
|
1.0
|
CB
|
C:HIS122
|
3.5
|
27.5
|
1.0
|
N
|
C:HIS122
|
3.9
|
25.0
|
1.0
|
O1
|
C:SO4318
|
3.9
|
52.1
|
0.5
|
OD1
|
C:ASP223
|
4.0
|
28.0
|
1.0
|
O3
|
C:SO4318
|
4.3
|
52.7
|
0.5
|
CA
|
C:HIS122
|
4.3
|
26.8
|
1.0
|
CB
|
C:ASP225
|
4.3
|
23.1
|
1.0
|
N
|
C:ALA121
|
4.3
|
21.9
|
1.0
|
NE2
|
C:HIS122
|
4.3
|
30.5
|
1.0
|
CD2
|
C:HIS122
|
4.3
|
30.0
|
1.0
|
CB
|
C:ASP223
|
4.3
|
25.0
|
1.0
|
O
|
C:HOH482
|
4.4
|
25.6
|
1.0
|
OD2
|
C:ASP124
|
4.5
|
35.8
|
1.0
|
CB
|
C:ASP120
|
4.5
|
23.3
|
1.0
|
OD1
|
C:ASP124
|
4.7
|
33.3
|
1.0
|
CB
|
C:ALA121
|
4.8
|
23.3
|
1.0
|
ND1
|
C:HIS97
|
4.8
|
29.3
|
1.0
|
C
|
C:ALA121
|
4.8
|
23.6
|
1.0
|
O
|
C:HIS122
|
4.9
|
29.2
|
1.0
|
CA
|
C:ALA121
|
4.9
|
22.5
|
1.0
|
CA
|
C:ASP120
|
5.0
|
21.9
|
1.0
|
CG
|
C:ASP124
|
5.0
|
30.4
|
1.0
|
|
Magnesium binding site 6 out
of 12 in 6nfp
Go back to
Magnesium Binding Sites List in 6nfp
Magnesium binding site 6 out
of 12 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg305
b:34.0
occ:0.50
|
O4
|
C:SO4318
|
2.0
|
40.3
|
0.5
|
OD2
|
C:ASP124
|
2.1
|
35.8
|
1.0
|
OD2
|
C:ASP120
|
2.2
|
30.5
|
1.0
|
ND1
|
C:HIS97
|
2.3
|
29.3
|
1.0
|
OD2
|
C:ASP223
|
2.5
|
30.7
|
1.0
|
MG
|
C:MG304
|
2.8
|
29.2
|
0.5
|
CG
|
C:ASP120
|
3.0
|
26.0
|
1.0
|
CG
|
C:HIS97
|
3.1
|
24.3
|
1.0
|
CG
|
C:ASP124
|
3.2
|
30.4
|
1.0
|
OD1
|
C:ASP120
|
3.2
|
27.0
|
1.0
|
CE1
|
C:HIS97
|
3.3
|
26.0
|
1.0
|
S
|
C:SO4318
|
3.3
|
59.9
|
0.5
|
CB
|
C:HIS97
|
3.3
|
22.8
|
1.0
|
O3
|
C:SO4318
|
3.5
|
52.7
|
0.5
|
OD1
|
C:ASP124
|
3.6
|
33.3
|
1.0
|
CG
|
C:ASP223
|
3.7
|
26.2
|
1.0
|
O1
|
C:SO4318
|
4.1
|
52.1
|
0.5
|
CB
|
C:ASP223
|
4.1
|
25.0
|
1.0
|
O2
|
C:SO4318
|
4.3
|
55.2
|
0.5
|
CD2
|
C:HIS97
|
4.3
|
23.4
|
1.0
|
NE2
|
C:HIS97
|
4.4
|
24.6
|
1.0
|
CB
|
C:ASP120
|
4.4
|
23.3
|
1.0
|
CB
|
C:HIS122
|
4.5
|
27.5
|
1.0
|
CB
|
C:ASP124
|
4.5
|
29.5
|
1.0
|
O
|
C:HIS137
|
4.6
|
22.9
|
1.0
|
NE1
|
C:TRP118
|
4.6
|
28.2
|
1.0
|
OD2
|
C:ASP225
|
4.6
|
29.7
|
1.0
|
ND1
|
C:HIS122
|
4.6
|
30.5
|
1.0
|
CZ2
|
C:TRP118
|
4.7
|
28.1
|
1.0
|
OD1
|
C:ASP223
|
4.8
|
28.0
|
1.0
|
O
|
C:HIS122
|
4.8
|
29.2
|
1.0
|
CA
|
C:HIS97
|
4.9
|
21.3
|
1.0
|
CG
|
C:GLU268
|
4.9
