Sodium in PDB 4xo4: Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine
Enzymatic activity of Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine
All present enzymatic activity of Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine:
3.4.11.2;
Protein crystallography data
The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine, PDB code: 4xo4
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)
|
19.95 /
2.18
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
120.509,
120.509,
170.283,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
13.2 /
17
|
Other elements in 4xo4:
The structure of Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine 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- Methionine
(pdb code 4xo4). 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 E. Coli Aminopeptidase N in Complex with L- Methionine, PDB code: 4xo4:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
Sodium binding site 1 out
of 7 in 4xo4
Go back to
Sodium Binding Sites List in 4xo4
Sodium binding site 1 out
of 7 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine
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- Methionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na905
b:24.2
occ:1.00
|
O
|
A:GLY335
|
2.3
|
19.7
|
1.0
|
O
|
A:HOH1674
|
2.3
|
31.9
|
1.0
|
O
|
A:SER332
|
2.5
|
20.2
|
1.0
|
O
|
A:HOH1573
|
2.5
|
23.2
|
1.0
|
O
|
A:HOH1515
|
2.6
|
23.2
|
1.0
|
O
|
A:ASP333
|
2.7
|
20.7
|
1.0
|
C
|
A:ASP333
|
3.4
|
21.1
|
1.0
|
C
|
A:GLY335
|
3.4
|
21.2
|
1.0
|
C
|
A:SER332
|
3.6
|
20.5
|
1.0
|
O
|
A:HOH1256
|
3.6
|
45.5
|
1.0
|
CA
|
A:ASP333
|
3.7
|
19.5
|
1.0
|
N
|
A:GLY335
|
3.9
|
21.4
|
1.0
|
N
|
A:ARG337
|
3.9
|
20.2
|
1.0
|
O
|
A:HOH1625
|
3.9
|
43.8
|
1.0
|
N
|
A:ASP333
|
4.1
|
19.1
|
1.0
|
O
|
A:HOH1292
|
4.2
|
34.7
|
1.0
|
C
|
A:LEU334
|
4.2
|
21.7
|
1.0
|
N
|
A:LEU334
|
4.3
|
19.8
|
1.0
|
CA
|
A:GLY335
|
4.3
|
20.8
|
1.0
|
N
|
A:SER336
|
4.3
|
22.8
|
1.0
|
CA
|
A:SER336
|
4.4
|
23.1
|
1.0
|
C
|
A:SER336
|
4.5
|
22.1
|
1.0
|
CB
|
A:ARG337
|
4.5
|
21.2
|
1.0
|
CA
|
A:ARG337
|
4.7
|
21.4
|
1.0
|
O
|
A:LEU334
|
4.7
|
21.6
|
1.0
|
CA
|
A:LEU334
|
4.7
|
21.7
|
1.0
|
CA
|
A:SER332
|
4.8
|
20.3
|
1.0
|
|
Sodium binding site 2 out
of 7 in 4xo4
Go back to
Sodium Binding Sites List in 4xo4
Sodium binding site 2 out
of 7 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine
