Manganese in PDB 2ef5: Crystal Structure of the Arginase From Thermus Thermophilus
Enzymatic activity of Crystal Structure of the Arginase From Thermus Thermophilus
All present enzymatic activity of Crystal Structure of the Arginase From Thermus Thermophilus:
3.5.3.1;
Protein crystallography data
The structure of Crystal Structure of the Arginase From Thermus Thermophilus, PDB code: 2ef5
was solved by
T.S.Kumarevel,
P.Karthe,
S.Kuramitsu,
S.Yokoyama,
Riken Structuralgenomics/Proteomics Initiative (Rsgi),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
19.98 /
2.00
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
150.795,
97.478,
126.463,
90.00,
108.66,
90.00
|
|
R / Rfree (%)
|
23.3 /
23.6
|
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 the Arginase From Thermus Thermophilus
(pdb code 2ef5). 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 the Arginase From Thermus Thermophilus, PDB code: 2ef5:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Manganese binding site 1 out
of 12 in 2ef5
Go back to
Manganese Binding Sites List in 2ef5
Manganese binding site 1 out
of 12 in the Crystal Structure of the Arginase From Thermus Thermophilus
 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 the Arginase From Thermus Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1101
b:42.2
occ:1.00
|
OD2
|
A:ASP220
|
2.2
|
28.5
|
1.0
|
|
OD1
|
A:ASP119
|
2.2
|
22.4
|
1.0
|
|
OD2
|
A:ASP218
|
2.5
|
27.2
|
1.0
|
|
ND1
|
A:HIS121
|
2.8
|
30.3
|
1.0
|
|
MN
|
A:MN1102
|
2.9
|
28.2
|
1.0
|
|
CG
|
A:ASP220
|
3.0
|
22.6
|
1.0
|
|
CG
|
A:ASP119
|
3.1
|
22.0
|
1.0
|
|
OD1
|
A:ASP220
|
3.1
|
23.8
|
1.0
|
|
CG
|
A:ASP218
|
3.1
|
23.3
|
1.0
|
|
O
|
A:HOH3048
|
3.2
|
44.1
|
1.0
|
|
OD2
|
A:ASP119
|
3.3
|
22.9
|
1.0
|
|
OD1
|
A:ASP218
|
3.6
|
23.1
|
1.0
|
|
CG
|
A:HIS121
|
3.7
|
29.2
|
1.0
|
|
CE1
|
A:HIS121
|
3.7
|
32.0
|
1.0
|
|
CB
|
A:HIS121
|
3.8
|
26.4
|
1.0
|
|
O
|
A:HOH3067
|
3.8
|
27.4
|
1.0
|
|
O
|
A:HOH3049
|
4.0
|
45.0
|
1.0
|
|
N
|
A:HIS121
|
4.0
|
21.0
|
1.0
|
|
CB
|
A:ASP218
|
4.1
|
20.5
|
1.0
|
|
CB
|
A:ASP220
|
4.4
|
20.0
|
1.0
|
|
N
|
A:ALA120
|
4.4
|
19.1
|
1.0
|
|
CB
|
A:ASP119
|
4.5
|
20.9
|
1.0
|
|
CA
|
A:HIS121
|
4.5
|
24.0
|
1.0
|
|
OD2
|
A:ASP123
|
4.6
|
22.7
|
1.0
|
|