|
24.8
|
1.0
|
CG
|
C:HIS122
|
5.0
|
28.5
|
1.0
|
CE2
|
C:TRP118
|
5.0
|
27.0
|
1.0
|
|
Magnesium binding site 7 out
of 12 in 6nfp
Go back to
Magnesium Binding Sites List in 6nfp
Magnesium binding site 7 out
of 12 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg302
b:31.9
occ:0.50
|
O3
|
D:SO4310
|
2.0
|
43.5
|
0.5
|
OD1
|
D:ASP120
|
2.2
|
27.9
|
1.0
|
OD2
|
D:ASP225
|
2.2
|
31.0
|
1.0
|
ND1
|
D:HIS122
|
2.3
|
34.7
|
1.0
|
OD2
|
D:ASP223
|
2.5
|
31.6
|
1.0
|
CG
|
D:ASP225
|
2.8
|
26.4
|
1.0
|
OD1
|
D:ASP225
|
2.8
|
27.1
|
1.0
|
MG
|
D:MG303
|
2.9
|
35.3
|
0.5
|
CG
|
D:ASP120
|
3.1
|
27.3
|
1.0
|
S
|
D:SO4310
|
3.2
|
64.1
|
0.5
|
CE1
|
D:HIS122
|
3.2
|
34.0
|
1.0
|
CG
|
D:HIS122
|
3.2
|
31.9
|
1.0
|
O1
|
D:SO4310
|
3.3
|
57.3
|
0.5
|
OD2
|
D:ASP120
|
3.3
|
31.9
|
1.0
|
CG
|
D:ASP223
|
3.4
|
28.4
|
1.0
|
CB
|
D:HIS122
|
3.5
|
29.9
|
1.0
|
N
|
D:HIS122
|
3.9
|
24.3
|
1.0
|
OD1
|
D:ASP223
|
3.9
|
27.3
|
1.0
|
O4
|
D:SO4310
|
4.0
|
53.2
|
0.5
|
O2
|
D:SO4310
|
4.2
|
50.5
|
0.5
|
O
|
D:HOH426
|
4.3
|
30.7
|
1.0
|
CB
|
D:ASP225
|
4.3
|
22.7
|
1.0
|
CA
|
D:HIS122
|
4.3
|
27.0
|
1.0
|
NE2
|
D:HIS122
|
4.3
|
33.2
|
1.0
|
N
|
D:ALA121
|
4.3
|
23.4
|
1.0
|
CD2
|
D:HIS122
|
4.3
|
34.3
|
1.0
|
CB
|
D:ASP223
|
4.4
|
25.6
|
1.0
|
CB
|
D:ASP120
|
4.5
|
24.4
|
1.0
|
OD2
|
D:ASP124
|
4.5
|
38.4
|
1.0
|
OD1
|
D:ASP124
|
4.7
|
32.3
|
1.0
|
CB
|
D:ALA121
|
4.8
|
22.4
|
1.0
|
ND1
|
D:HIS97
|
4.8
|
30.0
|
1.0
|
C
|
D:ALA121
|
4.8
|
24.6
|
1.0
|
CA
|
D:ALA121
|
4.9
|
22.5
|
1.0
|
O
|
D:HIS122
|
4.9
|
29.8
|
1.0
|
CA
|
D:ASP120
|
4.9
|
23.3
|
1.0
|
CG
|
D:ASP124
|
5.0
|
33.0
|
1.0
|
|
Magnesium binding site 8 out
of 12 in 6nfp
Go back to
Magnesium Binding Sites List in 6nfp
Magnesium binding site 8 out
of 12 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg303
b:35.3
occ:0.50
|
O3
|
D:SO4310
|
2.0
|
43.5
|
0.5
|
OD2
|
D:ASP120
|
2.1
|
31.9
|
1.0
|
OD2
|
D:ASP124
|
2.2
|
38.4
|
1.0
|
ND1
|
D:HIS97
|
2.3
|
30.0
|
1.0
|
OD2
|
D:ASP223
|
2.5
|
31.6
|
1.0
|
MG
|
D:MG302
|
2.9
|
31.9
|
0.5
|
CG
|
D:ASP120
|
3.1
|
27.3
|
1.0
|
CG
|
D:HIS97
|
3.1
|
26.6
|
1.0
|
CG
|
D:ASP124
|
3.2
|
33.0
|
1.0
|
CB
|
D:HIS97
|
