Sodium in PDB 6geh: Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
Protein crystallography data
The structure of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility., PDB code: 6geh
was solved by
I.B.Trindade,
J.P.M.Silva,
P.Matias,
E.Moe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.62 /
1.15
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.098,
77.753,
44.917,
90.00,
109.64,
90.00
|
R / Rfree (%)
|
14.5 /
17.4
|
Other elements in 6geh:
The structure of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility. also contains other interesting chemical elements:
Sodium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
24;
Binding sites:
The binding sites of Sodium atom in the Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
(pdb code 6geh). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 24 binding sites of Sodium where determined in the
Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility., PDB code: 6geh:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Sodium binding site 1 out
of 24 in 6geh
Go back to
Sodium Binding Sites List in 6geh
Sodium binding site 1 out
of 24 in the Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na610
b:38.9
occ:1.00
|
H
|
A:GLU191
|
2.2
|
26.0
|
1.0
|
O
|
A:HOH1047
|
2.6
|
29.3
|
1.0
|
HB
|
A:THR189
|
2.8
|
25.6
|
1.0
|
HB3
|
A:ALA190
|
2.9
|
24.9
|
1.0
|
HB2
|
A:GLU191
|
3.0
|
28.2
|
1.0
|
N
|
A:GLU191
|
3.0
|
21.7
|
1.0
|
HB3
|
A:GLU191
|
3.2
|
28.2
|
1.0
|
H
|
A:ALA190
|
3.2
|
25.6
|
1.0
|
O
|
A:HOH861
|
3.3
|
28.6
|
1.0
|
CB
|
A:GLU191
|
3.5
|
23.5
|
1.0
|
N
|
A:ALA190
|
3.5
|
21.3
|
1.0
|
CB
|
A:THR189
|
3.6
|
21.3
|
1.0
|
CB
|
A:ALA190
|
3.7
|
20.7
|
1.0
|
CA
|
A:GLU191
|
3.8
|
21.5
|
1.0
|
OG1
|
A:THR189
|
3.9
|
20.9
|
1.0
|
C
|
A:ALA190
|
3.9
|
20.2
|
1.0
|
CA
|
A:ALA190
|
3.9
|
20.4
|
1.0
|
O
|
A:HOH764
|
4.0
|
21.4
|
1.0
|
C
|
A:THR189
|
4.2
|
20.4
|
1.0
|
HB2
|
A:ALA190
|
4.2
|
24.9
|
1.0
|
HA
|
A:GLU191
|
4.3
|
25.8
|
1.0
|
HB1
|
A:ALA190
|
4.4
|
24.9
|
1.0
|
CA
|
A:THR189
|
4.5
|
20.4
|
1.0
|
HG21
|
A:THR189
|
4.6
|
26.4
|
1.0
|
HA
|
A:THR189
|
4.6
|
24.5
|
1.0
|
H
|
A:GLN192
|
4.6
|
24.2
|
0.6
|
H
|
