Sodium in PDB 6cl5: Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701
Protein crystallography data
The structure of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701, PDB code: 6cl5
was solved by
S.A.Buth,
M.M.Shneider,
P.G.Leiman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.69 /
2.32
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
144.504,
155.031,
200.481,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16.9 /
20.6
|
Other elements in 6cl5:
The structure of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701
(pdb code 6cl5). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the
Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701, PDB code: 6cl5:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
Sodium binding site 1 out
of 6 in 6cl5
Go back to
Sodium Binding Sites List in 6cl5
Sodium binding site 1 out
of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na803
b:65.6
occ:1.00
|
O
|
A:LEU688
|
2.3
|
77.4
|
1.0
|
|
O
|
A:HIS627
|
2.3
|
83.1
|
1.0
|
|
OE1
|
A:GLN690
|
2.4
|
70.7
|
1.0
|
|
OD1
|
A:ASP626
|
2.5
|
81.5
|
1.0
|
|
OE1
|
A:GLU684
|
2.5
|
78.6
|
1.0
|
|
O
|
A:HOH1136
|
3.0
|
66.9
|
1.0
|
|
H
|
A:HIS627
|
3.0
|
80.6
|
1.0
|
|
HB3
|
A:HIS627
|
3.0
|
71.5
|
1.0
|
|
HE22
|
A:GLN690
|
3.1
|
92.4
|
1.0
|
|
CD
|
A:GLN690
|
3.1
|
75.3
|
1.0
|
|
HA
|
A:ALA689
|
3.3
|
0.7
|
1.0
|
|
C
|
A:HIS627
|
3.4
|
87.8
|
1.0
|
|
NE2
|
A:GLN690
|
3.4
|
77.0
|
1.0
|
|
C
|
A:LEU688
|
3.4
|
88.4
|
1.0
|
|
CD
|
A:GLU684
|
3.4
|
76.7
|
1.0
|
|
H
|
A:GLN690
|
3.5
|
84.6
|
1.0
|
|
CG
|
A:ASP626
|
3.5
|
77.7
|
1.0
|
|
N
|
A:HIS627
|
3.6
|
67.1
|
1.0
|
|
OE2
|
A:GLU684
|
3.7
|
79.8
|
1.0
|
|
CA
|
A:HIS627
|
3.8
|
73.2
|
1.0
|
|
CB
|
A:HIS627
|
3.8
|
59.9
|
1.0
|
|
O
|
A:HOH1014
|
3.9
|
85.4
|
1.0
|
|
OD2
|
A:ASP626
|
3.9
|
91.5
|
1.0
|
|
CA
|
A:ALA689
|
4.1
|
84.7
|
1.0
|
|
N
|
A:GLN690
|
4.1
|
70.4
|
1.0
|
|
HE21
|
A:GLN690
|
4.1
|
92.4
|
1.0
|
|
N
|
A:ALA689
|
4.1
|
83.4
|
1.0
|
|
H
|
A:LEU688
|
4.2
|
0.9
|
1.0
|
|
HB2
|
A:HIS627
|
4.2
|
71.5
|
1.0
|
|
N
|
A:LEU688
|
4.3
|
0.7
|
1.0
|
|
CG
|
A:GLN690
|
4.3
|
63.7
|
1.0
|
|
HG3
|
A:GLN690
|
4.4
|
76.1
|
1.0
|
|
C
|
A:ALA689
|
4.4
|
80.7
|
1.0
|
|
CA
|
A:LEU688
|
4.4
|
89.2
|
1.0
|
|
H
|
A:GLY629
|
4.5
|
0.7
|
1.0
|
|
HA
|
A:PRO628
|
4.5
|
94.4
|
1.0
|
|
N
|
A:PRO628
|
4.5
|
79.8
|
1.0
|
|
HA
|
A:ASP626
|
4.6
|
92.3
|
1.0
|
|
HB2
|
A:GLN690
|
4.7
|
81.7
|
1.0
|
|
C
|
A:ASP626
|
4.7
|
70.0
|
1.0
|
|
C
|
A:GLY687
|
4.7
|
0.6
|
1.0
|
|
HA
|
A:HIS627
|
4.7
|
88.0
|
1.0
|
|
HA2
|
A:GLY687
|
4.8
|
0.9
|
1.0
|
|
CG
|
A:GLU684
|
4.8
|
75.2
|
1.0
|
|
HB3
|
A:GLU684
|
4.8
|
79.3
|
1.0
|
|
CB
|
A:ASP626
|
4.8
|
81.1
|
1.0
|
|
HA
|
A:LEU688
|
4.9
|
0.1
|
1.0
|
|
CA
|
A:PRO628
|
4.9
|
78.6
|
1.0
|
|
CB
|
A:GLN690
|
4.9
|
68.0
|
1.0
|
|
H
|
A:ALA689
|
5.0
|
0.2
|
1.0
|
|
CG
|
A:HIS627
|
5.0
|
63.1
|
1.0
|
|
N
|
A:GLY629
|
5.0
|
85.5
|
1.0
|
|
CA
|
A:ASP626
|
5.0
|
76.8
|
1.0
|
|
Sodium binding site 2 out
of 6 in 6cl5