3.2
|
26.5
|
1.0
|
S
|
D:SO4310
|
3.2
|
64.1
|
0.5
|
OD1
|
D:ASP120
|
3.3
|
27.9
|
1.0
|
CE1
|
D:HIS97
|
3.3
|
28.8
|
1.0
|
O2
|
D:SO4310
|
3.4
|
50.5
|
0.5
|
OD1
|
D:ASP124
|
3.6
|
32.3
|
1.0
|
CG
|
D:ASP223
|
3.6
|
28.4
|
1.0
|
O4
|
D:SO4310
|
4.0
|
53.2
|
0.5
|
CB
|
D:ASP223
|
4.1
|
25.6
|
1.0
|
CD2
|
D:HIS97
|
4.3
|
25.6
|
1.0
|
O1
|
D:SO4310
|
4.3
|
57.3
|
0.5
|
NE2
|
D:HIS97
|
4.4
|
26.0
|
1.0
|
CB
|
D:ASP120
|
4.5
|
24.4
|
1.0
|
CB
|
D:ASP124
|
4.5
|
30.4
|
1.0
|
CB
|
D:HIS122
|
4.5
|
29.9
|
1.0
|
O
|
D:HIS137
|
4.5
|
27.1
|
1.0
|
NE1
|
D:TRP118
|
4.6
|
28.0
|
1.0
|
CZ2
|
D:TRP118
|
4.7
|
27.8
|
1.0
|
ND1
|
D:HIS122
|
4.7
|
34.7
|
1.0
|
OD2
|
D:ASP225
|
4.7
|
31.0
|
1.0
|
OD1
|
D:ASP223
|
4.7
|
27.3
|
1.0
|
CA
|
D:HIS97
|
4.7
|
25.0
|
1.0
|
CG
|
D:GLU268
|
4.9
|
23.8
|
1.0
|
O
|
D:HIS122
|
4.9
|
29.8
|
1.0
|
CE2
|
D:TRP118
|
5.0
|
26.6
|
1.0
|
|
Magnesium binding site 9 out
of 12 in 6nfp
Go back to
Magnesium Binding Sites List in 6nfp
Magnesium binding site 9 out
of 12 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg303
b:34.5
occ:0.50
|
O1
|
E:SO4312
|
2.1
|
41.2
|
0.5
|
OD2
|
E:ASP225
|
2.1
|
30.5
|
1.0
|
OD1
|
E:ASP120
|
2.2
|
28.1
|
1.0
|
ND1
|
E:HIS122
|
2.3
|
31.6
|
1.0
|
OD2
|
E:ASP223
|
2.7
|
31.4
|
1.0
|
CG
|
E:ASP225
|
2.8
|
27.5
|
1.0
|
MG
|
E:MG304
|
2.8
|
35.1
|
0.5
|
OD1
|
E:ASP225
|
2.9
|
25.8
|
1.0
|
CG
|
E:ASP120
|
3.0
|
26.5
|
1.0
|
CG
|
E:HIS122
|
3.2
|
29.6
|
1.0
|
CE1
|
E:HIS122
|
3.2
|
33.1
|
1.0
|
S
|
E:SO4312
|
3.2
|
57.3
|
0.5
|
OD2
|
E:ASP120
|
3.3
|
30.8
|
1.0
|
O3
|
E:SO4312
|
3.4
|
52.7
|
0.5
|
CB
|
E:HIS122
|
3.4
|
29.1
|
1.0
|
CG
|
E:ASP223
|
3.4
|
26.6
|
1.0
|
N
|
E:HIS122
|
3.9
|
25.3
|
1.0
|
OD1
|
E:ASP223
|
4.0
|
26.1
|
1.0
|
O2
|
E:SO4312
|
4.0
|
51.3
|
0.5
|
CA
|
E:HIS122
|
4.3
|
27.5
|
1.0
|
O4
|
E:SO4312
|
4.3
|
48.8
|
0.5
|
CD2
|
E:HIS122
|
4.3
|
32.9
|
1.0
|
CB
|
E:ASP225
|
4.3
|
24.4
|
1.0
|
NE2
|
E:HIS122
|
4.3
|
34.2
|
1.0
|
CB
|
E:ASP223
|
4.4
|
24.2
|
1.0
|
N
|
E:ALA121
|
4.4
|
22.5
|
1.0
|
O
|
E:HOH481
|
4.4
|
28.0
|
1.0
|
OD2
|
E:ASP124
|
4.4
|
35.4
|
1.0
|
CB
|
E:ASP120
|
4.4
|
25.2
|
1.0
|
OD1
|
E:ASP124
|
4.7
|
30.1
|
1.0
|
ND1
