Sodium in PDB 9f7m: Blastococcus Orn Bound to Pgg
Protein crystallography data
The structure of Blastococcus Orn Bound to Pgg, PDB code: 9f7m
was solved by
S.Mortensen,
H.Sondermann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.28 /
1.65
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
79.57,
117.701,
99.466,
90,
93.62,
90
|
R / Rfree (%)
|
17.1 /
19.1
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Blastococcus Orn Bound to Pgg
(pdb code 9f7m). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the
Blastococcus Orn Bound to Pgg, PDB code: 9f7m:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 10 in 9f7m
Go back to
Sodium Binding Sites List in 9f7m
Sodium binding site 1 out
of 10 in the Blastococcus Orn Bound to Pgg
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na301
b:25.8
occ:0.76
|
OD2
|
A:ASP165
|
2.3
|
41.9
|
1.0
|
OP1
|
I:G603
|
2.3
|
23.2
|
0.9
|
OE2
|
A:GLU14
|
2.3
|
36.5
|
1.0
|
O
|
A:HOH498
|
2.4
|
37.9
|
1.0
|
O
|
A:HOH546
|
3.1
|
37.3
|
1.0
|
OD2
|
A:ASP12
|
3.1
|
32.9
|
1.0
|
CG
|
A:ASP165
|
3.2
|
38.7
|
1.0
|
OD1
|
A:ASP12
|
3.2
|
32.0
|
1.0
|
CD
|
A:GLU14
|
3.4
|
32.0
|
1.0
|
CG
|
A:ASP12
|
3.5
|
30.1
|
1.0
|
P
|
I:G603
|
3.6
|
22.0
|
0.9
|
OE1
|
A:GLU14
|
3.7
|
26.1
|
1.0
|
CB
|
A:ASP165
|
3.7
|
28.8
|
1.0
|
NA
|
I:NA701
|
3.8
|
21.8
|
0.7
|
O
|
A:HOH550
|
4.0
|
34.4
|
1.0
|
O
|
A:HOH427
|
4.0
|
42.7
|
1.0
|
OD1
|
A:ASP165
|
4.2
|
43.5
|
1.0
|
O5'
|
I:G603
|
4.2
|
23.9
|
1.0
|
O
|
I:HOH805
|
4.3
|
43.7
|
1.0
|
OP2
|
I:G603
|
4.3
|
20.1
|
0.8
|
O
|
A:HOH563
|
4.4
|
47.0
|
1.0
|
O
|
A:HOH604
|
4.4
|
46.7
|
1.0
|
C5'
|
I:G603
|
4.5
|
24.4
|
0.9
|
O
|
A:CYS13
|
4.5
|
24.8
|
1.0
|
O
|
I:HOH804
|
4.6
|
39.7
|
1.0
|
CG
|
A:GLU14
|
4.7
|
28.6
|
1.0
|
O3'
|
I:G602
|
4.7
|
23.0
|
0.9
|
O
|
A:HOH452
|
4.8
|
26.9
|
1.0
|
CB
|
A:ASP12
|
4.9
|
23.4
|
1.0
|
|
Sodium binding site 2 out
of 10 in 9f7m
Go back to
Sodium Binding Sites List in 9f7m
Sodium binding site 2 out
of 10 in the Blastococcus Orn Bound to Pgg
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Na701
b:21.8
occ:0.74
|
O
|
A:HOH418
|
2.2
|
28.1
|
1.0
|
OD1
|
A:ASP12
|
2.3
|
32.0
|
1.0
|
O
|
A:HOH550
|
2.4
|
34.4
|
1.0
|
O
|
A:HOH452
|
2.4
|
26.9
|
1.0
|
OP1
|
I:G603
|
2.4
|
