Sodium in PDB 4xn7: Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid
Enzymatic activity of Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid
All present enzymatic activity of Crystal Structure 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 E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid, PDB code: 4xn7
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)
|
49.25 /
2.22
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
120.690,
120.690,
170.460,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.9 /
24.6
|
Other elements in 4xn7:
The structure of Crystal Structure 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 E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid
(pdb code 4xn7). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3- Diaminopropionic Acid, PDB code: 4xn7:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 4xn7
Go back to
Sodium Binding Sites List in 4xn7
Sodium binding site 1 out
of 4 in the Crystal Structure 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 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:28.4
occ:1.00
|
O
|
A:HOH1371
|
2.2
|
21.3
|
1.0
|
O
|
A:GLY335
|
2.4
|
19.2
|
1.0
|
O
|
A:SER332
|
2.7
|
19.1
|
1.0
|
O
|
A:HOH1332
|
2.7
|
12.7
|
1.0
|
O
|
A:ASP333
|
2.9
|
18.2
|
1.0
|
C
|
A:GLY335
|
3.6
|
18.4
|
1.0
|
C
|
A:ASP333
|
3.6
|
17.0
|
1.0
|
O
|
A:HOH1147
|
3.7
|
28.2
|
1.0
|
O
|
A:HOH1301
|
3.9
|
20.8
|
1.0
|
C
|
A:SER332
|
3.9
|
17.5
|
1.0
|
O
|
A:HOH1391
|
3.9
|
35.7
|
1.0
|
N
|
A:ARG337
|
3.9
|
18.5
|
1.0
|
CA
|
A:ASP333
|
4.0
|
16.9
|
1.0
|
N
|
A:GLY335
|
4.2
|
18.9
|
1.0
|
N
|
A:ASP333
|
4.4
|
17.1
|
1.0
|
N
|
A:SER336
|
4.4
|
18.3
|
1.0
|
CA
|
A:GLY335
|
4.5
|
18.3
|
1.0
|
N
|
A:LEU334
|
4.5
|
17.4
|
1.0
|
C
|
A:LEU334
|
4.5
|
18.6
|
1.0
|
CA
|
A:SER336
|
4.5
|
18.7
|
1.0
|
C
|
A:SER336
|
4.6
|
18.9
|
1.0
|
CB
|
A:ARG337
|
4.6
|
18.2
|
1.0
|
O
|
A:HOH1362
|
4.7
|
30.7
|
1.0
|
CA
|
A:ARG337
|
4.8
|
18.7
|
1.0
|
CA
|
A:LEU334
|
5.0
|
17.9
|
1.0
|
O
|
A:LEU334
|
5.0
|
19.2
|
1.0
|
|
Sodium binding site 2 out
of 4 in 4xn7
Go back to
Sodium Binding Sites List in 4xn7
Sodium binding site 2 out
of 4 in the Crystal Structure 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 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:31.1
occ:1.00
|
O
|
A:HOH1419
|
2.3
|
26.5
|
1.0
|
O1
|
A:GOL924
|
2.5
|
49.3
|
1.0
|
OD1
|
A:ASP452
|
2.6
|
20.1
|
1.0
|
O
|
A:HOH1344
|
2.7
|
18.8
|
1.0
|
O
|
A:ASP452
|
2.8
|
18.4
|
1.0
|
O2
|
A:GOL924
|
3.0
|
56.9
|
1.0
|
C1
|
A:GOL924
|
3.3
|
52.6
|
1.0
|
O
|
A:HOH1372
|
3.5
|
27.3
|
1.0
|
C
|
A:ASP452
|
3.7
|
18.2
|
1.0
|
CG
|
A:ASP452
|
3.7
|
20.4
|
1.0
|
C2
|
A:GOL924
|
3.8
|
53.5
|
1.0
|
N
|
A:ASP452
|
4.3
|
19.7
|
1.0
|
CA
|
A:ASP452
|
