Sodium in PDB 3h09: The Structure of Haemophilus Influenzae IGA1 Protease
Enzymatic activity of The Structure of Haemophilus Influenzae IGA1 Protease
All present enzymatic activity of The Structure of Haemophilus Influenzae IGA1 Protease:
3.4.21.72;
Protein crystallography data
The structure of The Structure of Haemophilus Influenzae IGA1 Protease, PDB code: 3h09
was solved by
T.A.Johnson,
J.Qiu,
A.G.Plaut,
T.Holyoak,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.18 /
1.75
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.385,
131.872,
111.813,
90.00,
113.11,
90.00
|
R / Rfree (%)
|
16.1 /
19
|
Sodium Binding Sites:
The binding sites of Sodium atom in the The Structure of Haemophilus Influenzae IGA1 Protease
(pdb code 3h09). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
The Structure of Haemophilus Influenzae IGA1 Protease, PDB code: 3h09:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 3h09
Go back to
Sodium Binding Sites List in 3h09
Sodium binding site 1 out
of 4 in the The Structure of Haemophilus Influenzae IGA1 Protease
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of The Structure of Haemophilus Influenzae IGA1 Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na2300
b:20.6
occ:1.00
|
O
|
A:THR338
|
2.2
|
4.1
|
1.0
|
O
|
A:HOH1047
|
2.3
|
18.2
|
1.0
|
O
|
A:HOH1873
|
2.3
|
19.2
|
1.0
|
O
|
A:HOH1631
|
2.4
|
12.8
|
1.0
|
O
|
A:ASP335
|
2.5
|
4.3
|
1.0
|
O
|
A:HOH1366
|
2.5
|
15.0
|
1.0
|
O
|
A:HOH1763
|
3.4
|
34.6
|
1.0
|
C
|
A:THR338
|
3.5
|
3.7
|
1.0
|
C
|
A:ASP335
|
3.7
|
4.7
|
1.0
|
OD1
|
A:ASP335
|
4.1
|
11.8
|
1.0
|
CG2
|
A:THR338
|
4.1
|
8.9
|
1.0
|
O
|
A:LYS336
|
4.1
|
5.1
|
1.0
|
N
|
A:THR338
|
4.2
|
4.0
|
1.0
|
CG
|
A:ASP335
|
4.3
|
9.6
|
1.0
|
C
|
A:LYS336
|
4.3
|
4.8
|
1.0
|
OD2
|
A:ASP335
|
4.3
|
12.8
|
1.0
|
CA
|
A:THR338
|
4.3
|
5.3
|
1.0
|
O
|
A:HOH1532
|
4.4
|
17.9
|
1.0
|
N
|
A:ALA339
|
4.4
|
3.0
|
1.0
|
C
|
A:ALA339
|
4.5
|
4.4
|
1.0
|
CA
|
A:LYS336
|
4.5
|
4.7
|
1.0
|
O
|
A:ALA339
|
4.5
|
5.6
|
1.0
|
N
|
A:LYS336
|
4.5
|
3.9
|
1.0
|
CA
|
A:ALA339
|
4.5
|
3.7
|
1.0
|
CA
|
A:ASP335
|
4.6
|
5.8
|
1.0
|
CB
|
A:THR338
|
4.8
|
6.2
|
1.0
|
O
|
A:HOH1673
|
4.8
|
25.7
|
1.0
|
O
|
A:HOH1546
|
4.9
|
22.0
|
1.0
|
N
|
A:ASP337
|
4.9
|
4.1
|
1.0
|
N
|
A:GLY340
|
5.0
|
4.2
|
1.0
|
|
Sodium binding site 2 out
of 4 in 3h09
Go back to
Sodium Binding Sites List in 3h09
Sodium binding site 2 out
of 4 in the The Structure of Haemophilus Influenzae IGA1 Protease
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of The Structure of Haemophilus Influenzae IGA1 Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na2100
b:28.7
occ:1.00
|
O
|
B:HOH1569
|
2.3
|
16.8
|
1.0
|
O
|
B:THR338
|
2.3
|
5.6
|
1.0
|
O
|
B:HOH1192
|
2.3
|
21.2
|
1.0
|
O
|
B:ASP335
|
2.3
|
6.2
|
1.0
|
O
|
B:HOH1496
|
2.4
|
18.7
|
1.0
|
O
|
B:HOH1441
|
2.5
|
12.8
|
1.0
|
O
|
B:HOH1764
|
3.5
|
23.7
|
1.0
|
C
|
B:ASP335
|
3.5
|
6.5
|
1.0
|
C
|
B:THR338
|
3.6
|
5.1
|
1.0
|
CG2
|
B:THR338
|
4.0
|
6.4
|
1.0
|
O
|
B:LYS336
|
4.0
|
6.0
|
1.0
|
OD1
|