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- Methionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na906
b:22.6
occ:1.00
|
O
|
A:HOH1668
|
2.2
|
33.1
|
1.0
|
O
|
A:LEU138
|
2.3
|
19.3
|
1.0
|
O
|
A:ILE20
|
2.3
|
19.6
|
1.0
|
O
|
A:HOH1482
|
2.4
|
18.2
|
1.0
|
OE1
|
A:GLN19
|
2.4
|
20.2
|
1.0
|
CD
|
A:GLN19
|
3.3
|
20.3
|
1.0
|
C
|
A:LEU138
|
3.4
|
19.2
|
1.0
|
C
|
A:ILE20
|
3.4
|
18.6
|
1.0
|
N
|
A:LEU138
|
3.5
|
18.6
|
1.0
|
O
|
A:HOH1715
|
3.9
|
42.9
|
1.0
|
N
|
A:ILE20
|
4.0
|
18.0
|
1.0
|
CA
|
A:LEU138
|
4.0
|
19.5
|
1.0
|
CB
|
A:GLN19
|
4.1
|
19.7
|
1.0
|
O
|
A:HOH1702
|
4.1
|
38.8
|
1.0
|
NE2
|
A:GLN19
|
4.2
|
17.5
|
1.0
|
N
|
A:THR21
|
4.2
|
18.9
|
1.0
|
CG
|
A:GLN19
|
4.2
|
20.2
|
1.0
|
CA
|
A:THR21
|
4.2
|
19.3
|
1.0
|
C
|
A:VAL137
|
4.3
|
18.1
|
1.0
|
CA
|
A:ILE20
|
4.3
|
18.4
|
1.0
|
CG1
|
A:VAL137
|
4.4
|
17.8
|
1.0
|
N
|
A:ALA139
|
4.4
|
17.8
|
1.0
|
CA
|
A:VAL137
|
4.5
|
17.3
|
1.0
|
CB
|
A:LEU138
|
4.6
|
22.1
|
1.0
|
CA
|
A:ALA139
|
4.7
|
19.1
|
1.0
|
CA
|
A:GLN19
|
4.7
|
18.5
|
1.0
|
C
|
A:GLN19
|
4.7
|
19.7
|
1.0
|
CG2
|
A:THR21
|
4.9
|
22.5
|
1.0
|
CB
|
A:ALA139
|
5.0
|
18.7
|
1.0
|
|
Sodium binding site 3 out
of 7 in 4xo4
Go back to
Sodium Binding Sites List in 4xo4
Sodium binding site 3 out
of 7 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine
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- Methionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na907
b:28.0
occ:1.00
|
OE2
|
A:GLU264
|
2.7
|
20.3
|
1.0
|
OH
|
A:TYR185
|
2.7
|
15.7
|
1.0
|
OD1
|
A:ASN306
|
2.8
|
18.0
|
1.0
|
O
|
A:GLY305
|
3.2
|
16.6
|
1.0
|
C
|
A:GLY305
|
3.2
|
16.7
|
1.0
|
CA
|
A:GLY305
|
3.3
|
15.5
|
1.0
|
CG
|
A:GLU264
|
3.4
|
17.7
|
1.0
|
CD
|
A:GLU264
|
3.4
|
19.9
|
1.0
|
CE1
|
A:TYR185
|
3.5
|
15.5
|
1.0
|
CD
|
A:LYS319
|
3.6
|
17.0
|
1.0
|
CZ
|
A:TYR185
|
3.6
|
16.9
|
1.0
|
CD2
|
A:LEU186
|
3.8
|
17.2
|
1.0
|
CE
|
A:LYS319
|
3.8
|
15.8
|
1.0
|
N
|
A:ASN306
|
3.9
|
16.9
|
1.0
|
NZ
|
A:LYS319
|
4.0
|
15.6
|
1.0
|
CG
|
A:ASN306
|
4.0
|
16.8
|
1.0
|
CD1
|
A:LEU186
|
4.2
|
19.9
|
1.0
|
ND1
|
A:HIS301
|
4.2
|
15.8
|
1.0
|
CG
|
A:LEU186
|
4.4
|
18.6
|
1.0
|
CA
|
A:ASN306
|
4.5
|
17.4
|
1.0
|
CG
|
A:HIS301
|
4.5
|
14.7
|
1.0
|
OE1
|
A:GLU264
|
4.6
|
21.7
|
1.0
|
O
|
A:HIS301
|
4.7
|
15.0
|
1.0
|
CB
|
A:HIS301
|
4.7
|
14.3
|
1.0
|
N
|
A:GLY305
|
4.7
|
14.9
|
1.0
|
CE1
|
A:HIS301
|
4.7
|
16.3
|
1.0
|
CD1
|
A:TYR185
|
4.8
|
15.4
|
1.0
|
CE2
|
A:TYR185
|
4.9
|
15.5
|
1.0
|
CG