A:GLN192
|
4.6
|
24.2
|
0.4
|
CG2
|
A:THR189
|
4.7
|
22.0
|
1.0
|
O
|
A:HOH1086
|
4.7
|
37.2
|
1.0
|
HG1
|
A:THR189
|
4.7
|
25.1
|
1.0
|
CG
|
A:GLU191
|
4.9
|
27.1
|
1.0
|
HA
|
A:ALA190
|
4.9
|
24.5
|
1.0
|
HG22
|
A:THR189
|
4.9
|
26.4
|
1.0
|
OE1
|
A:GLU191
|
4.9
|
32.6
|
1.0
|
|
Sodium binding site 2 out
of 24 in 6geh
Go back to
Sodium Binding Sites List in 6geh
Sodium binding site 2 out
of 24 in the Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na611
b:22.7
occ:1.00
|
HG
|
A:SER238
|
2.0
|
15.5
|
1.0
|
O
|
A:HOH1055
|
2.4
|
56.8
|
1.0
|
O
|
A:HOH708
|
2.6
|
60.8
|
1.0
|
OG
|
A:SER238
|
2.7
|
12.9
|
1.0
|
NA
|
A:NA619
|
2.7
|
22.8
|
1.0
|
OG
|
A:SER239
|
2.8
|
10.2
|
0.6
|
HG2
|
A:PRO236
|
3.2
|
13.0
|
0.4
|
HB3
|
A:SER239
|
3.2
|
13.7
|
0.5
|
HG
|
A:SER239
|
3.2
|
12.2
|
0.6
|
HE22
|
A:GLN212
|
3.3
|
15.8
|
1.0
|
HA
|
A:SER239
|
3.5
|
12.3
|
0.5
|
HB2
|
A:PRO236
|
3.5
|
14.6
|
0.6
|
HG3
|
A:PRO236
|
3.6
|
13.0
|
0.4
|
HA
|
A:SER239
|
3.6
|
11.9
|
0.6
|
N
|
A:SER239
|
3.7
|
10.2
|
0.6
|
N
|
A:SER239
|
3.7
|
10.5
|
0.5
|
HB2
|
A:SER238
|
3.7
|
14.3
|
1.0
|
CB
|
A:SER238
|
3.8
|
11.9
|
1.0
|
CG
|
A:PRO236
|
3.8
|
10.8
|
0.4
|
C
|
A:SER238
|
3.8
|
11.0
|
1.0
|
CB
|
A:SER239
|
3.9
|
10.4
|
0.6
|
H
|
A:SER239
|
3.9
|
12.3
|
0.6
|
H
|
A:SER239
|
3.9
|
12.6
|
0.5
|
CA
|
A:SER239
|
3.9
|
9.9
|
0.6
|
CA
|
A:SER239
|
3.9
|
10.2
|
0.5
|
HG2
|
A:PRO236
|
3.9
|
16.2
|
0.6
|
CB
|
A:SER239
|
3.9
|
11.4
|
0.5
|
O
|
A:SER238
|
4.2
|
13.6
|
1.0
|
NE2
|
A:GLN212
|
4.2
|
13.2
|
1.0
|
O
|
A:HOH1118
|
4.2
|
42.0
|
1.0
|
HB2
|
A:SER239
|
4.3
|
13.7
|
0.5
|
CB
|
A:PRO236
|
4.3
|
12.2
|
0.6
|
HB2
|
A:PRO236
|
4.3
|
12.5
|
0.4
|
HH11
|
A:ARG125
|
4.3
|
20.1
|
1.0
|
CA
|
A:SER238
|
4.4
|
11.1
|
1.0
|
HB2
|
A:SER239
|
4.4
|
12.5
|
0.6
|
OE1
|
A:GLN212
|
4.4
|
11.7
|
1.0
|
HB3
|
A:SER239
|
4.5
|
12.5
|
0.6
|
HB3
|
A:SER238
|
4.5
|
14.3
|
1.0
|
CG
|
A:PRO236
|
4.6
|
13.5
|
0.6
|
HB3
|
A:PRO236
|
4.6
|
14.6
|
0.6
|
O
|
A:HOH956
|
4.6
|
27.7
|
1.0
|
CB
|
A:PRO236
|
4.7
|
10.4
|
0.4
|
CD
|
A:GLN212
|
4.8
|
11.9
|
1.0
|
HE21
|
A:GLN212
|
4.8
|
15.8
|
1.0
|
H
|
A:SER238
|
4.8
|
12.7
|
0.4
|
O
|
A:HOH738
|
4.8
|
15.5
|