OD1
|
A:ASP123
|
4.6
|
24.8
|
1.0
|
|
CD2
|
A:HIS121
|
4.8
|
31.3
|
1.0
|
|
NE2
|
A:HIS121
|
4.9
|
33.5
|
1.0
|
|
C
|
A:ALA120
|
4.9
|
20.9
|
1.0
|
|
ND1
|
A:HIS97
|
4.9
|
21.1
|
1.0
|
|
CG
|
A:GLU263
|
5.0
|
26.1
|
1.0
|
|
CA
|
A:ASP119
|
5.0
|
18.1
|
1.0
|
|
Manganese binding site 2 out
of 12 in 2ef5
Go back to
Manganese Binding Sites List in 2ef5
Manganese binding site 2 out
of 12 in the Crystal Structure of the Arginase From Thermus Thermophilus
 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 the Arginase From Thermus Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn1102
b:28.2
occ:1.00
|
OD2
|
A:ASP119
|
2.1
|
22.9
|
1.0
|
|
ND1
|
A:HIS97
|
2.2
|
21.1
|
1.0
|
|
OD2
|
A:ASP123
|
2.2
|
22.7
|
1.0
|
|
OD2
|
A:ASP218
|
2.4
|
27.2
|
1.0
|
|
MN
|
A:MN1101
|
2.9
|
42.2
|
1.0
|
|
CG
|
A:ASP119
|
3.1
|
22.0
|
1.0
|
|
CG
|
A:ASP123
|
3.1
|
24.6
|
1.0
|
|
CE1
|
A:HIS97
|
3.1
|
21.6
|
1.0
|
|
CG
|
A:HIS97
|
3.2
|
23.2
|
1.0
|
|
OD1
|
A:ASP123
|
3.3
|
24.8
|
1.0
|
|
OD1
|
A:ASP119
|
3.4
|
22.4
|
1.0
|
|
CG
|
A:ASP218
|
3.5
|
23.3
|
1.0
|
|
CB
|
A:HIS97
|
3.5
|
21.4
|
1.0
|
|
O
|
A:HOH3048
|
3.7
|
44.1
|
1.0
|
|
CB
|
A:ASP218
|
3.9
|
20.5
|
1.0
|
|
NE1
|
A:TRP117
|
4.1
|
19.8
|
1.0
|
|
NE2
|
A:HIS97
|
4.3
|
22.4
|
1.0
|
|
CD2
|
A:HIS97
|
4.3
|
21.0
|
1.0
|
|
CB
|
A:ASP119
|
4.4
|
20.9
|
1.0
|
|
O
|
A:HOH3049
|
4.4
|
45.0
|
1.0
|
|
CB
|
A:ASP123
|
4.5
|
24.8
|
1.0
|
|
OD1
|
A:ASP218
|
4.6
|
23.1
|
1.0
|
|
CG
|
A:GLU263
|
4.7
|
26.1
|
1.0
|
|
CZ2
|
A:TRP117
|
4.7
|
20.9
|
1.0
|
|
CE2
|
A:TRP117
|
4.7
|
20.8
|
1.0
|
|
O
|
A:HIS136
|
4.8
|
34.2
|
1.0
|
|
Manganese binding site 3 out
of 12 in 2ef5
Go back to
Manganese Binding Sites List in 2ef5
Manganese binding site 3 out
of 12 in the Crystal Structure of the Arginase From Thermus Thermophilus
 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 the Arginase From Thermus Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1601
b:38.1
occ:1.00
|
OD1
|
B:ASP119
|
2.2
|
16.6
|
1.0
|
|
OD2
|
B:ASP220
|
2.3
|
26.8
|
1.0
|
|
OD2
|
B:ASP218
|
2.6
|
21.9
|
1.0
|
|
ND1
|
B:HIS121
|
2.7
|
28.7
|
1.0
|
|
MN
|
B:MN1602
|
3.0
|
33.0
|
1.0
|
|
CG
|
B:ASP220
|
3.0
|
20.7
|
1.0
|
|
CG
|
B:ASP119
|
3.0
|
14.9
|
1.0
|
|
OD1
|
B:ASP220
|
3.1
|
20.4
|
1.0
|
|