23.2
|
0.9
|
O3'
|
I:G602
|
2.6
|
23.0
|
0.9
|
P
|
I:G603
|
3.2
|
22.0
|
0.9
|
CG
|
A:ASP12
|
3.6
|
30.1
|
1.0
|
NA
|
A:NA301
|
3.8
|
25.8
|
0.8
|
C3'
|
I:G602
|
3.9
|
21.8
|
1.0
|
O
|
A:HOH518
|
3.9
|
25.9
|
1.0
|
O2'
|
I:G602
|
3.9
|
21.1
|
0.8
|
O
|
A:HOH492
|
4.1
|
30.3
|
1.0
|
OD2
|
A:ASP113
|
4.1
|
27.3
|
1.0
|
O
|
A:HOH498
|
4.1
|
37.9
|
1.0
|
C5'
|
I:G603
|
4.2
|
24.4
|
0.9
|
C4'
|
I:G602
|
4.2
|
21.1
|
0.9
|
O5'
|
I:G603
|
4.2
|
23.9
|
1.0
|
OD2
|
A:ASP12
|
4.3
|
32.9
|
1.0
|
OD1
|
A:ASP113
|
4.3
|
26.6
|
1.0
|
O
|
A:CYS13
|
4.3
|
24.8
|
1.0
|
O
|
A:ASN108
|
4.3
|
22.0
|
1.0
|
OP2
|
I:G603
|
4.4
|
20.1
|
0.8
|
C2'
|
I:G602
|
4.5
|
19.1
|
1.0
|
CB
|
A:ASP12
|
4.6
|
23.4
|
1.0
|
CG
|
A:ASP113
|
4.6
|
26.9
|
1.0
|
O
|
I:HOH802
|
4.8
|
27.4
|
1.0
|
C5'
|
I:G602
|
4.8
|
21.3
|
1.0
|
N
|
A:CYS13
|
4.8
|
23.3
|
1.0
|
CA
|
A:ASP12
|
4.8
|
23.8
|
1.0
|
|
Sodium binding site 3 out
of 10 in 9f7m
Go back to
Sodium Binding Sites List in 9f7m
Sodium binding site 3 out
of 10 in the Blastococcus Orn Bound to Pgg
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Na701
b:24.5
occ:0.76
|
O
|
B:HOH308
|
2.3
|
30.2
|
1.0
|
OD1
|
B:ASP12
|
2.3
|
28.1
|
1.0
|
O
|
B:HOH463
|
2.4
|
35.6
|
1.0
|
O
|
B:HOH398
|
2.4
|
26.2
|
1.0
|
OP1
|
J:G603
|
2.6
|
28.4
|
1.0
|
O3'
|
J:G602
|
2.6
|
22.5
|
1.0
|
P
|
J:G603
|
3.2
|
23.6
|
1.0
|
CG
|
B:ASP12
|
3.5
|
27.9
|
1.0
|
C3'
|
J:G602
|
3.8
|
22.6
|
1.0
|
O2'
|
J:G602
|
3.8
|
22.9
|
1.0
|
OD2
|
B:ASP12
|
4.0
|
31.3
|
1.0
|
C4'
|
J:G602
|
4.0
|
22.2
|
1.0
|
O
|
J:HOH801
|
4.0
|
26.1
|
1.0
|
O
|
B:HOH442
|
4.1
|
27.0
|
1.0
|
C5'
|
J:G603
|
4.1
|
23.4
|
1.0
|
OD2
|
B:ASP113
|
4.2
|
29.4
|
1.0
|
O5'
|
J:G603
|
4.2
|
25.1
|
1.0
|
O
|
B:HOH372
|
4.2
|
29.2
|
1.0
|
OD1
|
B:ASP113
|
4.3
|
29.0
|
1.0
|
O
|
B:ASN108
|
4.3
|
24.3
|
1.0
|
O
|
B:CYS13
|
4.3
|
23.8
|
1.0
|
C2'
|
J:G602
|
4.4
|
22.4
|
1.0
|
OP2
|
J:G603
|
4.5
|
24.8
|
1.0
|
CG
|
B:ASP113
|
4.7
|
29.8
|
1.0
|
C5'
|
J:G602
|
4.7
|
22.6
|
1.0
|
CB
|
B:ASP12
|
4.7
|
24.6
|
1.0
|
O
|
J:HOH803
|
4.8
|
31.7
|
1.0
|
N
|
B:CYS13
|
4.8
|
24.7
|
1.0
|
CA
|
B:ASP12
|
5.0
|
24.3
|
1.0
|
|
Sodium binding site 4 out
of 10 in 9f7m
Go back to
Sodium Binding Sites List in 9f7m
Sodium binding site 4 out