1.0
|
HD2
|
A:PRO236
|
4.8
|
14.4
|
0.6
|
HE2
|
A:PHE128
|
4.9
|
22.4
|
1.0
|
H
|
A:SER238
|
4.9
|
12.7
|
0.6
|
HD2
|
A:PRO236
|
4.9
|
13.0
|
0.4
|
N
|
A:SER238
|
5.0
|
10.6
|
1.0
|
|
Sodium binding site 3 out
of 24 in 6geh
Go back to
Sodium Binding Sites List in 6geh
Sodium binding site 3 out
of 24 in the Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na612
b:26.7
occ:1.00
|
O
|
A:HOH860
|
2.6
|
26.9
|
1.0
|
O
|
A:ILE22
|
2.7
|
14.0
|
1.0
|
NA
|
A:NA613
|
2.9
|
39.8
|
1.0
|
HA
|
A:ILE22
|
3.2
|
15.7
|
1.0
|
O
|
A:HOH866
|
3.2
|
36.0
|
1.0
|
HG23
|
A:ILE22
|
3.4
|
19.9
|
1.0
|
HB3
|
A:GLN166
|
3.4
|
17.1
|
1.0
|
O
|
A:HOH1120
|
3.5
|
50.2
|
1.0
|
C
|
A:ILE22
|
3.6
|
13.6
|
1.0
|
CA
|
A:ILE22
|
3.8
|
13.1
|
1.0
|
HG22
|
A:ILE22
|
3.9
|
19.9
|
1.0
|
HE21
|
A:GLN166
|
3.9
|
23.1
|
1.0
|
NE2
|
A:GLN166
|
4.0
|
19.2
|
1.0
|
CG2
|
A:ILE22
|
4.0
|
16.6
|
1.0
|
HE22
|
A:GLN166
|
4.0
|
23.1
|
1.0
|
O
|
A:HOH948
|
4.1
|
36.5
|
1.0
|
O
|
A:HOH1117
|
4.2
|
34.0
|
1.0
|
CB
|
A:GLN166
|
4.4
|
14.2
|
1.0
|
O
|
A:GLN166
|
4.4
|
13.8
|
1.0
|
HD13
|
A:ILE22
|
4.5
|
19.7
|
1.0
|
CD
|
A:GLN166
|
4.5
|
15.8
|
1.0
|
O
|
A:GLU21
|
4.5
|
12.1
|
0.6
|
O
|
A:GLU21
|
4.5
|
14.5
|
0.4
|
CB
|
A:ILE22
|
4.6
|
14.4
|
1.0
|
HD12
|
A:ILE22
|
4.6
|
19.7
|
1.0
|
HB2
|
A:GLN166
|
4.8
|
17.1
|
1.0
|
N
|
A:SER23
|
4.8
|
12.9
|
1.0
|
HG21
|
A:ILE22
|
4.9
|
19.9
|
1.0
|
CG
|
A:GLN166
|
4.9
|
15.4
|
1.0
|
CD1
|
A:ILE22
|
5.0
|
16.4
|
1.0
|
HA
|
A:SER23
|
5.0
|
16.1
|
1.0
|
HG2
|
A:GLN166
|
5.0
|
18.5
|
1.0
|
|
Sodium binding site 4 out
of 24 in 6geh
Go back to
Sodium Binding Sites List in 6geh
Sodium binding site 4 out
of 24 in the Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na613
b:39.8
occ:1.00
|
O
|
A:HOH1120
|
2.7
|
50.2
|
1.0
|
HA
|
A:ILE22
|
2.8
|
15.7
|
1.0
|
NA
|
A:NA612
|
2.9
|
26.7
|
1.0
|
O
|
A:GLU21
|
2.9
|
12.1
|
0.6
|
HD13
|
A:ILE22
|
3.1
|
19.7
|
1.0
|
O
|
A:GLU21
|
3.2
|
14.5
|
0.4
|
HG22
|
A:ILE20
|
3.4
|
20.0
|
1.0
|
HG21
|
A:ILE20
|
3.7
|
20.0
|
1.0
|
CA
|
A:ILE22
|
3.8
|
13.1
|
1.0
|
CD1
|
A:ILE22
|
3.9
|
16.4
|
1.0
|
C
|
A:GLU21
|
3.9
|
12.4
|
0.6
|
HD12
|
A:ILE22
|
4.0
|
19.7
|
1.0
|
CG2
|
A:ILE20