OD2
|
B:ASP119
|
3.2
|
16.8
|
1.0
|
|
CG
|
B:ASP218
|
3.2
|
18.9
|
1.0
|
|
CG
|
B:HIS121
|
3.6
|
26.1
|
1.0
|
|
OD1
|
B:ASP218
|
3.7
|
22.1
|
1.0
|
|
CB
|
B:HIS121
|
3.7
|
23.7
|
1.0
|
|
CE1
|
B:HIS121
|
3.7
|
30.1
|
1.0
|
|
O
|
B:HOH3101
|
3.9
|
31.0
|
1.0
|
|
N
|
B:HIS121
|
3.9
|
18.4
|
1.0
|
|
O
|
B:HOH3082
|
4.1
|
49.6
|
1.0
|
|
CB
|
B:ASP218
|
4.1
|
15.7
|
1.0
|
|
N
|
B:ALA120
|
4.3
|
16.0
|
1.0
|
|
CA
|
B:HIS121
|
4.4
|
21.1
|
1.0
|
|
CB
|
B:ASP220
|
4.4
|
20.2
|
1.0
|
|
CB
|
B:ASP119
|
4.4
|
13.3
|
1.0
|
|
OD2
|
B:ASP123
|
4.5
|
25.9
|
1.0
|
|
OD1
|
B:ASP123
|
4.6
|
27.7
|
1.0
|
|
CD2
|
B:HIS121
|
4.8
|
28.3
|
1.0
|
|
NE2
|
B:HIS121
|
4.8
|
31.2
|
1.0
|
|
C
|
B:ALA120
|
4.9
|
17.8
|
1.0
|
|
O
|
B:HIS121
|
4.9
|
22.4
|
1.0
|
|
CA
|
B:ASP119
|
4.9
|
14.0
|
1.0
|
|
CB
|
B:ALA120
|
5.0
|
15.2
|
1.0
|
|
CG
|
B:ASP123
|
5.0
|
24.8
|
1.0
|
|
ND1
|
B:HIS97
|
5.0
|
16.8
|
1.0
|
|
Manganese binding site 4 out
of 12 in 2ef5
Go back to
Manganese Binding Sites List in 2ef5
Manganese binding site 4 out
of 12 in the Crystal Structure of the Arginase From Thermus Thermophilus
 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 the Arginase From Thermus Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn1602
b:33.0
occ:1.00
|
OD2
|
B:ASP119
|
2.1
|
16.8
|
1.0
|
|
ND1
|
B:HIS97
|
2.2
|
16.8
|
1.0
|
|
OD2
|
B:ASP123
|
2.2
|
25.9
|
1.0
|
|
OD2
|
B:ASP218
|
2.4
|
21.9
|
1.0
|
|
MN
|
B:MN1601
|
3.0
|
38.1
|
1.0
|
|
CG
|
B:ASP119
|
3.1
|
14.9
|
1.0
|
|
CG
|
B:ASP123
|
3.1
|
24.8
|
1.0
|
|
CE1
|
B:HIS97
|
3.1
|
18.0
|
1.0
|
|
CG
|
B:HIS97
|
3.2
|
18.2
|
1.0
|
|
OD1
|
B:ASP123
|
3.3
|
27.7
|
1.0
|
|
OD1
|
B:ASP119
|
3.4
|
16.6
|
1.0
|
|
CB
|
B:HIS97
|
3.5
|
17.9
|
1.0
|
|
CG
|
B:ASP218
|
3.5
|
18.9
|
1.0
|
|
CB
|
B:ASP218
|
3.9
|
15.7
|
1.0
|
|
NE1
|
B:TRP117
|
4.2
|
17.2
|
1.0
|
|
NE2
|
B:HIS97
|
4.3
|
19.4
|
1.0
|
|
CD2
|
B:HIS97
|
4.3
|
17.6
|
1.0
|
|
CB
|
B:ASP119
|
4.4
|
13.3
|
1.0
|
|
O
|
B:HOH3082
|
4.5
|
49.6
|
1.0
|
|
CB
|
B:ASP123
|
4.5
|
22.9
|
1.0
|
|
OD1
|
B:ASP218
|
4.6
|
22.1
|
1.0
|
|
CG
|
B:GLU263
|
4.6
|
21.6
|
1.0
|
|
CZ2
|
B:TRP117
|
4.7
|
16.5
|
1.0
|
|
CE2
|
B:TRP117
|
4.8
|
16.4
|
1.0
|
|
O
|
B:HIS136
|
4.8
|
32.5
|
1.0
|
|
CA
|
B:HIS97
|
5.0
|
19.8
|
1.0
|
|
Manganese binding site 5 out