of 10 in the Blastococcus Orn Bound to Pgg
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na301
b:27.8
occ:0.68
|
OP1
|
K:G603
|
2.3
|
25.7
|
1.0
|
OE2
|
C:GLU14
|
2.3
|
36.4
|
1.0
|
OD2
|
C:ASP165
|
2.5
|
44.6
|
1.0
|
OD2
|
C:ASP12
|
2.7
|
37.2
|
1.0
|
O
|
C:HOH529
|
2.9
|
41.7
|
1.0
|
CG
|
C:ASP165
|
3.3
|
39.2
|
1.0
|
OD1
|
C:ASP12
|
3.4
|
31.6
|
1.0
|
CD
|
C:GLU14
|
3.4
|
33.0
|
1.0
|
CG
|
C:ASP12
|
3.4
|
32.8
|
1.0
|
P
|
K:G603
|
3.6
|
23.1
|
1.0
|
OE1
|
C:GLU14
|
3.7
|
27.5
|
1.0
|
CB
|
C:ASP165
|
3.7
|
29.3
|
1.0
|
NA
|
K:NA701
|
3.9
|
22.4
|
0.7
|
O5'
|
K:G603
|
4.2
|
25.8
|
1.0
|
O
|
C:HOH553
|
4.3
|
42.8
|
1.0
|
OD1
|
C:ASP165
|
4.3
|
40.3
|
1.0
|
O
|
K:HOH809
|
4.3
|
36.0
|
1.0
|
OP2
|
K:G603
|
4.3
|
23.2
|
1.0
|
O
|
C:CYS13
|
4.5
|
24.7
|
1.0
|
C5'
|
K:G603
|
4.5
|
26.0
|
1.0
|
O
|
K:HOH808
|
4.5
|
42.2
|
1.0
|
CG
|
C:GLU14
|
4.7
|
27.7
|
1.0
|
O3'
|
K:G602
|
4.7
|
23.1
|
1.0
|
CB
|
C:ASP12
|
4.9
|
26.4
|
1.0
|
O
|
C:HOH459
|
4.9
|
26.9
|
1.0
|
CA
|
C:ALA162
|
5.0
|
30.2
|
1.0
|
|
Sodium binding site 5 out
of 10 in 9f7m
Go back to
Sodium Binding Sites List in 9f7m
Sodium binding site 5 out
of 10 in the Blastococcus Orn Bound to Pgg
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Na701
b:22.4
occ:0.70
|
OD1
|
C:ASP12
|
2.2
|
31.6
|
1.0
|
O
|
C:HOH406
|
2.3
|
30.4
|
1.0
|
O
|
C:HOH459
|
2.3
|
26.9
|
1.0
|
O
|
K:HOH809
|
2.3
|
36.0
|
1.0
|
OP1
|
K:G603
|
2.5
|
25.7
|
1.0
|
O3'
|
K:G602
|
2.6
|
23.1
|
1.0
|
P
|
K:G603
|
3.1
|
23.1
|
1.0
|
CG
|
C:ASP12
|
3.5
|
32.8
|
1.0
|
C3'
|
K:G602
|
3.8
|
22.3
|
1.0
|
O
|
C:HOH487
|
3.9
|
28.6
|
1.0
|
O2'
|
K:G602
|
3.9
|
26.7
|
1.0
|
NA
|
C:NA301
|
3.9
|
27.8
|
0.7
|
O
|
C:HOH479
|
4.0
|
31.6
|
1.0
|
C4'
|
K:G602
|
4.1
|
22.1
|
1.0
|
OD2
|
C:ASP113
|
4.1
|
28.5
|
1.0
|
OD2
|
C:ASP12
|
4.1
|
37.2
|
1.0
|
O5'
|
K:G603
|
4.1
|
25.8
|
1.0
|
C5'
|
K:G603
|
4.2
|
26.0
|
1.0
|
O
|
C:ASN108
|
4.2
|
22.9
|
1.0
|
O
|
C:CYS13
|
4.3
|
24.7
|
1.0
|
OP2
|
K:G603
|
4.3
|
23.2
|
1.0
|
OD1
|
C:ASP113
|
4.3
|
29.9
|
1.0
|
C2'
|
K:G602
|
4.5
|
25.8
|
1.0
|
CB
|
C:ASP12
|
4.6
|
26.4
|
1.0
|
O
|
K:HOH802
|
4.6
|
29.3
|
1.0
|
CG
|
C:ASP113
|
4.6
|
30.6
|
1.0
|
C5'
|
K:G602
|
4.7
|
24.2
|
1.0
|
N
|
C:CYS13
|
4.8
|
25.8
|
1.0
|
CA
|
C:ASP12
|