|
4.0
|
16.6
|
1.0
|
C
|
A:GLU21
|
4.0
|
13.0
|
0.4
|
HG23
|
A:ILE22
|
4.2
|
19.9
|
1.0
|
O
|
A:ILE22
|
4.3
|
14.0
|
1.0
|
N
|
A:ILE22
|
4.3
|
12.5
|
1.0
|
C
|
A:ILE22
|
4.4
|
13.6
|
1.0
|
HD11
|
A:ILE22
|
4.5
|
19.7
|
1.0
|
HG23
|
A:ILE20
|
4.5
|
20.0
|
1.0
|
CB
|
A:ILE22
|
4.7
|
14.4
|
1.0
|
CG1
|
A:ILE22
|
4.8
|
15.0
|
1.0
|
O
|
A:HOH1117
|
4.9
|
34.0
|
1.0
|
O
|
A:HOH860
|
4.9
|
26.9
|
1.0
|
CG2
|
A:ILE22
|
4.9
|
16.6
|
1.0
|
HB
|
A:ILE20
|
5.0
|
17.8
|
1.0
|
|
Sodium binding site 5 out
of 24 in 6geh
Go back to
Sodium Binding Sites List in 6geh
Sodium binding site 5 out
of 24 in the Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na614
b:26.3
occ:1.00
|
O
|
A:HOH838
|
2.6
|
19.2
|
1.0
|
OD2
|
A:ASP136
|
2.7
|
16.2
|
1.0
|
OE1
|
A:GLN221
|
2.8
|
17.3
|
1.0
|
HZ2
|
A:TRP246
|
2.9
|
19.5
|
1.0
|
HD12
|
A:LEU161
|
2.9
|
25.9
|
1.0
|
HE22
|
A:GLN221
|
3.1
|
21.0
|
1.0
|
HB2
|
A:GLU218
|
3.1
|
19.5
|
1.0
|
H
|
A:GLU218
|
3.2
|
17.5
|
1.0
|
HE1
|
A:TRP246
|
3.3
|
19.3
|
1.0
|
HB3
|
A:ASP136
|
3.3
|
14.8
|
1.0
|
HD22
|
A:LEU217
|
3.4
|
16.8
|
1.0
|
CD
|
A:GLN221
|
3.5
|
16.7
|
1.0
|
O2
|
A:GOL634
|
3.6
|
27.7
|
0.5
|
NE2
|
A:GLN221
|
3.6
|
17.5
|
1.0
|
HO2
|
A:GOL634
|
3.6
|
33.2
|
0.5
|
CG
|
A:ASP136
|
3.6
|
12.3
|
1.0
|
HB2
|
A:ASP136
|
3.6
|
14.8
|
1.0
|
CZ2
|
A:TRP246
|
3.7
|
16.3
|
1.0
|
CB
|
A:ASP136
|
3.7
|
12.3
|
1.0
|
CD1
|
A:LEU161
|
3.8
|
21.5
|
1.0
|
H31
|
A:GOL634
|
3.8
|
24.8
|
0.5
|
O
|
A:DMS607
|
3.8
|
19.6
|
0.5
|
NE1
|
A:TRP246
|
3.9
|
16.1
|
1.0
|
CB
|
A:GLU218
|
3.9
|
16.2
|
1.0
|
HD13
|
A:LEU161
|
3.9
|
25.9
|
1.0
|
HB3
|
A:GLU218
|
3.9
|
19.5
|
1.0
|
N
|
A:GLU218
|
3.9
|
14.6
|
1.0
|
HB2
|
A:LEU161
|
4.1
|
18.5
|
1.0
|
HD23
|
A:LEU217
|
4.1
|
16.8
|
1.0
|
CE2
|
A:TRP246
|
4.1
|
15.8
|
1.0
|
CD2
|
A:LEU217
|
4.2
|
14.0
|
1.0
|
HB3
|
A:LEU217
|
4.2
|
16.3
|
1.0
|
H11
|
A:DMS607
|
4.2
|
19.9
|
0.5
|
HD11
|
A:LEU161
|
4.3
|
25.9
|
1.0
|
HA
|
A:LEU217
|
4.3
|
15.6
|
1.0
|
HE21
|
A:GLN221
|
4.4
|
21.0
|
1.0
|
HD11
|
A:LEU184
|
4.5
|
23.2
|
1.0
|
OE1
|
A:GLN193
|
4.5
|
20.7
|
1.0
|
CA
|
A:GLU218
|
4.6
|
15.3
|
1.0
|
C2
|
A:GOL634
|
4.6
|
24.2
|
0.5
|
C3
|
A:GOL634
|
4.7
|
20.7