of 12 in 2ef5
Go back to
Manganese Binding Sites List in 2ef5
Manganese binding site 5 out
of 12 in the Crystal Structure of the Arginase From Thermus Thermophilus
 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 the Arginase From Thermus Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn1201
b:43.9
occ:1.00
|
OD1
|
D:ASP119
|
2.2
|
20.4
|
1.0
|
|
OD2
|
D:ASP220
|
2.2
|
27.4
|
1.0
|
|
OD2
|
D:ASP218
|
2.4
|
27.9
|
1.0
|
|
ND1
|
D:HIS121
|
2.8
|
30.3
|
1.0
|
|
MN
|
D:MN1202
|
2.9
|
30.7
|
1.0
|
|
CG
|
D:ASP220
|
3.0
|
22.5
|
1.0
|
|
OD1
|
D:ASP220
|
3.1
|
22.6
|
1.0
|
|
CG
|
D:ASP119
|
3.1
|
20.9
|
1.0
|
|
CG
|
D:ASP218
|
3.1
|
24.3
|
1.0
|
|
OD2
|
D:ASP119
|
3.2
|
22.3
|
1.0
|
|
O
|
D:HOH3054
|
3.3
|
53.5
|
1.0
|
|
OD1
|
D:ASP218
|
3.6
|
24.0
|
1.0
|
|
CG
|
D:HIS121
|
3.6
|
29.8
|
1.0
|
|
CB
|
D:HIS121
|
3.7
|
27.0
|
1.0
|
|
CE1
|
D:HIS121
|
3.8
|
32.1
|
1.0
|
|
O
|
D:HOH3073
|
3.9
|
34.1
|
1.0
|
|
N
|
D:HIS121
|
4.0
|
23.6
|
1.0
|
|
CB
|
D:ASP218
|
4.0
|
20.9
|
1.0
|
|
O
|
D:HOH3055
|
4.1
|
52.8
|
1.0
|
|
N
|
D:ALA120
|
4.4
|
20.2
|
1.0
|
|
CB
|
D:ASP220
|
4.4
|
21.9
|
1.0
|
|
CA
|
D:HIS121
|
4.4
|
25.8
|
1.0
|
|
CB
|
D:ASP119
|
4.5
|
19.3
|
1.0
|
|
OD2
|
D:ASP123
|
4.5
|
31.7
|
1.0
|
|
OD1
|
D:ASP123
|
4.7
|
32.1
|
1.0
|
|
CD2
|
D:HIS121
|
4.8
|
30.5
|
1.0
|
|
NE2
|
D:HIS121
|
4.9
|
32.7
|
1.0
|
|
C
|
D:ALA120
|
4.9
|
22.8
|
1.0
|
|
ND1
|
D:HIS97
|
4.9
|
18.6
|
1.0
|
|
CA
|
D:ASP119
|
4.9
|
19.0
|
1.0
|
|
CG
|
D:GLU263
|
4.9
|
24.2
|
1.0
|
|
CB
|
D:ALA120
|
5.0
|
21.7
|
1.0
|
|
Manganese binding site 6 out
of 12 in 2ef5
Go back to
Manganese Binding Sites List in 2ef5
Manganese binding site 6 out
of 12 in the Crystal Structure of the Arginase From Thermus Thermophilus
 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 the Arginase From Thermus Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn1202
b:30.7
occ:1.00
|
OD2
|
D:ASP119
|
2.1
|
22.3
|
1.0
|
|
OD2
|
D:ASP123
|
2.2
|
31.7
|
1.0
|
|
ND1
|
D:HIS97
|
2.3
|
18.6
|
1.0
|
|
OD2
|
D:ASP218
|
2.5
|
27.9
|
1.0
|
|
MN
|
D:MN1201
|
2.9
|
43.9
|
1.0
|
|
CG
|
D:ASP119
|
3.0
|
20.9
|
1.0
|
|
CG
|
D:ASP123
|
3.1
|
30.3
|
1.0
|
|
CE1
|
D:HIS97
|
3.2
|
20.1
|
1.0
|
|
CG
|
D:HIS97
|
3.3
|
20.5
|
1.0
|
|
OD1
|
D:ASP123
|
