Sodium in PDB 4xmt: Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid
Enzymatic activity of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid
All present enzymatic activity of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid:
3.4.11.2;
Protein crystallography data
The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid, PDB code: 4xmt
was solved by
A.Addlagatta,
R.Gumpena,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
21.14 /
2.00
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
120.473,
120.473,
170.620,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
12.8 /
16.9
|
Other elements in 4xmt:
The structure of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid
(pdb code 4xmt). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the
Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid, PDB code: 4xmt:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
Sodium binding site 1 out
of 7 in 4xmt
Go back to
Sodium Binding Sites List in 4xmt
Sodium binding site 1 out
of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na903
b:25.2
occ:1.00
|
O
|
A:HOH1877
|
2.1
|
34.3
|
1.0
|
O
|
A:GLY335
|
2.3
|
19.5
|
1.0
|
O
|
A:HOH1776
|
2.4
|
26.6
|
1.0
|
O
|
A:SER332
|
2.4
|
17.8
|
1.0
|
O
|
A:HOH1588
|
2.5
|
19.3
|
1.0
|
O
|
A:ASP333
|
2.7
|
16.2
|
1.0
|
O
|
A:HOH1014
|
3.1
|
25.8
|
0.5
|
C
|
A:ASP333
|
3.3
|
19.4
|
1.0
|
C
|
A:GLY335
|
3.4
|
18.6
|
1.0
|
C
|
A:SER332
|
3.5
|
18.8
|
1.0
|
CA
|
A:ASP333
|
3.7
|
18.7
|
1.0
|
N
|
A:GLY335
|
3.8
|
17.0
|
1.0
|
N
|
A:ARG337
|
4.0
|
19.4
|
1.0
|
N
|
A:ASP333
|
4.1
|
18.8
|
1.0
|
C
|
A:LEU334
|
4.2
|
19.6
|
1.0
|
O
|
A:HOH1529
|
4.2
|
27.9
|
1.0
|
N
|
A:LEU334
|
4.2
|
17.5
|
1.0
|
CA
|
A:GLY335
|
4.2
|
19.0
|
1.0
|
O
|
A:HOH2077
|
4.3
|
44.0
|
1.0
|
O
|
A:HOH1775
|
4.3
|
48.5
|
1.0
|
N
|
A:SER336
|
4.3
|
19.9
|
1.0
|
O
|
A:HOH1943
|
4.4
|
37.2
|
1.0
|
CA
|
A:SER336
|
4.5
|
19.5
|
1.0
|
O
|
A:HOH1500
|
4.5
|
32.3
|
1.0
|
C
|
A:SER336
|
4.6
|
18.6
|
1.0
|
CB
|
A:ARG337
|
4.6
|
20.3
|
1.0
|
CA
|
A:LEU334
|
4.7
|
19.4
|
1.0
|
O
|
A:LEU334
|
4.8
|
19.2
|
1.0
|
CA
|
A:SER332
|
4.8
|
17.2
|
1.0
|
CA
|
A:ARG337
|
4.8
|
20.8
|
1.0
|
|
Sodium binding site 2 out
of 7 in 4xmt
Go back to