|
E:HIS97
|
4.8
|
29.1
|
1.0
|
C
|
E:ALA121
|
4.8
|
24.8
|
1.0
|
O
|
E:HIS122
|
4.9
|
29.3
|
1.0
|
CB
|
E:ALA121
|
4.9
|
24.5
|
1.0
|
CG
|
E:ASP124
|
5.0
|
31.2
|
1.0
|
CA
|
E:ASP120
|
5.0
|
22.9
|
1.0
|
CA
|
E:ALA121
|
5.0
|
22.6
|
1.0
|
|
Magnesium binding site 10 out
of 12 in 6nfp
Go back to
Magnesium Binding Sites List in 6nfp
Magnesium binding site 10 out
of 12 in the 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of 1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg304
b:35.1
occ:0.50
|
O1
|
E:SO4312
|
2.1
|
41.2
|
0.5
|
OD2
|
E:ASP120
|
2.1
|
30.8
|
1.0
|
OD2
|
E:ASP124
|
2.2
|
35.4
|
1.0
|
ND1
|
E:HIS97
|
2.3
|
29.1
|
1.0
|
OD2
|
E:ASP223
|
2.5
|
31.4
|
1.0
|
MG
|
E:MG303
|
2.8
|
34.5
|
0.5
|
CG
|
E:ASP120
|
3.1
|
26.5
|
1.0
|
CG
|
E:HIS97
|
3.1
|
25.2
|
1.0
|
CG
|
E:ASP124
|
3.2
|
31.2
|
1.0
|
CB
|
E:HIS97
|
3.2
|
24.3
|
1.0
|
S
|
E:SO4312
|
3.3
|
57.3
|
0.5
|
CE1
|
E:HIS97
|
3.3
|
29.2
|
1.0
|
OD1
|
E:ASP120
|
3.3
|
28.1
|
1.0
|
O4
|
E:SO4312
|
3.5
|
48.8
|
0.5
|
OD1
|
E:ASP124
|
3.6
|
30.1
|
1.0
|
CG
|
E:ASP223
|
3.6
|
26.6
|
1.0
|
O2
|
E:SO4312
|
3.9
|
51.3
|
0.5
|
CB
|
E:ASP223
|
4.1
|
24.2
|
1.0
|
CD2
|
E:HIS97
|
4.3
|
24.6
|
1.0
|
O3
|
E:SO4312
|
4.3
|
52.7
|
0.5
|
NE2
|
E:HIS97
|
4.4
|
25.2
|
1.0
|
CB
|
E:ASP120
|
4.4
|
25.2
|
1.0
|
CB
|
E:HIS122
|
4.5
|
29.1
|
1.0
|
CB
|
E:ASP124
|
4.5
|
29.3
|
1.0
|
O
|
E:HIS137
|
4.5
|
27.4
|
1.0
|
NE1
|
E:TRP118
|
4.6
|
24.9
|
1.0
|
OD2
|
E:ASP225
|
4.6
|
30.5
|
1.0
|
ND1
|
E:HIS122
|
4.7
|
31.6
|
1.0
|
CZ2
|
E:TRP118
|
4.7
|
25.7
|
1.0
|
OD1
|
E:ASP223
|
4.7
|
26.1
|
1.0
|
CA
|
E:HIS97
|
4.7
|
24.0
|
1.0
|
CG
|
E:GLU268
|
4.9
|
27.1
|
1.0
|
O
|
E:HIS122
|
4.9
|
29.3
|
1.0
|
CE2
|
E:TRP118
|
5.0
|
24.3
|
1.0
|
CG
|
E:HIS122
|
5.0
|
29.6
|
1.0
|
|
Reference:
G.Minasov,
Z.Wawrzak,
E.Evdokimova,
S.Grimshaw,
K.Kwon,
A.Savchenko,
K.J.F.Satchell,
A.Joachimiak,
Center For Structural Genomics Of Infectious Diseases(Csgid).
1.7 Angstrom Resolution Crystal Structure of Arginase From Bacillus Subtilis Subsp. Subtilis Str. 168 To Be Published.
Page generated: Tue Oct 1 12:40:00 2024
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