|
0.5
|
HB3
|
A:LEU161
|
4.7
|
18.5
|
1.0
|
CB
|
A:LEU161
|
4.7
|
15.4
|
1.0
|
HD21
|
A:LEU217
|
4.8
|
16.8
|
1.0
|
OD1
|
A:ASP136
|
4.8
|
12.1
|
1.0
|
CG
|
A:LEU161
|
4.8
|
19.2
|
1.0
|
CH2
|
A:TRP246
|
4.8
|
16.8
|
1.0
|
HG3
|
A:GLU218
|
4.8
|
21.1
|
1.0
|
C
|
A:LEU217
|
4.9
|
14.3
|
1.0
|
S
|
A:DMS607
|
4.9
|
16.0
|
0.5
|
CA
|
A:LEU217
|
4.9
|
13.0
|
1.0
|
CB
|
A:LEU217
|
4.9
|
13.6
|
1.0
|
CG
|
A:GLN221
|
4.9
|
16.1
|
1.0
|
C1
|
A:DMS607
|
4.9
|
16.6
|
0.5
|
HH2
|
A:TRP246
|
4.9
|
20.1
|
1.0
|
H2
|
A:GOL634
|
4.9
|
29.1
|
0.5
|
HG
|
A:LEU161
|
5.0
|
23.1
|
1.0
|
HA
|
A:GLU218
|
5.0
|
18.4
|
1.0
|
O
|
A:HOH1032
|
5.0
|
24.3
|
1.0
|
HH12
|
A:ARG248
|
5.0
|
27.4
|
1.0
|
|
Sodium binding site 6 out
of 24 in 6geh
Go back to
Sodium Binding Sites List in 6geh
Sodium binding site 6 out
of 24 in the Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na615
b:20.4
occ:1.00
|
HE
|
A:ARG149
|
2.1
|
17.6
|
1.0
|
O
|
A:ARG149
|
2.7
|
13.0
|
1.0
|
O
|
A:HOH1081
|
2.8
|
17.0
|
0.4
|
HA
|
A:ARG149
|
2.9
|
12.9
|
1.0
|
NE
|
A:ARG149
|
2.9
|
14.7
|
1.0
|
HB3
|
A:ARG149
|
3.0
|
14.4
|
1.0
|
O
|
A:HOH990
|
3.0
|
33.5
|
1.0
|
O
|
A:HOH1081
|
3.1
|
15.4
|
0.6
|
HH21
|
A:ARG149
|
3.1
|
20.4
|
1.0
|
O
|
A:HOH989
|
3.4
|
17.8
|
0.6
|
CA
|
A:ARG149
|
3.5
|
10.7
|
1.0
|
C
|
A:ARG149
|
3.5
|
11.5
|
1.0
|
O
|
A:HOH883
|
3.6
|
19.6
|
0.5
|
HD2
|
A:ARG149
|
3.6
|
16.2
|
1.0
|
CB
|
A:ARG149
|
3.6
|
12.0
|
1.0
|
NH2
|
A:ARG149
|
3.7
|
17.0
|
1.0
|
CD
|
A:ARG149
|
3.8
|
13.5
|
1.0
|
CZ
|
A:ARG149
|
3.8
|
15.3
|
1.0
|
HD2
|
A:PHE126
|
3.9
|
20.5
|
1.0
|
HB3
|
A:PHE126
|
4.0
|
18.3
|
1.0
|
O
|
A:HOH989
|
4.0
|
15.7
|
0.4
|
O
|
A:HOH883
|
4.2
|
16.7
|
0.5
|
CG
|
A:ARG149
|
4.3
|
12.2
|
1.0
|
CD2
|
A:PHE126
|
4.4
|
17.1
|
1.0
|
HB2
|
A:ARG149
|
4.4
|
14.4
|
1.0
|
HH22
|
A:ARG149
|
4.5
|
20.4
|
1.0
|
HD3
|
A:ARG149
|
4.6
|
16.2
|
1.0
|
HB2
|
A:PHE126
|
4.6
|
18.3
|
1.0
|
CB
|
A:PHE126
|
4.7
|
15.3
|
1.0
|
HG3
|
A:ARG149
|
4.7
|
14.7
|
1.0
|
N
|
A:LEU150
|
4.7
|
11.0
|
1.0
|
N
|
A:ARG149
|
4.8
|
10.0
|
1.0
|
CG
|
A:PHE126
|
4.9
|
15.6
|
1.0
|
O
|
A:LYS148
|
4.9
|
10.6
|
0.6
|
O
|
A:LYS148
|
4.9
|
9.4
|
0.4
|
|
Sodium binding site 7 out