Sodium Binding Sites List in 4xmt
Sodium binding site 2 out
of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na904
b:41.6
occ:1.00
|
O
|
A:HOH1897
|
2.2
|
47.8
|
1.0
|
O
|
A:HOH1893
|
2.4
|
43.8
|
1.0
|
OD1
|
A:ASP452
|
2.4
|
23.9
|
1.0
|
O
|
A:ASP452
|
2.5
|
23.9
|
1.0
|
O
|
A:HOH1885
|
2.5
|
44.1
|
1.0
|
O
|
A:HOH1639
|
2.6
|
31.1
|
1.0
|
C
|
A:ASP452
|
3.3
|
24.4
|
1.0
|
NA
|
A:NA907
|
3.4
|
50.9
|
1.0
|
CG
|
A:ASP452
|
3.5
|
23.4
|
1.0
|
O
|
A:HOH1844
|
3.7
|
33.8
|
1.0
|
N
|
A:ASP452
|
3.8
|
22.2
|
1.0
|
CA
|
A:ASP452
|
3.9
|
21.1
|
1.0
|
O
|
A:HOH1880
|
4.1
|
48.4
|
1.0
|
CB
|
A:ASP452
|
4.3
|
22.9
|
1.0
|
N
|
A:ASP453
|
4.3
|
25.4
|
1.0
|
O
|
A:HOH1872
|
4.4
|
49.8
|
1.0
|
OD2
|
A:ASP452
|
4.4
|
24.9
|
1.0
|
O
|
A:HOH1758
|
4.5
|
31.1
|
1.0
|
CA
|
A:ASP453
|
4.5
|
26.4
|
1.0
|
|
Sodium binding site 3 out
of 7 in 4xmt
Go back to
Sodium Binding Sites List in 4xmt
Sodium binding site 3 out
of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na905
b:42.5
occ:1.00
|
O
|
A:HOH1653
|
2.5
|
44.5
|
1.0
|
O
|
A:HOH1718
|
2.7
|
25.4
|
1.0
|
O
|
A:HOH1491
|
2.8
|
36.9
|
1.0
|
O
|
A:HOH1393
|
2.8
|
26.7
|
1.0
|
O
|
A:GLY56
|
2.9
|
18.3
|
1.0
|
N
|
A:GLY79
|
3.6
|
21.7
|
1.0
|
C
|
A:GLY56
|
3.7
|
18.9
|
1.0
|
CA
|
A:GLY79
|
3.7
|
23.2
|
1.0
|
O
|
A:HOH1940
|
3.8
|
57.8
|
1.0
|
CA
|
A:GLU57
|
4.0
|
19.4
|
1.0
|
OH
|
A:TYR130
|
4.1
|
26.7
|
1.0
|
N
|
A:ALA80
|
4.1
|
18.9
|
1.0
|
C
|
A:GLY79
|
4.1
|
22.2
|
1.0
|
N
|
A:GLU57
|
4.2
|
16.5
|
1.0
|
O
|
A:GLU77
|
4.2
|
23.2
|
1.0
|
N
|
A:ASP58
|
4.3
|
19.3
|
1.0
|
C
|
A:GLU57
|
4.6
|
20.0
|
1.0
|
OE1
|
A:GLU57
|
4.7
|
24.6
|
1.0
|
C
|
A:GLU78
|
4.7
|
24.8
|
1.0
|
CA
|
A:GLY56
|
4.7
|
17.2
|
1.0
|
CE1
|
A:TYR130
|
4.8
|
22.6
|
1.0
|
CZ
|
A:TYR130
|
4.9
|
23.8
|
1.0
|
O
|
A:GLY79
|
4.9
|
18.3
|
1.0
|
CD
|
A:GLU57
|
5.0
|
25.3
|
1.0
|
|
Sodium binding site 4 out
of 7 in 4xmt
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Sodium Binding Sites List in 4xmt
Sodium binding site 4 out
of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na906
b:33.3
occ:1.00
|
O
|
A:HOH1728
|
2.4
|
30.6
|
1.0
|
O
|
A:LEU138
|
2.5
|
18.3
|
1.0
|
O
|
A:HOH1965
|
2.5
|
36.0
|
1.0
|
OE1
|
A:GLN19
|
2.6
|
22.2
|
1.0
|
O
|
A:ILE20