4.8
|
24.3
|
1.0
|
|
Sodium binding site 6 out
of 10 in 9f7m
Go back to
Sodium Binding Sites List in 9f7m
Sodium binding site 6 out
of 10 in the Blastococcus Orn Bound to Pgg
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Na701
b:23.5
occ:0.70
|
O
|
D:HOH1432
|
2.3
|
29.4
|
1.0
|
OD1
|
D:ASP12
|
2.3
|
26.1
|
1.0
|
O
|
D:HOH1465
|
2.4
|
26.2
|
1.0
|
O
|
L:HOH811
|
2.5
|
33.6
|
1.0
|
OP1
|
L:G603
|
2.5
|
28.3
|
1.0
|
O3'
|
L:G602
|
2.5
|
25.3
|
1.0
|
P
|
L:G603
|
3.1
|
24.5
|
1.0
|
CG
|
D:ASP12
|
3.5
|
29.9
|
1.0
|
O2'
|
L:G602
|
3.7
|
26.8
|
1.0
|
C3'
|
L:G602
|
3.7
|
23.1
|
1.0
|
C4'
|
L:G602
|
3.9
|
23.4
|
1.0
|
O
|
D:HOH1530
|
4.0
|
26.1
|
1.0
|
OD2
|
D:ASP12
|
4.1
|
30.9
|
1.0
|
O
|
D:HOH1487
|
4.1
|
27.8
|
1.0
|
C5'
|
L:G603
|
4.1
|
24.1
|
1.0
|
O
|
D:HOH1407
|
4.1
|
28.0
|
1.0
|
O5'
|
L:G603
|
4.1
|
25.1
|
1.0
|
OD1
|
D:ASP113
|
4.1
|
27.4
|
1.0
|
O
|
D:CYS13
|
4.2
|
26.1
|
1.0
|
OD2
|
D:ASP113
|
4.3
|
28.7
|
1.0
|
O
|
D:ASN108
|
4.3
|
24.5
|
1.0
|
OP2
|
L:G603
|
4.3
|
24.0
|
1.0
|
C2'
|
L:G602
|
4.4
|
22.9
|
1.0
|
C5'
|
L:G602
|
4.6
|
22.1
|
1.0
|
CG
|
D:ASP113
|
4.6
|
26.5
|
1.0
|
CB
|
D:ASP12
|
4.7
|
23.5
|
1.0
|
O
|
L:HOH804
|
4.7
|
26.1
|
1.0
|
N
|
D:CYS13
|
4.7
|
26.6
|
1.0
|
CA
|
D:ASP12
|
4.9
|
25.3
|
1.0
|
|
Sodium binding site 7 out
of 10 in 9f7m
Go back to
Sodium Binding Sites List in 9f7m
Sodium binding site 7 out
of 10 in the Blastococcus Orn Bound to Pgg
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Na701
b:23.4
occ:0.85
|
OD1
|
E:ASP12
|
2.3
|
24.7
|
1.0
|
O
|
E:HOH321
|
2.4
|
27.7
|
1.0
|
O
|
E:HOH367
|
2.4
|
23.7
|
1.0
|
O
|
E:HOH466
|
2.5
|
31.2
|
1.0
|
OP1
|
M:G603
|
2.5
|
25.7
|
1.0
|
O3'
|
M:G602
|
2.5
|
21.8
|
1.0
|
P
|
M:G603
|
3.1
|
23.6
|
1.0
|
CG
|
E:ASP12
|
3.5
|
25.7
|
1.0
|
O2'
|
M:G602
|
3.7
|
25.3
|
1.0
|
C3'
|
M:G602
|
3.7
|
19.6
|
1.0
|
C4'
|
M:G602
|
4.0
|
21.1
|
1.0
|
O
|
E:HOH304
|
4.0
|
25.2
|
1.0
|
OD2
|
E:ASP12
|
4.0
|
26.9
|
1.0
|
C5'
|
M:G603
|
4.1
|
24.2
|
1.0
|
O5'
|
M:G603
|
4.1
|
24.9
|
1.0
|
OD2
|
E:ASP113
|
4.1
|
27.4
|
1.0
|
O
|
E:HOH435
|
4.1
|
27.0
|
1.0
|
O
|
E:HOH365
|
4.2
|
27.3
|
1.0
|
O
|
E:CYS13
|
4.2
|
24.1
|
1.0
|
OD1
|
E:ASP113
|
4.3
|
29.1
|
1.0
|
O
|
E:ASN108
|
4.3
|
22.5
|
1.0
|
OP2
|
M:G603
|