3.3
|
32.1
|
1.0
|
|
OD1
|
D:ASP119
|
3.4
|
20.4
|
1.0
|
|
CB
|
D:HIS97
|
3.5
|
20.1
|
1.0
|
|
CG
|
D:ASP218
|
3.5
|
24.3
|
1.0
|
|
O
|
D:HOH3054
|
3.7
|
53.5
|
1.0
|
|
CB
|
D:ASP218
|
4.0
|
20.9
|
1.0
|
|
NE1
|
D:TRP117
|
4.2
|
23.4
|
1.0
|
|
NE2
|
D:HIS97
|
4.3
|
22.6
|
1.0
|
|
CB
|
D:ASP119
|
4.4
|
19.3
|
1.0
|
|
CD2
|
D:HIS97
|
4.4
|
19.6
|
1.0
|
|
O
|
D:HOH3055
|
4.4
|
52.8
|
1.0
|
|
CB
|
D:ASP123
|
4.5
|
30.4
|
1.0
|
|
OD1
|
D:ASP218
|
4.6
|
24.0
|
1.0
|
|
CG
|
D:GLU263
|
4.7
|
24.2
|
1.0
|
|
CZ2
|
D:TRP117
|
4.7
|
24.9
|
1.0
|
|
O
|
D:HIS136
|
4.8
|
35.2
|
1.0
|
|
CE2
|
D:TRP117
|
4.8
|
23.5
|
1.0
|
|
CB
|
D:HIS121
|
4.9
|
27.0
|
1.0
|
|
OD2
|
D:ASP220
|
5.0
|
27.4
|
1.0
|
|
Manganese binding site 7 out
of 12 in 2ef5
Go back to
Manganese Binding Sites List in 2ef5
Manganese binding site 7 out
of 12 in the Crystal Structure of the Arginase From Thermus Thermophilus
 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 the Arginase From Thermus Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn1301
b:30.8
occ:1.00
|
OD2
|
E:ASP220
|
2.1
|
24.2
|
1.0
|
|
OD1
|
E:ASP119
|
2.2
|
17.4
|
1.0
|
|
OD2
|
E:ASP218
|
2.5
|
19.4
|
1.0
|
|
ND1
|
E:HIS121
|
2.7
|
28.9
|
1.0
|
|
CG
|
E:ASP220
|
2.9
|
17.8
|
1.0
|
|
OD1
|
E:ASP220
|
3.0
|
17.5
|
1.0
|
|
MN
|
E:MN1302
|
3.1
|
16.4
|
1.0
|
|
CG
|
E:ASP119
|
3.1
|
13.9
|
1.0
|
|
CG
|
E:ASP218
|
3.1
|
18.7
|
1.0
|
|
O
|
E:HOH3096
|
3.3
|
54.7
|
1.0
|
|
OD2
|
E:ASP119
|
3.3
|
15.4
|
1.0
|
|
OD1
|
E:ASP218
|
3.6
|
20.1
|
1.0
|
|
CE1
|
E:HIS121
|
3.7
|
30.8
|
1.0
|
|
CG
|
E:HIS121
|
3.7
|
26.1
|
1.0
|
|
CB
|
E:HIS121
|
3.8
|
22.1
|
1.0
|
|
O
|
E:HOH3113
|
3.9
|
27.6
|
1.0
|
|
N
|
E:HIS121
|
4.0
|
16.9
|
1.0
|
|
CB
|
E:ASP218
|
4.0
|
15.2
|
1.0
|
|
O
|
E:HOH3097
|
4.1
|
45.0
|
1.0
|
|
N
|
E:ALA120
|
4.3
|
14.5
|
1.0
|
|
CB
|
E:ASP220
|
4.3
|
16.6
|
1.0
|
|
CB
|
E:ASP119
|
4.5
|
15.2
|
1.0
|
|
CA
|
E:HIS121
|
4.5
|
19.5
|
1.0
|
|
OD2
|
E:ASP123
|
4.7
|
20.5
|
1.0
|
|
NE2
|
E:HIS121
|
4.8
|
30.7
|
1.0
|
|
CD2
|
E:HIS121
|
4.8
|
27.6
|
1.0
|
|
OD1
|
E:ASP123
|
4.8
|
23.8
|
1.0
|
|
C
|
E:ALA120
|
4.9
|
15.6
|
1.0
|
|
CB
|
E:ALA120
|
4.9
|
13.1
|
1.0
|
|
CA
|
E:ASP119
|
4.9
|
13.3
|
1.0
|
|
CA
|
E:ALA120
|
4.9
|
14.6
|
1.0
|
|
Manganese binding site 8 out
