Sodium in PDB 6i9o: Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis
Protein crystallography data
The structure of Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis, PDB code: 6i9o
was solved by
T.N.Trinh,
C.Cambillau,
A.Roussel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.35 /
1.55
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
208.030,
52.220,
66.560,
90.00,
108.38,
90.00
|
R / Rfree (%)
|
18.4 /
21.1
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis
(pdb code 6i9o). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis, PDB code: 6i9o:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 6i9o
Go back to
Sodium Binding Sites List in 6i9o
Sodium binding site 1 out
of 4 in the Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:34.6
occ:1.00
|
O
|
A:HOH350
|
2.3
|
54.1
|
1.0
|
O
|
A:ALA117
|
2.3
|
35.4
|
1.0
|
O
|
A:LEU123
|
2.3
|
38.1
|
1.0
|
O
|
A:HIS120
|
2.4
|
34.7
|
1.0
|
O
|
A:HOH459
|
2.5
|
41.7
|
1.0
|
O
|
A:HOH425
|
2.7
|
40.4
|
1.0
|
C
|
A:ALA117
|
3.3
|
35.8
|
1.0
|
C
|
A:HIS120
|
3.5
|
36.4
|
1.0
|
C
|
A:LEU123
|
3.6
|
37.4
|
1.0
|
O
|
A:ASP121
|
3.7
|
46.0
|
1.0
|
CA
|
A:ALA117
|
3.8
|
31.9
|
1.0
|
CA
|
A:ASP121
|
3.8
|
38.4
|
1.0
|
C
|
A:ASP121
|
3.8
|
42.8
|
1.0
|
N
|
A:ASP121
|
4.0
|
35.5
|
1.0
|
CB
|
A:ALA117
|
4.0
|
32.7
|
1.0
|
N
|
A:LEU123
|
4.1
|
33.7
|
1.0
|
CA
|
A:LEU123
|
4.4
|
32.8
|
1.0
|
O
|
A:HOH468
|
4.4
|
42.3
|
1.0
|
N
|
A:GLU118
|
4.4
|
31.5
|
1.0
|
CD
|
A:LYS124
|
4.5
|
63.7
|
1.0
|
NZ
|
A:LYS124
|
4.5
|
83.7
|
1.0
|
N
|
A:LYS124
|
4.5
|
34.0
|
1.0
|
N
|
A:PHE122
|
4.6
|
36.1
|
1.0
|
CA
|
A:HIS120
|
4.6
|
32.2
|
1.0
|
N
|
A:HIS120
|
4.6
|
31.9
|
1.0
|
CA
|
A:LYS124
|
4.7
|
33.3
|
1.0
|
CA
|
A:GLU118
|
4.9
|
31.2
|
1.0
|
CE
|
A:LYS124
|
4.9
|
75.8
|
1.0
|
CB
|
A:LEU123
|
4.9
|
31.6
|
1.0
|
O
|
A:HOH397
|
4.9
|
39.4
|
1.0
|
|
Sodium binding site 2 out
of 4 in 6i9o
Go back to
Sodium Binding Sites List in 6i9o
Sodium binding site 2 out
of 4 in the Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na202
b:29.2
occ:1.00
|
O
|
B:LEU123
|
2.2
|
32.1
|
1.0
|
O
|
B:ALA117
|
2.3
|
27.5
|
1.0
|
O
|
B:HOH329
|
2.4
|
41.1
|
1.0
|
O
|
B:HOH438
|
2.4
|
42.2
|
1.0
|
O
|
B:HIS120
|
2.4
|
30.2
|
1.0
|
O
|
B:HOH453
|
2.5
|
33.5
|
1.0
|
C
|
B:ALA117
|
3.3
|
28.7
|
1.0
|
C
|
B:LEU123
|
3.4
|
32.3
|
1.0
|
C
|
B:HIS120
|
3.5
|
30.7
|
1.0
|
CA
|
B:ALA117
|
3.8
|
25.9
|
1.0
|
CA
|
B:ASP121
|
3.9
|
32.9
|
1.0
|
C
|
B:ASP121
|
4.0
|
38.8
|
1.0
|
CB
|
B:ALA117
|
4.0
|
27.2
|
1.0
|
N
|
B:LEU123
|
4.0
|
28.5
|
1.0
|
O
|
B:HOH489
|
4.0
|
51.6
|
1.0
|
O
|
B:ASP121
|
4.1
|
43.9
|
1.0
|
N
|
B:ASP121
|
4.1
|
30.8
|
1.0
|
CA
|
B:LEU123
|
4.3
|
27.9
|
1.0
|
O
|
B:HOH469
|
4.4
|
37.0
|
1.0
|
N
|
B:LYS124
|
4.4
|
29.9
|
1.0
|
N
|
B:GLU118
|
4.5
|
26.8
|
1.0
|
N
|
B:HIS120
|
4.6
|
26.2
|
1.0
|
CA
|