4.3
|
23.5
|
1.0
|
C2'
|
M:G602
|
4.4
|
23.0
|
1.0
|
CG
|
E:ASP113
|
4.6
|
30.0
|
1.0
|
CB
|
E:ASP12
|
4.7
|
21.6
|
1.0
|
C5'
|
M:G602
|
4.7
|
24.2
|
1.0
|
N
|
E:CYS13
|
4.8
|
20.9
|
1.0
|
O
|
M:HOH802
|
4.9
|
29.0
|
1.0
|
CA
|
E:ASP12
|
5.0
|
20.5
|
1.0
|
|
Sodium binding site 8 out
of 10 in 9f7m
Go back to
Sodium Binding Sites List in 9f7m
Sodium binding site 8 out
of 10 in the Blastococcus Orn Bound to Pgg
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
N:Na701
b:23.7
occ:0.83
|
OD1
|
F:ASP12
|
2.3
|
30.2
|
1.0
|
O
|
F:HOH319
|
2.3
|
25.5
|
1.0
|
O
|
F:HOH358
|
2.4
|
25.6
|
1.0
|
O
|
F:HOH378
|
2.4
|
31.5
|
1.0
|
OP1
|
N:G603
|
2.4
|
28.0
|
1.0
|
O3'
|
N:G602
|
2.6
|
26.0
|
1.0
|
P
|
N:G603
|
3.1
|
28.7
|
1.0
|
CG
|
F:ASP12
|
3.5
|
32.5
|
1.0
|
C3'
|
N:G602
|
3.8
|
24.6
|
1.0
|
O2'
|
N:G602
|
3.8
|
27.1
|
1.0
|
O
|
F:HOH311
|
4.0
|
34.9
|
1.0
|
O
|
F:HOH330
|
4.0
|
38.8
|
1.0
|
C4'
|
N:G602
|
4.0
|
22.6
|
1.0
|
O
|
F:HOH347
|
4.0
|
29.8
|
1.0
|
OD2
|
F:ASP113
|
4.1
|
30.2
|
1.0
|
C5'
|
N:G603
|
4.1
|
27.9
|
1.0
|
O5'
|
N:G603
|
4.1
|
26.4
|
1.0
|
OD2
|
F:ASP12
|
4.2
|
35.4
|
1.0
|
O
|
F:CYS13
|
4.2
|
26.6
|
1.0
|
OD1
|
F:ASP165
|
4.2
|
41.8
|
1.0
|
OP2
|
N:G603
|
4.3
|
28.5
|
1.0
|
OD1
|
F:ASP113
|
4.3
|
31.1
|
1.0
|
O
|
F:ASN108
|
4.3
|
23.0
|
1.0
|
C2'
|
N:G602
|
4.4
|
25.3
|
1.0
|
O
|
F:HOH315
|
4.5
|
36.1
|
1.0
|
CB
|
F:ASP12
|
4.6
|
25.0
|
1.0
|
CG
|
F:ASP113
|
4.6
|
29.5
|
1.0
|
C5'
|
N:G602
|
4.6
|
21.7
|
1.0
|
N
|
F:CYS13
|
4.7
|
25.3
|
1.0
|
O
|
N:HOH804
|
4.7
|
28.6
|
1.0
|
CA
|
F:ASP12
|
4.8
|
25.4
|
1.0
|
CG
|
F:ASP165
|
4.9
|
38.4
|
1.0
|
OD2
|
F:ASP165
|
4.9
|
38.3
|
1.0
|
|
Sodium binding site 9 out
of 10 in 9f7m
Go back to
Sodium Binding Sites List in 9f7m
Sodium binding site 9 out
of 10 in the Blastococcus Orn Bound to Pgg
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
O:Na701
b:22.3
occ:0.75
|
OD1
|
G:ASP12
|
2.3
|
29.6
|
1.0
|
O
|
G:HOH323
|
2.3
|
30.1
|
1.0
|
O
|
G:HOH361
|
2.4
|
31.6
|
1.0
|
O
|
G:HOH422
|
2.4
|
36.5
|
1.0
|
OP1
|
O:G603
|
2.5
|
27.6
|
1.0
|
O3'
|
O:G602
|
2.6
|
26.2
|
1.0
|
P
|
O:G603
|
3.2
|
26.7
|
1.0
|
CG
|
G:ASP12
|
3.5
|
28.5
|
1.0
|
C3'
|
O:G602
|
3.8
|
26.2
|
1.0
|
O2'
|
O:G602
|
3.8
|
27.3
|
1.0
|
O
|
O:HOH801
