Magnesium in PDB 5d8n: Tomato Leucine Aminopeptidase Mutant - K354E
Enzymatic activity of Tomato Leucine Aminopeptidase Mutant - K354E
All present enzymatic activity of Tomato Leucine Aminopeptidase Mutant - K354E:
3.4.11.1;
3.4.11.5;
Protein crystallography data
The structure of Tomato Leucine Aminopeptidase Mutant - K354E, PDB code: 5d8n
was solved by
K.T.Duprez,
M.A.Scranton,
L.L.Walling,
L.Fan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.15
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
127.112,
165.193,
168.275,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.3 /
17.9
|
Other elements in 5d8n:
The structure of Tomato Leucine Aminopeptidase Mutant - K354E also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Tomato Leucine Aminopeptidase Mutant - K354E
(pdb code 5d8n). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the
Tomato Leucine Aminopeptidase Mutant - K354E, PDB code: 5d8n:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
Magnesium binding site 1 out
of 7 in 5d8n
Go back to
Magnesium Binding Sites List in 5d8n
Magnesium binding site 1 out
of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg604
b:47.6
occ:1.00
|
O
|
A:HOH862
|
1.9
|
37.1
|
1.0
|
O
|
A:HOH945
|
2.1
|
42.5
|
1.0
|
O
|
A:HOH787
|
2.2
|
30.3
|
1.0
|
O
|
A:HOH1085
|
2.3
|
44.1
|
1.0
|
O
|
A:ILE74
|
2.4
|
34.3
|
1.0
|
O
|
A:HOH705
|
2.5
|
40.7
|
1.0
|
C
|
A:ILE74
|
3.5
|
30.4
|
1.0
|
N
|
A:ILE74
|
3.6
|
28.6
|
1.0
|
O
|
A:HOH733
|
3.8
|
29.9
|
1.0
|
CA
|
A:ILE74
|
4.0
|
29.1
|
1.0
|
OE2
|
A:GLU249
|
4.1
|
33.0
|
1.0
|
OE1
|
A:GLU249
|
4.2
|
28.5
|
1.0
|
O
|
A:HOH1013
|
4.3
|
45.2
|
1.0
|
CB
|
A:ILE74
|
4.3
|
26.1
|
1.0
|
OE1
|
A:GLU242
|
4.5
|
41.9
|
1.0
|
CD
|
A:GLU249
|
4.5
|
29.6
|
1.0
|
N
|
A:GLY75
|
4.6
|
33.4
|
1.0
|
O
|
A:HOH1007
|
4.7
|
46.8
|
1.0
|
C
|
A:SER73
|
4.7
|
28.4
|
0.5
|
C
|
A:SER73
|
4.7
|
28.7
|
0.5
|
CA
|
A:GLY75
|
4.9
|
32.4
|
1.0
|
|
Magnesium binding site 2 out
of 7 in 5d8n
Go back to
Magnesium Binding Sites List in 5d8n
Magnesium binding site 2 out
of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg605
b:50.3
occ:1.00
|
O
|
A:ALA264
|
2.1
|
22.5
|
1.0
|
O
|
A:HOH893
|
2.2
|
34.0
|
1.0
|
O
|
A:HOH997
|
2.2
|
35.7
|
1.0
|
O
|
A:HOH960
|
2.2
|
37.8
|
1.0
|
O
|
A:VAL262
|
2.3
|
18.9
|
1.0
|
O
|