|
2.7
|
23.9
|
1.0
|
CD
|
A:GLN19
|
3.4
|
21.2
|
1.0
|
C
|
A:LEU138
|
3.5
|
19.1
|
1.0
|
C
|
A:ILE20
|
3.6
|
21.7
|
1.0
|
N
|
A:LEU138
|
3.7
|
16.2
|
1.0
|
CB
|
A:GLN19
|
4.0
|
18.6
|
1.0
|
O
|
A:HOH1972
|
4.0
|
19.9
|
0.5
|
CA
|
A:THR21
|
4.1
|
18.4
|
1.0
|
CA
|
A:LEU138
|
4.1
|
17.7
|
1.0
|
N
|
A:ILE20
|
4.1
|
19.6
|
1.0
|
CG
|
A:GLN19
|
4.1
|
20.1
|
1.0
|
N
|
A:THR21
|
4.2
|
18.6
|
1.0
|
NE2
|
A:GLN19
|
4.3
|
20.3
|
1.0
|
O
|
A:HOH1514
|
4.4
|
34.1
|
1.0
|
CG2
|
A:THR21
|
4.4
|
21.9
|
1.0
|
C
|
A:VAL137
|
4.5
|
17.3
|
1.0
|
O
|
A:HOH1898
|
4.5
|
48.0
|
1.0
|
N
|
A:ALA139
|
4.6
|
17.8
|
1.0
|
CB
|
A:LEU138
|
4.6
|
19.5
|
1.0
|
CA
|
A:ILE20
|
4.6
|
18.9
|
1.0
|
O
|
A:HOH2022
|
4.6
|
19.8
|
0.5
|
CA
|
A:GLN19
|
4.7
|
18.0
|
1.0
|
CA
|
A:VAL137
|
4.7
|
16.5
|
1.0
|
CG1
|
A:VAL137
|
4.7
|
18.1
|
1.0
|
C
|
A:GLN19
|
4.8
|
20.6
|
1.0
|
CB
|
A:THR21
|
4.9
|
20.7
|
1.0
|
CA
|
A:ALA139
|
4.9
|
16.9
|
1.0
|
O
|
A:HOH1614
|
5.0
|
29.4
|
1.0
|
|
Sodium binding site 5 out
of 7 in 4xmt
Go back to
Sodium Binding Sites List in 4xmt
Sodium binding site 5 out
of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na907
b:50.9
occ:1.00
|
O
|
A:HOH1844
|
2.3
|
33.8
|
1.0
|
O
|
A:HOH1897
|
2.4
|
47.8
|
1.0
|
O
|
A:HOH1179
|
2.5
|
30.5
|
1.0
|
OH
|
A:TYR544
|
2.7
|
23.0
|
1.0
|
O
|
A:HOH1872
|
2.8
|
49.8
|
1.0
|
OD1
|
A:ASP452
|
2.9
|
23.9
|
1.0
|
CZ
|
A:TYR544
|
3.4
|
20.4
|
1.0
|
NA
|
A:NA904
|
3.4
|
41.6
|
1.0
|
CG
|
A:ASP452
|
3.7
|
23.4
|
1.0
|
OD2
|
A:ASP452
|
3.7
|
24.9
|
1.0
|
O
|
A:HOH1995
|
4.0
|
43.0
|
1.0
|
CE1
|
A:TYR544
|
4.0
|
21.3
|
1.0
|
O
|
A:HOH1639
|
4.1
|
31.1
|
1.0
|
CE2
|
A:TYR544
|
4.1
|
22.5
|
1.0
|
NE2
|
A:GLN550
|
4.2
|
33.0
|
1.0
|
O
|
A:LYS545
|
4.3
|
23.7
|
1.0
|
OE1
|
A:GLN550
|
4.6
|
23.5
|
1.0
|
O
|
A:HOH1669
|
4.6
|
39.1
|
1.0
|
O
|
A:HOH1885
|
4.7
|
44.1
|
1.0
|
CD
|
A:GLN550
|
4.8
|
24.9
|
1.0
|
|
Sodium binding site 6 out
of 7 in 4xmt
Go back to
Sodium Binding Sites List in 4xmt
Sodium binding site 6 out
of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na908
b:46.4
occ:1.00
|
O
|
A:HOH1808
|
2.4
|
58.9
|
1.0
|
O
|
A:HOH1865
|
2.4
|
47.5
|
1.0
|
O
|
A:HOH1191
|
2.4
|
32.9
|
1.0
|
O
|
A:HOH1646
|
2.5
|
49.2
|
1.0
|
O
|