of 24 in 6geh
Go back to
Sodium Binding Sites List in 6geh
Sodium binding site 7 out
of 24 in the Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na616
b:18.6
occ:1.00
|
O
|
A:HOH909
|
2.7
|
23.0
|
1.0
|
OG1
|
A:THR63
|
2.7
|
12.8
|
1.0
|
HG23
|
A:THR63
|
3.0
|
14.9
|
1.0
|
HG21
|
A:THR63
|
3.2
|
14.9
|
1.0
|
HG1
|
A:THR63
|
3.3
|
15.3
|
1.0
|
CG2
|
A:THR63
|
3.4
|
12.5
|
1.0
|
CB
|
A:THR63
|
3.7
|
11.6
|
1.0
|
HA
|
A:THR63
|
4.3
|
13.9
|
1.0
|
HB2
|
A:ASN68
|
4.3
|
19.9
|
1.0
|
HG22
|
A:THR63
|
4.4
|
14.9
|
1.0
|
HB
|
A:THR63
|
4.4
|
13.9
|
1.0
|
HD21
|
A:ASN68
|
4.4
|
20.8
|
1.0
|
O
|
A:HOH987
|
4.6
|
33.9
|
1.0
|
CA
|
A:THR63
|
4.6
|
11.6
|
1.0
|
O
|
A:HOH878
|
4.6
|
16.9
|
1.0
|
O
|
A:HOH913
|
4.8
|
18.6
|
1.0
|
|
Sodium binding site 8 out
of 24 in 6geh
Go back to
Sodium Binding Sites List in 6geh
Sodium binding site 8 out
of 24 in the Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na617
b:21.2
occ:1.00
|
H
|
A:HIS174
|
2.2
|
14.7
|
1.0
|
HA
|
A:GLN173
|
2.6
|
14.9
|
1.0
|
O
|
A:HOH827
|
2.7
|
24.9
|
0.5
|
O
|
A:HOH1094
|
2.7
|
25.5
|
1.0
|
O
|
A:HOH1000
|
2.8
|
19.6
|
1.0
|
O
|
A:HOH827
|
2.8
|
14.1
|
0.5
|
N
|
A:HIS174
|
3.0
|
12.2
|
1.0
|
HB2
|
A:GLN173
|
3.1
|
17.5
|
1.0
|
O
|
A:HIS174
|
3.1
|
13.7
|
1.0
|
CA
|
A:GLN173
|
3.4
|
12.4
|
1.0
|
O
|
A:HOH1108
|
3.6
|
44.5
|
1.0
|
O
|
A:HOH821
|
3.6
|
15.3
|
0.5
|
CB
|
A:GLN173
|
3.7
|
14.6
|
1.0
|
C
|
A:GLN173
|
3.7
|
12.4
|
1.0
|
O
|
A:HOH848
|
3.8
|
20.6
|
1.0
|
O
|
A:HOH1056
|
3.9
|
40.5
|
1.0
|
C
|
A:HIS174
|
3.9
|
11.8
|
1.0
|
HB3
|
A:GLN173
|
4.0
|
17.5
|
1.0
|
CA
|
A:HIS174
|
4.0
|
11.9
|
1.0
|
O
|
A:HOH962
|
4.1
|
29.3
|
0.4
|
O
|
A:HOH821
|
4.2
|
12.9
|
0.5
|
O
|
A:HOH1069
|
4.4
|
19.0
|
1.0
|
HB3
|
A:HIS174
|
4.4
|
14.2
|
1.0
|
O
|
A:HOH791
|
4.4
|
16.2
|
1.0
|
N
|
A:GLN173
|
4.6
|
12.7
|
1.0
|
CB
|
A:HIS174
|
4.8
|
11.9
|
1.0
|
HA
|
A:HIS174
|
4.8
|
14.3
|
1.0
|
O
|
A:LEU177
|
4.8
|
17.0
|
1.0
|
HE22
|
A:GLN173
|
4.8
|
18.5
|
1.0
|
O
|
A:SER172
|
4.8
|
12.7
|
1.0
|
HG23
|
A:THR179
|
4.8
|
21.8
|
1.0
|
O
|
A:GLN173
|
4.9
|
12.5
|
1.0
|
O
|
A:HOH979
|
4.9
|
25.1
|
1.0
|
|
Sodium binding site 9 out
of 24 in 6geh