B:HIS120
|
4.6
|
27.6
|
1.0
|
CA
|
B:LYS124
|
4.6
|
29.9
|
1.0
|
N
|
B:PHE122
|
4.7
|
31.4
|
1.0
|
CB
|
B:LEU123
|
4.8
|
26.8
|
1.0
|
CA
|
B:GLU118
|
4.9
|
28.6
|
1.0
|
O
|
B:HOH389
|
5.0
|
33.2
|
1.0
|
|
Sodium binding site 3 out
of 4 in 6i9o
Go back to
Sodium Binding Sites List in 6i9o
Sodium binding site 3 out
of 4 in the Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na202
b:46.0
occ:1.00
|
O
|
C:ALA117
|
2.2
|
36.3
|
1.0
|
O
|
C:LEU123
|
2.2
|
45.2
|
1.0
|
O
|
C:HIS120
|
2.2
|
41.3
|
1.0
|
O
|
C:HOH357
|
2.8
|
69.2
|
1.0
|
O
|
C:HOH433
|
2.9
|
56.2
|
1.0
|
C
|
C:ALA117
|
3.2
|
36.9
|
1.0
|
C
|
C:HIS120
|
3.3
|
42.5
|
1.0
|
C
|
C:LEU123
|
3.4
|
44.8
|
1.0
|
CA
|
C:ALA117
|
3.6
|
33.7
|
1.0
|
O
|
C:ASP121
|
3.8
|
55.1
|
1.0
|
CA
|
C:ASP121
|
3.8
|
46.2
|
1.0
|
C
|
C:ASP121
|
3.8
|
52.1
|
1.0
|
N
|
C:ASP121
|
3.9
|
42.7
|
1.0
|
N
|
C:LEU123
|
3.9
|
41.6
|
1.0
|
CB
|
C:ALA117
|
3.9
|
35.4
|
1.0
|
CA
|
C:LEU123
|
4.2
|
40.8
|
1.0
|
N
|
C:GLU118
|
4.4
|
32.5
|
1.0
|
CA
|
C:HIS120
|
4.4
|
36.6
|
1.0
|
N
|
C:HIS120
|
4.5
|
35.1
|
1.0
|
N
|
C:LYS124
|
4.5
|
40.9
|
1.0
|
N
|
C:PHE122
|
4.5
|
46.4
|
1.0
|
NZ
|
C:LYS124
|
4.5
|
0.2
|
1.0
|
O
|
C:HOH442
|
4.6
|
49.2
|
1.0
|
CD
|
C:LYS124
|
4.6
|
74.6
|
1.0
|
CB
|
C:LEU123
|
4.7
|
38.6
|
1.0
|
CA
|
C:LYS124
|
4.7
|
40.4
|
1.0
|
CA
|
C:GLU118
|
4.9
|
32.5
|
1.0
|
CE
|
C:LYS124
|
4.9
|
91.6
|
1.0
|
C
|
C:PHE122
|
5.0
|
47.2
|
1.0
|
N
|
C:ALA117
|
5.0
|
32.5
|
1.0
|
|
Sodium binding site 4 out
of 4 in 6i9o
Go back to
Sodium Binding Sites List in 6i9o
Sodium binding site 4 out
of 4 in the Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na202
b:37.4
occ:1.00
|
O
|
D:ALA117
|
2.2
|
35.8
|
1.0
|
O
|
D:HIS120
|
2.2
|
39.4
|
1.0
|
O
|
D:LEU123
|
2.4
|
37.0
|
1.0
|
O
|
D:HOH431
|
2.7
|
47.2
|
1.0
|
C
|
D:ALA117
|
3.3
|
35.1
|
1.0
|
C
|
D:HIS120
|
3.3
|
38.7
|
1.0
|
C
|
D:LEU123
|
3.6
|
38.9
|
1.0
|
CA
|
D:ASP121
|
3.8
|
38.9
|
1.0
|
CA
|
D:ALA117
|
3.8
|
29.6
|
1.0
|
O
|
D:ASP121
|
3.8
|
46.6
|
1.0
|
C
|
D:ASP121
|
3.9
|
44.7
|
1.0
|
N
|
D:ASP121
|
3.9
|
37.9
|
1.0
|
N
|
D:LEU123
|
4.0
|
37.0
|
1.0
|
CB
|
D:ALA117
|
4.1
|
31.1
|
1.0
|
CA
|
D:LEU123
|
4.3
|
34.1
|
1.0
|
CA
|
D:HIS120
|
4.4
|
34.5
|
1.0
|
N
|
D:HIS120
|
4.4
|
34.2
|
1.0
|
N
|
D:GLU118
|
4.4
|
32.5
|
1.0
|
NZ
|
D:LYS124
|
4.5
|
64.2
|
1.0
|
N
|
D:PHE122
|
4.6
|
39.7
|
1.0
|
CD
|
D:LYS124
|
4.6
|
52.5
|
1.0
|
N
|
D:LYS124
|
4.6
|
35.7
|
1.0
|
O
|
D:HOH370
|
4.7
|
51.7
|
1.0
|
CA
|
D:GLU118
|
4.8
|
34.1
|
1.0
|
CB
|
D:LEU123
|
4.8
|
31.2
|
1.0
|
CA
|
D:LYS124
|
4.8
|
35.4
|
1.0
|
C
|
D:GLU118
|
4.9
|
38.1
|
1.0
|
CE
|
D:LYS124
|
4.9
|
59.5
|
1.0
|
|
Reference:
T.N.Trinh,
C.Cambillau,
A.Roussel.
Structure of A PG1058 Domain, A Protein of T9SS From Porphyromonas Gingivalis To Be Published.
Page generated: Tue Dec 15 12:23:53 2020
|