of 12 in 2ef5
Go back to
Manganese Binding Sites List in 2ef5
Manganese binding site 8 out
of 12 in the Crystal Structure of the Arginase From Thermus Thermophilus
 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 the Arginase From Thermus Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn1302
b:16.4
occ:1.00
|
OD2
|
E:ASP119
|
2.1
|
15.4
|
1.0
|
|
OD2
|
E:ASP123
|
2.2
|
20.5
|
1.0
|
|
ND1
|
E:HIS97
|
2.3
|
14.3
|
1.0
|
|
OD2
|
E:ASP218
|
2.5
|
19.4
|
1.0
|
|
MN
|
E:MN1301
|
3.1
|
30.8
|
1.0
|
|
CG
|
E:ASP119
|
3.1
|
13.9
|
1.0
|
|
CG
|
E:ASP123
|
3.1
|
19.2
|
1.0
|
|
CG
|
E:HIS97
|
3.2
|
15.6
|
1.0
|
|
CE1
|
E:HIS97
|
3.2
|
13.5
|
1.0
|
|
OD1
|
E:ASP123
|
3.3
|
23.8
|
1.0
|
|
OD1
|
E:ASP119
|
3.4
|
17.4
|
1.0
|
|
CB
|
E:HIS97
|
3.5
|
16.0
|
1.0
|
|
CG
|
E:ASP218
|
3.5
|
18.7
|
1.0
|
|
O
|
E:HOH3096
|
3.7
|
54.7
|
1.0
|
|
CB
|
E:ASP218
|
4.0
|
15.2
|
1.0
|
|
NE1
|
E:TRP117
|
4.2
|
17.2
|
1.0
|
|
NE2
|
E:HIS97
|
4.3
|
17.9
|
1.0
|
|
CD2
|
E:HIS97
|
4.4
|
15.2
|
1.0
|
|
O
|
E:HOH3097
|
4.4
|
45.0
|
1.0
|
|
CB
|
E:ASP119
|
4.4
|
15.2
|
1.0
|
|
CB
|
E:ASP123
|
4.5
|
18.2
|
1.0
|
|
OD1
|
E:ASP218
|
4.6
|
20.1
|
1.0
|
|
CG
|
E:GLU263
|
4.7
|
21.5
|
1.0
|
|
CZ2
|
E:TRP117
|
4.7
|
17.4
|
1.0
|
|
O
|
E:HIS136
|
4.8
|
27.2
|
1.0
|
|
CE2
|
E:TRP117
|
4.8
|
17.0
|
1.0
|
|
OD2
|
E:ASP220
|
5.0
|
24.2
|
1.0
|
|
CA
|
E:HIS97
|
5.0
|
16.7
|
1.0
|
|
Manganese binding site 9 out
of 12 in 2ef5
Go back to
Manganese Binding Sites List in 2ef5
Manganese binding site 9 out
of 12 in the Crystal Structure of the Arginase From Thermus Thermophilus
 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 the Arginase From Thermus Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn1401
b:47.3
occ:1.00
|
OD2
|
F:ASP220
|
2.3
|
28.9
|
1.0
|
|
OD1
|
F:ASP119
|
2.3
|
25.8
|
1.0
|
|
OD2
|
F:ASP218
|
2.4
|
27.3
|
1.0
|
|
ND1
|
F:HIS121
|
2.8
|
30.4
|
1.0
|
|
MN
|
F:MN1402
|
2.9
|
31.4
|
1.0
|
|
CG
|
F:ASP119
|
3.1
|
25.9
|
1.0
|
|
CG
|
F:ASP220
|
3.1
|
24.7
|
1.0
|
|
CG
|
F:ASP218
|
3.2
|
26.6
|
1.0
|
|
O
|
F:HOH3072
|
3.2
|
50.1
|
1.0
|
|
OD2
|
F:ASP119
|
3.2
|
27.4
|
1.0
|
|
OD1
|
F:ASP220
|
3.2
|
24.4
|
1.0
|
|
CG
|
F:HIS121
|
3.6
|
30.1
|
1.0
|
|
OD1
|
F:ASP218
|
3.6
|
27.8
|
1.0
|
|
CB
|
F:HIS121
|
3.8
|
26.3
|