|
A:LYS319
|
4.9
|
16.8
|
1.0
|
CB
|
A:ASN306
|
4.9
|
16.9
|
1.0
|
CB
|
A:GLU264
|
4.9
|
17.5
|
1.0
|
ND2
|
A:ASN306
|
4.9
|
18.0
|
1.0
|
OG1
|
A:THR309
|
5.0
|
20.5
|
1.0
|
|
Sodium binding site 4 out
of 7 in 4xo4
Go back to
Sodium Binding Sites List in 4xo4
Sodium binding site 4 out
of 7 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine
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- Methionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na908
b:48.4
occ:1.00
|
OG
|
A:SER570
|
2.5
|
24.7
|
1.0
|
OD1
|
A:ASP566
|
2.6
|
24.4
|
1.0
|
O
|
A:HOH1665
|
2.7
|
35.6
|
1.0
|
O
|
A:HOH1713
|
2.7
|
42.9
|
1.0
|
O
|
A:ASP566
|
2.9
|
18.4
|
1.0
|
CG
|
A:ASP566
|
3.5
|
24.0
|
1.0
|
O
|
A:HOH1593
|
3.6
|
42.6
|
1.0
|
N
|
A:SER570
|
3.6
|
19.3
|
1.0
|
CB
|
A:SER570
|
3.7
|
20.5
|
1.0
|
NH2
|
A:ARG349
|
3.7
|
31.5
|
1.0
|
C
|
A:ASP566
|
3.8
|
20.9
|
1.0
|
NH1
|
A:ARG349
|
3.9
|
29.0
|
1.0
|
CA
|
A:SER570
|
3.9
|
20.4
|
1.0
|
CB
|
A:GLN569
|
3.9
|
25.2
|
1.0
|
CZ
|
A:ARG349
|
4.1
|
27.2
|
1.0
|
OD2
|
A:ASP566
|
4.1
|
31.7
|
1.0
|
CA
|
A:ASP566
|
4.2
|
19.8
|
1.0
|
C
|
A:GLN569
|
4.3
|
23.4
|
1.0
|
O
|
A:HOH1561
|
4.3
|
45.5
|
1.0
|
CB
|
A:ASP566
|
4.4
|
21.8
|
1.0
|
O
|
A:HOH1358
|
4.4
|
41.3
|
1.0
|
CA
|
A:GLN569
|
4.7
|
22.6
|
1.0
|
N
|
A:ALA567
|
4.8
|
20.1
|
1.0
|
CG
|
A:GLN569
|
5.0
|
26.7
|
1.0
|
|
Sodium binding site 5 out
of 7 in 4xo4
Go back to
Sodium Binding Sites List in 4xo4
Sodium binding site 5 out
of 7 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine
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 E. Coli Aminopeptidase N in Complex with L- Methionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na909
b:45.2
occ:1.00
|
OD1
|
A:ASP432
|
2.3
|
31.9
|
1.0
|
O
|
A:HOH1659
|
2.5
|
43.4
|
1.0
|
OG
|
A:SER434
|
2.5
|
34.7
|
1.0
|
O
|
A:HOH1357
|
2.6
|
37.3
|
1.0
|
OE1
|
A:GLU426
|
2.7
|
25.0
|
1.0
|
CD
|
A:GLU426
|
3.2
|
31.3
|
1.0
|
CG
|
A:ASP432
|
3.5
|
30.7
|
1.0
|
CB
|
A:SER434
|
3.7
|
24.3
|
1.0
|
OE2
|
A:GLU426
|
3.7
|
34.3
|
1.0
|
O
|
A:HOH1235
|
3.8
|
44.4
|
1.0
|
N
|
A:SER434
|
3.8
|
17.6
|
1.0
|
NH1
|
A:ARG437
|
4.0
|
47.1
|
0.5
|
N
|
A:LEU433
|
4.1
|
21.4
|
1.0
|
CA
|
A:SER434
|
4.1
|
21.6
|
1.0
|
CG
|
A:GLU426
|
4.2
|
30.0
|
1.0
|
OD2
|
A:ASP432
|
4.2
|
38.1
|
1.0
|
CA
|
A:ASP432
|
4.3
|
27.9
|
1.0
|
CB
|
A:ASP432
|
4.3
|
28.7
|
1.0
|
NH1
|
A:ARG437
|
4.6
|
12.6
|
0.5
|
C
|
A:ASP432
|
4.6
|
24.4
|
1.0
|
O
|