Go back to
Sodium Binding Sites List in 6geh
Sodium binding site 9 out
of 24 in the Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 9 of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na618
b:22.1
occ:1.00
|
H
|
A:ASN61
|
2.2
|
14.9
|
1.0
|
HA
|
A:VAL60
|
2.8
|
15.5
|
1.0
|
O
|
A:HOH1051
|
2.8
|
18.4
|
1.0
|
HB2
|
A:ALA70
|
2.9
|
19.0
|
1.0
|
N
|
A:ASN61
|
3.0
|
12.4
|
1.0
|
O
|
A:HOH1013
|
3.0
|
30.6
|
1.0
|
O
|
A:ASN68
|
3.0
|
14.4
|
1.0
|
OD1
|
A:ASN61
|
3.3
|
13.1
|
1.0
|
CG
|
A:ASN61
|
3.3
|
12.5
|
1.0
|
ND2
|
A:ASN61
|
3.4
|
13.8
|
1.0
|
HD21
|
A:ASN61
|
3.4
|
16.5
|
1.0
|
H
|
A:ALA70
|
3.5
|
17.3
|
1.0
|
CA
|
A:VAL60
|
3.5
|
12.9
|
1.0
|
HB
|
A:VAL60
|
3.5
|
15.7
|
1.0
|
N
|
A:ALA70
|
3.6
|
14.4
|
1.0
|
HA
|
A:ALA70
|
3.7
|
17.4
|
1.0
|
C
|
A:VAL60
|
3.7
|
12.6
|
1.0
|
CB
|
A:ALA70
|
3.7
|
15.9
|
1.0
|
HD22
|
A:ASN61
|
3.8
|
16.5
|
1.0
|
CA
|
A:ALA70
|
3.9
|
14.5
|
1.0
|
CA
|
A:ASN61
|
3.9
|
11.8
|
1.0
|
C
|
A:ALA69
|
4.0
|
14.6
|
1.0
|
CB
|
A:VAL60
|
4.0
|
13.1
|
1.0
|
CB
|
A:ASN61
|
4.0
|
12.6
|
1.0
|
HA
|
A:ALA69
|
4.0
|
17.8
|
1.0
|
HG12
|
A:VAL60
|
4.0
|
16.7
|
1.0
|
HB3
|
A:ASN61
|
4.1
|
15.2
|
1.0
|
O
|
A:HOH780
|
4.1
|
14.3
|
1.0
|
C
|
A:ASN68
|
4.2
|
14.3
|
1.0
|
O
|
A:ASN61
|
4.2
|
12.9
|
1.0
|
HB3
|
A:ALA70
|
4.3
|
19.0
|
1.0
|
HB1
|
A:ALA70
|
4.3
|
19.0
|
1.0
|
O
|
A:HOH942
|
4.4
|
30.3
|
1.0
|
C
|
A:ASN61
|
4.4
|
11.9
|
1.0
|
CA
|
A:ALA69
|
4.5
|
14.9
|
1.0
|
O
|
A:HOH1023
|
4.5
|
47.2
|
1.0
|
O
|
A:ALA69
|
4.5
|
16.9
|
1.0
|
CG1
|
A:VAL60
|
4.6
|
13.9
|
1.0
|
NA
|
A:NA621
|
4.6
|
23.6
|
1.0
|
O
|
A:THR59
|
4.7
|
18.0
|
1.0
|
N
|
A:VAL60
|
4.7
|
13.5
|
1.0
|
HA
|
A:ASN61
|
4.8
|
14.2
|
1.0
|
N
|
A:ALA69
|
4.8
|
14.3
|
1.0
|
O
|
A:VAL60
|
4.9
|
13.8
|
1.0
|
HB
|
A:THR63
|
4.9
|
13.9
|
1.0
|
HB2
|
A:ASN61
|
4.9
|
15.2
|
1.0
|
|
Sodium binding site 10 out
of 24 in 6geh
Go back to
Sodium Binding Sites List in 6geh
Sodium binding site 10 out
of 24 in the Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 10 of Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacterium Shewanella Reveals Unanticipated Functional Versatility. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na619