A:HOH748
|
2.3
|
20.9
|
1.0
|
C
|
A:ALA264
|
3.2
|
23.3
|
1.0
|
C
|
A:VAL262
|
3.3
|
19.4
|
1.0
|
C
|
A:ASN263
|
3.9
|
20.9
|
1.0
|
CA
|
A:PRO265
|
3.9
|
21.4
|
1.0
|
N
|
A:PRO265
|
4.0
|
22.2
|
1.0
|
N
|
A:ALA264
|
4.0
|
20.3
|
1.0
|
CA
|
A:VAL262
|
4.0
|
19.1
|
1.0
|
O
|
A:HOH795
|
4.0
|
26.1
|
1.0
|
O
|
A:LEU261
|
4.1
|
20.5
|
1.0
|
O
|
A:ASN263
|
4.1
|
23.7
|
1.0
|
O
|
A:HOH881
|
4.1
|
44.4
|
1.0
|
CA
|
A:ALA264
|
4.2
|
20.6
|
1.0
|
O
|
A:HOH754
|
4.3
|
40.4
|
1.0
|
N
|
A:ASN263
|
4.3
|
20.2
|
1.0
|
C
|
A:PRO265
|
4.4
|
20.4
|
1.0
|
O
|
A:HOH952
|
4.5
|
40.4
|
1.0
|
CA
|
A:ASN263
|
4.5
|
19.7
|
1.0
|
O
|
A:HOH843
|
4.7
|
49.1
|
1.0
|
N
|
A:ALA266
|
4.7
|
20.2
|
1.0
|
CG1
|
A:VAL262
|
4.8
|
19.3
|
1.0
|
O
|
A:ASP367
|
4.8
|
36.8
|
1.0
|
C
|
A:LEU261
|
4.9
|
20.4
|
1.0
|
N
|
A:VAL262
|
4.9
|
20.1
|
1.0
|
O
|
A:LYS365
|
5.0
|
51.3
|
1.0
|
|
Magnesium binding site 3 out
of 7 in 5d8n
Go back to
Magnesium Binding Sites List in 5d8n
Magnesium binding site 3 out
of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg608
b:38.0
occ:1.00
|
O
|
B:VAL262
|
2.1
|
18.1
|
1.0
|
O
|
B:HOH762
|
2.1
|
38.2
|
1.0
|
O
|
B:HOH980
|
2.2
|
38.7
|
1.0
|
O
|
B:HOH1022
|
2.2
|
32.5
|
1.0
|
O
|
B:ALA264
|
2.3
|
21.0
|
1.0
|
O
|
B:HOH715
|
2.3
|
21.5
|
1.0
|
C
|
B:VAL262
|
3.2
|
17.7
|
1.0
|
C
|
B:ALA264
|
3.4
|
21.5
|
1.0
|
CA
|
B:VAL262
|
3.8
|
18.5
|
1.0
|
C
|
B:ASN263
|
4.0
|
18.1
|
1.0
|
O
|
B:HOH943
|
4.0
|
18.6
|
1.0
|
O
|
B:LEU261
|
4.1
|
16.0
|
1.0
|
N
|
B:ALA264
|
4.1
|
18.3
|
1.0
|
CA
|
B:PRO265
|
4.2
|
20.8
|
1.0
|
N
|
B:PRO265
|
4.2
|
22.2
|
1.0
|
O
|
B:ASN263
|
4.2
|
17.8
|
1.0
|
N
|
B:ASN263
|
4.2
|
16.9
|
1.0
|
O
|
B:HOH945
|
4.3
|
36.5
|
1.0
|
CA
|
B:ALA264
|
4.4
|
19.9
|
1.0
|
O
|
B:HOH720
|
4.4
|
30.4
|
1.0
|
O
|
C:HOH1062
|
4.4
|
38.1
|
1.0
|
CG1
|
B:VAL262
|
4.5
|
19.0
|
1.0
|
CA
|
B:ASN263
|
4.5
|
17.6
|
1.0
|
O
|
B:ASP367
|
4.5
|
32.4
|
1.0
|
O
|
B:HOH825
|
4.6
|
50.7
|
1.0
|
O
|
B:LYS365
|
4.7
|
40.4
|
1.0
|
C
|
B:PRO265
|
4.8
|
19.2
|
1.0
|
N
|
B:VAL262
|
4.8
|
17.6
|
1.0
|
CB
|
B:VAL262
|
4.8
|
18.8
|
1.0
|
C
|
B:LEU261
|
4.8
|
16.6
|
1.0
|
|
Magnesium binding site 4 out
of 7 in 5d8n
Go back to
Magnesium Binding Sites List in 5d8n
Magnesium binding site 4 out
of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg609
b:49.9