B:ASP335
|
4.1
|
14.2
|
1.0
|
CG
|
B:ASP335
|
4.2
|
11.2
|
1.0
|
OD2
|
B:ASP335
|
4.2
|
14.6
|
1.0
|
O
|
B:HOH1167
|
4.2
|
17.5
|
1.0
|
C
|
B:LYS336
|
4.2
|
4.9
|
1.0
|
N
|
B:THR338
|
4.2
|
4.0
|
1.0
|
CA
|
B:LYS336
|
4.4
|
5.6
|
1.0
|
N
|
B:LYS336
|
4.4
|
5.2
|
1.0
|
CA
|
B:THR338
|
4.4
|
5.1
|
1.0
|
O
|
B:HOH1765
|
4.5
|
27.1
|
1.0
|
CA
|
B:ASP335
|
4.5
|
7.4
|
1.0
|
N
|
B:ALA339
|
4.5
|
3.9
|
1.0
|
O
|
B:ALA339
|
4.6
|
5.7
|
1.0
|
C
|
B:ALA339
|
4.6
|
4.6
|
1.0
|
CA
|
B:ALA339
|
4.6
|
4.8
|
1.0
|
O
|
B:HOH1469
|
4.7
|
26.1
|
1.0
|
CB
|
B:THR338
|
4.8
|
5.8
|
1.0
|
N
|
B:ASP337
|
4.9
|
4.3
|
1.0
|
CB
|
B:ASP335
|
5.0
|
7.8
|
1.0
|
|
Sodium binding site 3 out
of 4 in 3h09
Go back to
Sodium Binding Sites List in 3h09
Sodium binding site 3 out
of 4 in the The Structure of Haemophilus Influenzae IGA1 Protease
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of The Structure of Haemophilus Influenzae IGA1 Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na2200
b:30.5
occ:1.00
|
O
|
B:HOH1535
|
2.3
|
22.8
|
1.0
|
O
|
B:HOH1725
|
2.3
|
16.0
|
1.0
|
O
|
B:VAL491
|
2.3
|
7.3
|
1.0
|
O
|
B:HOH1751
|
2.4
|
13.6
|
1.0
|
O
|
B:HOH1228
|
2.5
|
24.9
|
1.0
|
O
|
B:HOH1203
|
2.7
|
21.0
|
1.0
|
C
|
B:VAL491
|
3.5
|
6.9
|
1.0
|
O
|
B:HOH1577
|
4.0
|
26.8
|
1.0
|
O
|
B:LYS512
|
4.1
|
9.7
|
1.0
|
O
|
B:HOH1077
|
4.1
|
29.6
|
1.0
|
N
|
B:VAL491
|
4.2
|
8.3
|
1.0
|
CA
|
B:VAL491
|
4.4
|
7.8
|
1.0
|
O
|
B:HOH1738
|
4.4
|
18.6
|
1.0
|
OE2
|
B:GLU467
|
4.4
|
17.7
|
1.0
|
CB
|
B:LYS492
|
4.4
|
4.8
|
1.0
|
N
|
B:LYS492
|
4.5
|
5.7
|
1.0
|
CG1
|
B:VAL491
|
4.5
|
9.3
|
1.0
|
CA
|
B:LYS492
|
4.6
|
5.1
|
1.0
|
|
Sodium binding site 4 out
of 4 in 3h09
Go back to
Sodium Binding Sites List in 3h09
Sodium binding site 4 out
of 4 in the The Structure of Haemophilus Influenzae IGA1 Protease
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of The Structure of Haemophilus Influenzae IGA1 Protease within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na2300
b:25.1
occ:1.00
|
O
|
B:HOH1045
|
2.3
|
21.5
|
1.0
|
O
|
B:HOH1810
|
2.3
|
22.4
|
1.0
|
O
|
B:HOH1397
|
2.4
|
13.2
|
1.0
|
OG1
|
B:THR52
|
2.5
|
9.2
|
1.0
|
O
|
B:THR52
|
2.5
|
6.1
|
1.0
|
C
|
B:THR52
|
3.3
|
6.1
|
1.0
|
O
|
B:HOH1519
|
3.4
|
34.1
|
1.0
|
N
|
B:THR52
|
3.6
|
6.2
|
1.0
|
CB
|
B:THR52
|
3.6
|
6.9
|
1.0
|
CA
|
B:THR52
|
3.7
|
6.6
|
1.0
|
O
|
B:HOH1416
|
4.1
|
35.8
|
1.0
|
O
|
B:HOH1217
|
4.2
|
26.5
|
1.0
|
ND2
|
B:ASN53
|
4.2
|
4.0
|
1.0
|
N
|
B:ASN53
|
4.4
|
4.8
|
1.0
|
CB
|
B:ASN53
|
4.5
|
5.3
|
1.0
|
CG2
|
B:THR52
|
4.8
|
7.4
|
1.0
|
CG
|
B:ASN53
|
4.8
|
3.8
|
1.0
|
CA
|
B:ASN53
|
4.9
|
4.3
|
1.0
|
C
|
B:ALA51
|
4.9
|
5.5
|
1.0
|
O
|
B:ASN53
|
5.0
|
4.2
|
1.0
|
|
Reference:
T.A.Johnson,
J.Qiu,
A.G.Plaut,
T.Holyoak.
Active-Site Gating Regulates Substrate Selectivity in A Chymotrypsin-Like Serine Protease the Structure of Haemophilus Influenzae Immunoglobulin A1 Protease. J.Mol.Biol. V. 389 559 2009.
ISSN: ISSN 0022-2836
PubMed: 19393662
DOI: 10.1016/J.JMB.2009.04.041
Page generated: Mon Oct 7 10:20:02 2024
|