|
4.0
|
30.0
|
1.0
|
OD2
|
G:ASP12
|
4.0
|
33.9
|
1.0
|
C4'
|
O:G602
|
4.0
|
22.9
|
1.0
|
O
|
G:HOH367
|
4.1
|
28.9
|
1.0
|
C5'
|
O:G603
|
4.1
|
30.5
|
1.0
|
O
|
G:HOH411
|
4.1
|
28.5
|
1.0
|
OD1
|
G:ASP113
|
4.1
|
29.4
|
1.0
|
O5'
|
O:G603
|
4.2
|
29.3
|
1.0
|
O
|
G:CYS13
|
4.2
|
28.2
|
1.0
|
O
|
G:ASN108
|
4.3
|
24.1
|
1.0
|
OD2
|
G:ASP113
|
4.3
|
30.4
|
1.0
|
OP2
|
O:G603
|
4.3
|
27.9
|
1.0
|
C2'
|
O:G602
|
4.4
|
24.9
|
1.0
|
O
|
O:HOH810
|
4.6
|
44.0
|
1.0
|
CB
|
G:ASP12
|
4.6
|
24.9
|
1.0
|
CG
|
G:ASP113
|
4.7
|
29.9
|
1.0
|
C5'
|
O:G602
|
4.7
|
26.5
|
1.0
|
O
|
O:HOH802
|
4.8
|
30.6
|
1.0
|
N
|
G:CYS13
|
4.8
|
27.6
|
1.0
|
CA
|
G:ASP12
|
5.0
|
27.8
|
1.0
|
|
Sodium binding site 10 out
of 10 in 9f7m
Go back to
Sodium Binding Sites List in 9f7m
Sodium binding site 10 out
of 10 in the Blastococcus Orn Bound to Pgg
 Mono view
 Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Blastococcus Orn Bound to Pgg within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
P:Na701
b:29.4
occ:0.93
|
OD1
|
H:ASP12
|
2.2
|
33.6
|
1.0
|
O
|
H:HOH358
|
2.4
|
32.9
|
1.0
|
O
|
H:HOH311
|
2.5
|
34.8
|
1.0
|
OP1
|
P:G603
|
2.5
|
34.4
|
1.0
|
O3'
|
P:G602
|
2.5
|
28.2
|
1.0
|
O
|
H:HOH413
|
2.6
|
35.1
|
1.0
|
P
|
P:G603
|
3.1
|
29.9
|
1.0
|
CG
|
H:ASP12
|
3.4
|
32.8
|
1.0
|
C3'
|
P:G602
|
3.8
|
29.3
|
1.0
|
O2'
|
P:G602
|
3.8
|
29.2
|
1.0
|
OD2
|
H:ASP12
|
3.9
|
36.6
|
1.0
|
O
|
H:HOH302
|
3.9
|
35.2
|
1.0
|
C4'
|
P:G602
|
4.0
|
29.8
|
1.0
|
O
|
H:HOH355
|
4.1
|
35.1
|
1.0
|
C5'
|
P:G603
|
4.1
|
25.6
|
1.0
|
O
|
H:CYS13
|
4.1
|
34.8
|
1.0
|
OD2
|
H:ASP113
|
4.1
|
36.7
|
1.0
|
O5'
|
P:G603
|
4.1
|
28.0
|
1.0
|
O
|
H:HOH392
|
4.2
|
31.4
|
1.0
|
OP2
|
P:G603
|
4.3
|
30.0
|
1.0
|
OD1
|
H:ASP113
|
4.4
|
34.4
|
1.0
|
O
|
H:ASN108
|
4.4
|
25.9
|
1.0
|
C2'
|
P:G602
|
4.4
|
27.6
|
1.0
|
CB
|
H:ASP12
|
4.5
|
31.1
|
1.0
|
C5'
|
P:G602
|
4.7
|
26.7
|
1.0
|
CG
|
H:ASP113
|
4.7
|
33.0
|
1.0
|
N
|
H:CYS13
|
4.7
|
30.7
|
1.0
|
CA
|
H:ASP12
|
4.9
|
29.3
|
1.0
|
O
|
P:HOH801
|
5.0
|
36.2
|
1.0
|
|
Reference:
S.Mortensen,
H.Sondermann.
Unique Dinucleases with Dna Specificity Are Associated with Genomic Islands in Actinomycetes and Clostridia To Be Published.
Page generated: Mon Aug 18 16:52:04 2025
|