occ:1.00
|
O
|
B:HOH830
|
2.0
|
36.2
|
1.0
|
O
|
B:HOH989
|
2.3
|
41.0
|
1.0
|
O
|
B:HOH1149
|
2.3
|
43.6
|
1.0
|
O
|
B:ILE74
|
2.4
|
23.9
|
1.0
|
O
|
B:HOH848
|
2.4
|
40.1
|
1.0
|
O
|
B:HOH739
|
2.4
|
26.5
|
1.0
|
C
|
B:ILE74
|
3.4
|
22.4
|
1.0
|
N
|
B:ILE74
|
3.8
|
24.2
|
1.0
|
O
|
B:HOH758
|
3.9
|
28.9
|
1.0
|
CA
|
B:ILE74
|
4.1
|
23.1
|
1.0
|
O
|
B:HOH1064
|
4.2
|
39.8
|
1.0
|
OE2
|
B:GLU249
|
4.3
|
23.2
|
1.0
|
OE1
|
B:GLU249
|
4.4
|
27.3
|
1.0
|
OE1
|
B:GLU242
|
4.4
|
33.9
|
1.0
|
CB
|
B:ILE74
|
4.4
|
21.2
|
1.0
|
O
|
B:HOH1144
|
4.5
|
42.6
|
1.0
|
N
|
B:GLY75
|
4.5
|
23.0
|
1.0
|
CD
|
B:GLU249
|
4.8
|
24.6
|
1.0
|
C
|
B:SER73
|
4.8
|
24.6
|
0.5
|
C
|
B:SER73
|
4.8
|
24.4
|
0.5
|
CA
|
B:GLY75
|
4.8
|
23.6
|
1.0
|
O
|
B:HOH1112
|
4.9
|
38.0
|
1.0
|
OG
|
B:SER73
|
4.9
|
29.4
|
0.5
|
|
Magnesium binding site 5 out
of 7 in 5d8n
Go back to
Magnesium Binding Sites List in 5d8n
Magnesium binding site 5 out
of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg610
b:47.1
occ:1.00
|
O
|
B:HOH1156
|
2.0
|
53.3
|
1.0
|
O
|
A:HOH973
|
2.1
|
41.9
|
1.0
|
O
|
B:HOH1063
|
2.2
|
44.0
|
1.0
|
O
|
B:HOH780
|
2.2
|
37.5
|
1.0
|
O
|
A:HOH1001
|
2.5
|
52.1
|
1.0
|
O
|
B:HOH778
|
2.7
|
41.2
|
1.0
|
O
|
B:HOH1103
|
3.5
|
45.5
|
1.0
|
OE1
|
B:GLU129
|
4.1
|
37.2
|
1.0
|
O
|
A:HOH1014
|
4.2
|
42.4
|
1.0
|
O
|
B:SER138
|
4.3
|
30.5
|
1.0
|
O
|
B:HOH951
|
4.3
|
28.0
|
1.0
|
CB
|
B:GLU129
|
4.5
|
31.6
|
1.0
|
CB
|
A:SER176
|
4.6
|
25.8
|
0.5
|
O
|
A:SER176
|
4.7
|
29.3
|
0.5
|
O
|
A:SER176
|
4.7
|
30.3
|
0.5
|
O
|
B:HOH787
|
4.7
|
27.4
|
1.0
|
O
|
B:HOH1123
|
4.8
|
48.0
|
1.0
|
CB
|
A:SER176
|
4.8
|
29.5
|
0.5
|
CD
|
B:GLU129
|
4.8
|
35.9
|
1.0
|
CG
|
B:GLU129
|
4.8
|
34.7
|
1.0
|
O
|
B:GLU129
|
4.9
|
27.3
|
1.0
|
OG
|
A:SER176
|
5.0
|
30.1
|
0.5
|
|
Magnesium binding site 6 out
of 7 in 5d8n
Go back to
Magnesium Binding Sites List in 5d8n
Magnesium binding site 6 out
of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg606
b:47.1
occ:1.00
|
O
|
C:HOH952
|
2.1
|
37.5
|
1.0
|
O
|
C:HOH955
|
2.2
|
43.1
|
1.0
|
O
|
C:HOH748
|
2.2
|
28.1
|
1.0
|
O
|
C:HOH1089
|
2.2
|
41.3
|
1.0
|
O
|
C:ILE74
|
2.2
|
31.3
|
1.0
|
O
|
C:HOH819
|
2.3
|
33.8
|
1.0
|
C
|
C:ILE74
|
3.3
|
28.6
|
1.0
|
N
|
C:ILE74
|
3.5
|
28.2
|
1.0
|
CA
|
C:ILE74
|
3.9
|
27.6
|
1.0
|