b:22.8
occ:1.00
|
HH11
|
A:ARG125
|
2.2
|
20.1
|
1.0
|
HD2
|
A:ARG125
|
2.7
|
16.7
|
1.0
|
NA
|
A:NA611
|
2.7
|
22.7
|
1.0
|
OE1
|
A:GLN212
|
2.8
|
11.7
|
1.0
|
NH1
|
A:ARG125
|
3.0
|
16.7
|
1.0
|
HD3
|
A:ARG125
|
3.1
|
16.7
|
1.0
|
HE22
|
A:GLN212
|
3.3
|
15.8
|
1.0
|
CD
|
A:ARG125
|
3.3
|
13.9
|
1.0
|
HH12
|
A:ARG125
|
3.4
|
20.1
|
1.0
|
HA
|
A:SER239
|
3.4
|
12.3
|
0.5
|
HA
|
A:SER239
|
3.5
|
11.9
|
0.6
|
CD
|
A:GLN212
|
3.6
|
11.9
|
1.0
|
NE2
|
A:GLN212
|
3.7
|
13.2
|
1.0
|
HG
|
A:SER238
|
3.8
|
15.5
|
1.0
|
O
|
A:SER238
|
3.9
|
13.6
|
1.0
|
CZ
|
A:ARG125
|
4.0
|
16.4
|
1.0
|
O
|
A:HOH1055
|
4.1
|
56.8
|
1.0
|
NE
|
A:ARG125
|
4.1
|
15.6
|
1.0
|
OG
|
A:SER239
|
4.2
|
10.2
|
0.6
|
O
|
A:HOH708
|
4.3
|
60.8
|
1.0
|
HB2
|
A:SER238
|
4.3
|
14.3
|
1.0
|
CA
|
A:SER239
|
4.3
|
9.9
|
0.6
|
CA
|
A:SER239
|
4.3
|
10.2
|
0.5
|
C
|
A:SER238
|
4.4
|
11.0
|
1.0
|
O
|
A:HOH956
|
4.4
|
27.7
|
1.0
|
HG2
|
A:ARG125
|
4.4
|
16.2
|
1.0
|
NA
|
A:NA631
|
4.5
|
19.7
|
1.0
|
OG
|
A:SER238
|
4.5
|
12.9
|
1.0
|
HE21
|
A:GLN212
|
4.5
|
15.8
|
1.0
|
CG
|
A:ARG125
|
4.5
|
13.5
|
1.0
|
N
|
A:SER239
|
4.6
|
10.2
|
0.6
|
N
|
A:SER239
|
4.6
|
10.5
|
0.5
|
O
|
A:HOH792
|
4.6
|
14.0
|
0.6
|
HE2
|
A:PHE128
|
4.6
|
22.4
|
1.0
|
HZ
|
A:PHE128
|
4.6
|
23.6
|
1.0
|
HB3
|
A:SER239
|
4.7
|
13.7
|
0.5
|
CZ
|
A:PHE128
|
4.7
|
19.6
|
1.0
|
CE2
|
A:PHE128
|
4.7
|
18.6
|
1.0
|
CB
|
A:SER239
|
4.8
|
10.4
|
0.6
|
HG
|
A:SER239
|
4.8
|
12.2
|
0.6
|
CB
|
A:SER238
|
4.8
|
11.9
|
1.0
|
HB2
|
A:SER239
|
4.9
|
13.7
|
0.5
|
CB
|
A:SER239
|
4.9
|
11.4
|
0.5
|
HB3
|
A:ARG125
|
4.9
|
16.1
|
1.0
|
CG
|
A:GLN212
|
4.9
|
11.8
|
1.0
|
HG3
|
A:GLN212
|
4.9
|
14.2
|
1.0
|
HE
|
A:ARG125
|
5.0
|
18.7
|
1.0
|
|
Reference:
I.B.Trindade,
J.M.Silva,
B.M.Fonseca,
T.Catarino,
M.Fujita,
P.M.Matias,
E.Moe,
R.O.Louro.
Structure and Reactivity of A Siderophore-Interacting Protein From the Marine Bacteriumshewanellareveals Unanticipated Functional Versatility. J. Biol. Chem. V. 294 157 2019.
ISSN: ESSN 1083-351X
PubMed: 30420426
DOI: 10.1074/JBC.RA118.005041
Page generated: Tue Oct 8 09:00:56 2024
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