1.0
|
|
CE1
|
F:HIS121
|
3.8
|
32.2
|
1.0
|
|
O
|
F:HOH3089
|
3.8
|
39.5
|
1.0
|
|
O
|
F:HOH3073
|
4.0
|
49.7
|
1.0
|
|
N
|
F:HIS121
|
4.1
|
22.4
|
1.0
|
|
CB
|
F:ASP218
|
4.1
|
22.2
|
1.0
|
|
N
|
F:ALA120
|
4.4
|
20.4
|
1.0
|
|
CB
|
F:ASP220
|
4.5
|
23.1
|
1.0
|
|
CB
|
F:ASP119
|
4.5
|
22.6
|
1.0
|
|
CA
|
F:HIS121
|
4.5
|
25.5
|
1.0
|
|
OD2
|
F:ASP123
|
4.6
|
30.9
|
1.0
|
|
OD1
|
F:ASP123
|
4.6
|
33.8
|
1.0
|
|
CD2
|
F:HIS121
|
4.8
|
31.8
|
1.0
|
|
NE2
|
F:HIS121
|
4.9
|
33.5
|
1.0
|
|
CG
|
F:GLU263
|
4.9
|
29.7
|
1.0
|
|
ND1
|
F:HIS97
|
4.9
|
22.9
|
1.0
|
|
C
|
F:ALA120
|
5.0
|
22.0
|
1.0
|
|
CG
|
F:ASP123
|
5.0
|
32.9
|
1.0
|
|
Manganese binding site 10 out
of 12 in 2ef5
Go back to
Manganese Binding Sites List in 2ef5
Manganese binding site 10 out
of 12 in the Crystal Structure of the Arginase From Thermus Thermophilus
 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 the Arginase From Thermus Thermophilus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mn1402
b:31.4
occ:1.00
|
OD2
|
F:ASP119
|
2.0
|
27.4
|
1.0
|
|
ND1
|
F:HIS97
|
2.3
|
22.9
|
1.0
|
|
OD2
|
F:ASP123
|
2.3
|
30.9
|
1.0
|
|
OD2
|
F:ASP218
|
2.4
|
27.3
|
1.0
|
|
MN
|
F:MN1401
|
2.9
|
47.3
|
1.0
|
|
CG
|
F:ASP119
|
3.1
|
25.9
|
1.0
|
|
CG
|
F:ASP123
|
3.2
|
32.9
|
1.0
|
|
CE1
|
F:HIS97
|
3.2
|
25.6
|
1.0
|
|
CG
|
F:HIS97
|
3.2
|
26.2
|
1.0
|
|
OD1
|
F:ASP123
|
3.3
|
33.8
|
1.0
|
|
OD1
|
F:ASP119
|
3.4
|
25.8
|
1.0
|
|
CG
|
F:ASP218
|
3.5
|
26.6
|
1.0
|
|
CB
|
F:HIS97
|
3.5
|
26.5
|
1.0
|
|
O
|
F:HOH3072
|
3.7
|
50.1
|
1.0
|
|
CB
|
F:ASP218
|
4.0
|
22.2
|
1.0
|
|
NE1
|
F:TRP117
|
4.2
|
22.6
|
1.0
|
|
NE2
|
F:HIS97
|
4.3
|
26.6
|
1.0
|
|
CB
|
F:ASP119
|
4.4
|
22.6
|
1.0
|
|
CD2
|
F:HIS97
|
4.4
|
25.3
|
1.0
|
|
O
|
F:HOH3073
|
4.4
|
49.7
|
1.0
|
|
CB
|
F:ASP123
|
4.6
|
30.7
|
1.0
|
|
OD1
|
F:ASP218
|
4.6
|
27.8
|
1.0
|
|
CG
|
F:GLU263
|
4.6
|
29.7
|
1.0
|
|
CZ2
|
F:TRP117
|
4.8
|
24.5
|
1.0
|
|
O
|
F:HIS136
|
4.8
|
39.1
|
1.0
|
|
CE2
|
F:TRP117
|
4.8
|
23.2
|
1.0
|
|
OD2
|
F:ASP220
|
5.0
|
28.9
|
1.0
|
|
CB
|
F:HIS121
|
5.0
|
26.3
|
1.0
|
|
Reference:
T.S.Kumarevel,
P.Karthe,
S.Kuramitsu,
S.Yokoyama.
Crystal Structure of the Arginase From Thermus Thermophilus To Be Published.
Page generated: Sat Oct 5 13:58:38 2024
|