OE2
|
C:GLU249
|
4.3
|
31.5
|
1.0
|
CB
|
C:ILE74
|
4.4
|
29.2
|
1.0
|
N
|
C:GLY75
|
4.4
|
28.5
|
1.0
|
O
|
C:HOH711
|
4.4
|
27.7
|
1.0
|
OE1
|
C:GLU249
|
4.4
|
30.1
|
1.0
|
C
|
C:SER73
|
4.5
|
28.3
|
0.5
|
C
|
C:SER73
|
4.6
|
28.5
|
0.5
|
OE1
|
C:GLU242
|
4.6
|
35.6
|
1.0
|
OG
|
C:SER73
|
4.8
|
29.3
|
0.5
|
CA
|
C:GLY75
|
4.8
|
33.4
|
1.0
|
CD
|
C:GLU249
|
4.8
|
30.3
|
1.0
|
CA
|
C:SER73
|
4.8
|
29.2
|
0.5
|
CA
|
C:SER73
|
4.9
|
29.4
|
0.5
|
|
Magnesium binding site 7 out
of 7 in 5d8n
Go back to
Magnesium Binding Sites List in 5d8n
Magnesium binding site 7 out
of 7 in the Tomato Leucine Aminopeptidase Mutant - K354E
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Tomato Leucine Aminopeptidase Mutant - K354E within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg607
b:43.9
occ:1.00
|
O
|
C:HOH857
|
2.0
|
39.3
|
1.0
|
O
|
C:HOH731
|
2.0
|
22.0
|
1.0
|
O
|
C:HOH1013
|
2.1
|
35.5
|
1.0
|
O
|
C:VAL262
|
2.3
|
22.9
|
1.0
|
O
|
C:HOH942
|
2.5
|
34.7
|
1.0
|
O
|
C:ALA264
|
2.5
|
24.0
|
1.0
|
C
|
C:VAL262
|
3.3
|
21.2
|
1.0
|
C
|
C:ALA264
|
3.6
|
20.6
|
1.0
|
CA
|
C:VAL262
|
3.7
|
20.5
|
1.0
|
O
|
C:HOH880
|
3.8
|
48.0
|
1.0
|
O
|
C:HOH804
|
3.9
|
46.4
|
1.0
|
O
|
C:HOH893
|
3.9
|
29.8
|
1.0
|
O
|
C:LEU261
|
4.0
|
22.6
|
1.0
|
O
|
C:ASP367
|
4.2
|
32.1
|
1.0
|
C
|
C:ASN263
|
4.3
|
20.5
|
1.0
|
N
|
C:ALA264
|
4.3
|
19.7
|
1.0
|
CG1
|
C:VAL262
|
4.4
|
20.3
|
1.0
|
CA
|
C:PRO265
|
4.4
|
21.6
|
1.0
|
N
|
C:ASN263
|
4.4
|
19.4
|
1.0
|
N
|
C:PRO265
|
4.4
|
22.0
|
1.0
|
O
|
C:HOH990
|
4.6
|
38.3
|
1.0
|
CA
|
C:ALA264
|
4.6
|
20.8
|
1.0
|
O
|
C:ASN263
|
4.6
|
20.6
|
1.0
|
CG
|
C:MET368
|
4.7
|
37.9
|
1.0
|
O
|
C:LYS365
|
4.7
|
43.2
|
1.0
|
CB
|
C:VAL262
|
4.7
|
21.6
|
1.0
|
N
|
C:VAL262
|
4.7
|
20.7
|
1.0
|
C
|
C:LEU261
|
4.8
|
20.9
|
1.0
|
CA
|
C:ASN263
|
4.8
|
19.7
|
1.0
|
O
|
C:HOH772
|
4.8
|
37.3
|
1.0
|
C
|
C:PRO265
|
4.8
|
20.9
|
1.0
|
|
Reference:
K.T.Duprez,
M.A.Scranton,
L.L.Walling,
L.Fan.
Structural Insights Into Chaperone-Activity Enhancement By A K354E Mutation in Tomato Acidic Leucine Aminopeptidase. Acta Crystallogr D Struct V. 72 694 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27139632
DOI: 10.1107/S205979831600509X
Page generated: Sun Sep 29 02:36:27 2024
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