A:HOH1572
|
4.6
|
33.2
|
1.0
|
C
|
A:LEU433
|
4.7
|
19.6
|
1.0
|
CA
|
A:LEU433
|
5.0
|
21.1
|
1.0
|
|
Sodium binding site 6 out
of 7 in 4xo4
Go back to
Sodium Binding Sites List in 4xo4
Sodium binding site 6 out
of 7 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine
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 E. Coli Aminopeptidase N in Complex with L- Methionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na910
b:42.4
occ:1.00
|
O
|
A:HOH1474
|
2.1
|
27.5
|
1.0
|
OD1
|
A:ASP452
|
2.4
|
29.0
|
1.0
|
O
|
A:HOH1669
|
2.5
|
30.9
|
1.0
|
O
|
A:ASP452
|
2.8
|
22.7
|
1.0
|
O
|
A:HOH1316
|
2.9
|
31.9
|
1.0
|
O
|
A:HOH1496
|
3.3
|
39.3
|
1.0
|
CG
|
A:ASP452
|
3.6
|
26.2
|
1.0
|
C
|
A:ASP452
|
3.6
|
23.5
|
1.0
|
O
|
A:HOH1035
|
3.6
|
38.6
|
1.0
|
N
|
A:ASP452
|
3.7
|
24.6
|
1.0
|
CA
|
A:MET903
|
3.9
|
45.0
|
1.0
|
CB
|
A:MET903
|
4.0
|
40.9
|
1.0
|
N
|
A:MET903
|
4.0
|
44.3
|
1.0
|
CA
|
A:ASP452
|
4.0
|
23.5
|
1.0
|
O
|
A:HOH1757
|
4.4
|
33.8
|
1.0
|
CB
|
A:ASP452
|
4.4
|
25.1
|
1.0
|
OD2
|
A:ASP452
|
4.5
|
23.9
|
1.0
|
N
|
A:ASP453
|
4.8
|
25.3
|
1.0
|
C
|
A:LYS451
|
4.8
|
27.1
|
1.0
|
O
|
A:HOH1345
|
4.9
|
23.2
|
1.0
|
O
|
A:HOH1397
|
5.0
|
34.9
|
1.0
|
|
Sodium binding site 7 out
of 7 in 4xo4
Go back to
Sodium Binding Sites List in 4xo4
Sodium binding site 7 out
of 7 in the Crystal Structure of E. Coli Aminopeptidase N in Complex with L- Methionine
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 E. Coli Aminopeptidase N in Complex with L- Methionine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na911
b:51.6
occ:1.00
|
O
|
A:HOH1647
|
2.5
|
35.8
|
1.0
|
OD1
|
A:ASN343
|
2.6
|
29.7
|
1.0
|
O
|
A:HOH1603
|
2.8
|
50.9
|
1.0
|
OE1
|
A:GLU615
|
2.9
|
32.6
|
1.0
|
OE2
|
A:GLU615
|
2.9
|
37.3
|
1.0
|
CD
|
A:GLU615
|
3.3
|
29.1
|
1.0
|
CG
|
A:ASN343
|
3.5
|
26.0
|
1.0
|
ND2
|
A:ASN343
|
3.8
|
29.8
|
1.0
|
NE
|
A:ARG346
|
3.8
|
25.4
|
1.0
|
CD
|
A:ARG346
|
4.3
|
24.0
|
1.0
|
CG2
|
A:THR618
|
4.5
|
31.0
|
1.0
|
CZ
|
A:ARG346
|
4.5
|
29.5
|
1.0
|
NH2
|
A:ARG346
|
4.7
|
30.3
|
1.0
|
CG
|
A:GLU615
|
4.8
|
25.6
|
1.0
|
CB
|
A:THR618
|
4.9
|
30.3
|
1.0
|
CB
|
A:ASN343
|
4.9
|
24.5
|
1.0
|
OG1
|
A:THR618
|
5.0
|
29.8
|
1.0
|
|
Reference:
A.Addlagatta,
R.Gumpena.
Crystal Structure of E. Coli Aminopeptidase N in Complex with L-Methionine To Be Published.
Page generated: Mon Oct 7 19:19:04 2024
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