4.4
|
19.1
|
1.0
|
OD2
|
A:ASP452
|
4.5
|
20.6
|
1.0
|
N
|
A:ASP453
|
4.5
|
19.1
|
1.0
|
CB
|
A:ASP452
|
4.6
|
19.8
|
1.0
|
O
|
A:HOH1269
|
4.7
|
32.6
|
1.0
|
CA
|
A:ASP453
|
4.8
|
20.1
|
1.0
|
C3
|
A:GOL924
|
5.0
|
51.2
|
1.0
|
|
Sodium binding site 3 out
of 4 in 4xn7
Go back to
Sodium Binding Sites List in 4xn7
Sodium binding site 3 out
of 4 in the Crystal Structure 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 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:38.3
occ:1.00
|
OE2
|
A:GLU627
|
2.8
|
24.5
|
0.8
|
O
|
A:HOH1392
|
3.0
|
40.1
|
1.0
|
O
|
A:GLY350
|
3.0
|
25.9
|
1.0
|
O
|
A:ASN623
|
3.1
|
20.6
|
1.0
|
CB
|
A:ALA354
|
3.6
|
16.2
|
1.0
|
O
|
A:HOH1172
|
3.7
|
26.0
|
1.0
|
CD
|
A:GLU627
|
3.7
|
24.2
|
0.8
|
C
|
A:ASN623
|
3.8
|
20.3
|
1.0
|
CA
|
A:ASN623
|
4.0
|
21.6
|
1.0
|
O3
|
A:GOL927
|
4.0
|
35.7
|
1.0
|
ND2
|
A:ASN623
|
4.0
|
27.7
|
1.0
|
C3
|
A:GOL927
|
4.0
|
40.3
|
1.0
|
CG
|
A:GLU627
|
4.0
|
22.8
|
0.8
|
CB
|
A:ASN623
|
4.1
|
22.6
|
1.0
|
CB
|
A:ALA626
|
4.1
|
18.7
|
1.0
|
C
|
A:GLY350
|
4.2
|
21.5
|
1.0
|
O2
|
A:GOL927
|
4.2
|
50.5
|
1.0
|
CG
|
A:ASN623
|
4.5
|
24.7
|
1.0
|
C2
|
A:GOL927
|
4.6
|
39.7
|
1.0
|
N
|
A:GLU627
|
4.7
|
19.5
|
1.0
|
OE1
|
A:GLU627
|
4.8
|
24.2
|
0.8
|
CA
|
A:LEU351
|
4.9
|
19.5
|
1.0
|
CA
|
A:ALA354
|
4.9
|
16.1
|
1.0
|
N
|
A:LEU351
|
4.9
|
20.2
|
1.0
|
|
Sodium binding site 4 out
of 4 in 4xn7
Go back to
Sodium Binding Sites List in 4xn7
Sodium binding site 4 out
of 4 in the Crystal Structure 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 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:23.9
occ:1.00
|
O
|
A:ILE20
|
2.4
|
16.1
|
1.0
|
O
|
A:LEU138
|
2.5
|
17.4
|
1.0
|
OE1
|
A:GLN19
|
2.5
|
17.9
|
1.0
|
O
|
A:HOH1338
|
2.5
|
15.0
|
1.0
|
C
|
A:ILE20
|
3.4
|
15.2
|
1.0
|
CD
|
A:GLN19
|
3.4
|
17.6
|
1.0
|
C
|
A:LEU138
|
3.5
|
16.5
|
1.0
|
O
|
A:HOH1445
|
3.6
|
32.4
|
1.0
|
N
|
A:LEU138
|
3.6
|
16.1
|
1.0
|
N
|
A:ILE20
|
3.9
|
17.2
|
1.0
|
CB
|
A:GLN19
|
3.9
|
18.3
|
1.0
|
CG
|
A:GLN19
|
4.1
|
18.1
|
1.0
|
CA
|
A:LEU138
|
4.1
|
16.6
|
1.0
|
N
|
A:THR21
|
4.2
|
14.6
|
1.0
|
CA
|
A:THR21
|
4.2
|
14.1
|
1.0
|
CA
|
A:ILE20
|
4.3
|
16.1
|
1.0
|
CG1
|
A:VAL137
|
4.3
|
14.1
|
1.0
|
NE2
|
A:GLN19
|
4.3
|
16.5
|
1.0
|
O
|
A:HOH1461
|
4.4
|
21.6
|
1.0
|
C
|
A:VAL137
|
4.4
|
15.6
|
1.0
|
N
|
A:ALA139
|
4.6
|
16.8
|
1.0
|
CA
|
A:VAL137
|
4.6
|
13.8
|
1.0
|
C
|
A:GLN19
|
4.6
|
18.0
|
1.0
|
CA
|
A:GLN19
|
4.6
|
17.8
|
1.0
|
CG2
|
A:THR21
|
4.6
|
14.6
|
1.0
|
CB
|
A:LEU138
|
4.6
|
17.0
|
1.0
|
CA
|
A:ALA139
|
4.9
|
16.7
|
1.0
|
|
Reference:
A.Addlagatta,
R.Gumpena.
Crystal Structure of E. Coli Aminopeptidase N in Complex with L-2,3-Diaminopropionic Acid To Be Published.
Page generated: Mon Oct 7 19:13:51 2024
|