A:HIS771
|
2.5
|
21.0
|
1.0
|
O
|
A:PHE774
|
2.5
|
21.3
|
1.0
|
C
|
A:HIS771
|
3.5
|
24.8
|
1.0
|
C
|
A:PHE774
|
3.6
|
22.8
|
1.0
|
O
|
A:ARG772
|
3.9
|
25.9
|
1.0
|
N
|
A:PHE774
|
4.0
|
21.7
|
1.0
|
CA
|
A:ARG772
|
4.0
|
26.6
|
1.0
|
C
|
A:ARG772
|
4.0
|
26.1
|
1.0
|
N
|
A:ARG772
|
4.1
|
24.1
|
1.0
|
CA
|
A:PHE774
|
4.3
|
21.5
|
1.0
|
O
|
A:GLN770
|
4.3
|
24.1
|
1.0
|
C
|
A:GLN770
|
4.5
|
26.3
|
1.0
|
N
|
A:HIS771
|
4.6
|
23.0
|
1.0
|
N
|
A:SER773
|
4.6
|
23.1
|
1.0
|
CB
|
A:PHE774
|
4.6
|
20.1
|
1.0
|
CA
|
A:HIS771
|
4.7
|
23.0
|
1.0
|
N
|
A:THR775
|
4.7
|
23.1
|
1.0
|
C
|
A:SER773
|
4.8
|
23.7
|
1.0
|
CA
|
A:THR775
|
4.9
|
22.3
|
1.0
|
O
|
A:LEU769
|
4.9
|
23.3
|
1.0
|
|
Sodium binding site 7 out
of 7 in 4xmt
Go back to
Sodium Binding Sites List in 4xmt
Sodium binding site 7 out
of 7 in the Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na909
b:48.4
occ:1.00
|
OD2
|
A:ASP24
|
2.2
|
26.6
|
0.5
|
OD1
|
A:ASP24
|
2.3
|
26.5
|
0.5
|
CG
|
A:ASP24
|
2.5
|
23.0
|
0.5
|
O
|
A:HOH2006
|
2.7
|
48.0
|
1.0
|
O
|
A:HOH1279
|
2.7
|
22.2
|
1.0
|
O
|
A:HOH1112
|
2.8
|
25.0
|
1.0
|
O
|
A:HOH1025
|
3.2
|
54.0
|
1.0
|
O
|
A:HOH1134
|
3.5
|
28.1
|
1.0
|
CB
|
A:ASP24
|
3.8
|
19.4
|
0.5
|
CB
|
A:ASP24
|
3.8
|
19.3
|
0.5
|
CB
|
A:ASP22
|
3.9
|
19.5
|
1.0
|
N
|
A:ASP24
|
4.0
|
17.2
|
1.0
|
C
|
A:ILE23
|
4.0
|
17.6
|
1.0
|
OG1
|
A:THR142
|
4.1
|
22.4
|
0.4
|
O
|
A:ILE23
|
4.2
|
16.7
|
1.0
|
N
|
A:ILE23
|
4.2
|
17.9
|
1.0
|
O
|
A:HOH1012
|
4.2
|
42.3
|
1.0
|
CA
|
A:ASP24
|
4.3
|
18.0
|
0.5
|
CA
|
A:ASP24
|
4.3
|
18.1
|
0.5
|
OD2
|
A:ASP24
|
4.4
|
29.4
|
0.5
|
C
|
A:ASP22
|
4.4
|
19.0
|
1.0
|
CA
|
A:ILE23
|
4.5
|
17.3
|
1.0
|
CG
|
A:ASP24
|
4.6
|
22.3
|
0.5
|
CA
|
A:ASP22
|
4.7
|
18.9
|
1.0
|
CG
|
A:ASP22
|
4.8
|
22.6
|
1.0
|
OD2
|
A:ASP22
|
4.8
|
21.7
|
1.0
|
CB
|
A:THR142
|
4.8
|
21.1
|
0.4
|
O
|
A:ARG140
|
4.9
|
18.3
|
1.0
|
OG1
|
A:THR142
|
4.9
|
19.8
|
0.6
|
O
|
A:ASP22
|
5.0
|
17.5
|
1.0
|
O
|
A:VAL39
|
5.0
|
17.3
|
1.0
|
|
Reference:
A.Addlagatta,
R.Gumpena.
Crystal Structure of MET260ALA Mutant of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid To Be Published.
Page generated: Mon Oct 7 19:09:55 2024
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