Go back to
Sodium Binding Sites List in 6cl5
Sodium binding site 2 out
of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na801
b:75.8
occ:1.00
|
O
|
B:HIS627
|
2.2
|
76.8
|
1.0
|
|
O
|
B:LEU688
|
2.4
|
88.3
|
1.0
|
|
OE1
|
B:GLU684
|
2.4
|
91.4
|
1.0
|
|
OE1
|
B:GLN690
|
2.5
|
73.1
|
1.0
|
|
OD1
|
B:ASP626
|
2.5
|
0.1
|
1.0
|
|
O
|
B:HOH924
|
3.0
|
72.5
|
1.0
|
|
O
|
B:HOH919
|
3.1
|
68.8
|
1.0
|
|
HB3
|
B:HIS627
|
3.1
|
90.1
|
1.0
|
|
HE22
|
B:GLN690
|
3.2
|
86.0
|
1.0
|
|
CD
|
B:GLU684
|
3.2
|
94.1
|
1.0
|
|
H
|
B:HIS627
|
3.2
|
94.7
|
1.0
|
|
HA
|
B:ALA689
|
3.2
|
0.2
|
1.0
|
|
OE2
|
B:GLU684
|
3.2
|
85.4
|
1.0
|
|
C
|
B:HIS627
|
3.3
|
77.9
|
1.0
|
|
CD
|
B:GLN690
|
3.3
|
71.8
|
1.0
|
|
C
|
B:LEU688
|
3.5
|
97.4
|
1.0
|
|
NE2
|
B:GLN690
|
3.5
|
71.6
|
1.0
|
|
CG
|
B:ASP626
|
3.6
|
0.1
|
1.0
|
|
N
|
B:HIS627
|
3.7
|
79.2
|
1.0
|
|
CA
|
B:HIS627
|
3.8
|
80.1
|
1.0
|
|
CB
|
B:HIS627
|
3.9
|
75.3
|
1.0
|
|
OD2
|
B:ASP626
|
3.9
|
0.1
|
1.0
|
|
CA
|
B:ALA689
|
4.0
|
95.1
|
1.0
|
|
H
|
B:GLN690
|
4.0
|
0.7
|
1.0
|
|
N
|
B:ALA689
|
4.2
|
87.9
|
1.0
|
|
HA
|
B:PRO628
|
4.3
|
96.9
|
1.0
|
|
HE21
|
B:GLN690
|
4.3
|
86.0
|
1.0
|
|
N
|
B:GLN690
|
4.4
|
94.7
|
1.0
|
|
N
|
B:PRO628
|
4.4
|
83.0
|
1.0
|
|
N
|
B:LEU688
|
4.4
|
96.9
|
1.0
|
|
HB2
|
B:HIS627
|
4.4
|
90.1
|
1.0
|
|
H
|
B:LEU688
|
4.4
|
0.3
|
1.0
|
|
C
|
B:ALA689
|
4.5
|
99.7
|
1.0
|
|
CA
|
B:LEU688
|
4.6
|
98.4
|
1.0
|
|
CG
|
B:GLN690
|
4.6
|
76.6
|
1.0
|
|
O
|
B:TYR686
|
4.6
|
0.9
|
1.0
|
|
CG
|
B:GLU684
|
4.6
|
88.0
|
1.0
|
|
CA
|
B:PRO628
|
4.6
|
80.7
|
1.0
|
|
HB2
|
B:GLN690
|
4.7
|
98.1
|
1.0
|
|
C
|
B:PRO628
|
4.7
|
88.9
|
1.0
|
|
C
|
B:ASP626
|
4.7
|
82.2
|
1.0
|
|
HA2
|
B:GLY687
|
4.7
|
0.7
|
1.0
|
|
C
|
B:GLY687
|
4.7
|
97.5
|
1.0
|
|
HA
|
B:HIS627
|
4.8
|
96.2
|
1.0
|
|
HG3
|
B:GLN690
|
4.8
|
92.0
|
1.0
|
|
HA
|
B:ASP626
|
4.8
|
0.5
|
1.0
|
|
HB3
|
B:GLU684
|
4.8
|
92.9
|
1.0
|
|
CB
|
B:ASP626
|
4.9
|
0.4
|
1.0
|
|
O
|
B:PRO628
|
4.9
|
90.7
|
1.0
|
|
CG
|
B:HIS627
|
4.9
|
79.3
|
1.0
|
|
HG2
|
B:GLU684
|
5.0
|
0.7
|
1.0
|
|
HA
|
B:LEU688
|
5.0
|
0.1
|
1.0
|
|
ND1
|
B:HIS627
|
5.0
|
73.2
|
1.0
|
|
Sodium binding site 3 out
of 6 in 6cl5
Go back to
Sodium Binding Sites List in 6cl5
Sodium binding site 3 out
of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na801
b:77.9
occ:1.00
|
O
|
C:LEU688
|
2.4
|
0.4
|
1.0
|
|
O
|
C:HOH963
|
2.4
|
59.2
|
1.0
|
|
OE1
|
C:GLN690
|
2.4
|
96.1
|
1.0
|
|
OE1
|
C:GLU684
|
2.5
|
0.5
|
1.0
|
|
O
|
C:HIS627
|
2.5
|
0.2
|
1.0
|
|
OD1
|
C:ASP626
|
2.5
|
0.7
|
1.0
|
|
HE22
|
C:GLN690
|
3.1
|
90.6
|
1.0
|
|
CD
|
C:GLN690
|
3.2
|
85.5
|
1.0
|
|
CD
|
C:GLU684
|
3.3
|
0.1
|
1.0
|
|
H
|
C:HIS627
|
3.4
|
0.5
|
1.0
|
|
OE2
|
C:GLU684
|
3.5
|
94.0
|
1.0
|
|
NE2
|
C:GLN690
|
3.5
|
75.5
|
1.0
|
|
C
|
C:LEU688
|
3.5
|
0.4
|
1.0
|
|
CG
|
C:ASP626
|
3.5
|
99.0
|
1.0
|
|
HB3
|
C:HIS627
|
3.6
|
0.3
|
1.0
|
|
C
|
C:HIS627
|
3.6
|
99.1
|
1.0
|
|
HA
|
C:ALA689
|
3.7
|
0.4
|
1.0
|
|
HA2
|
C:GLY687
|
3.7
|
0.5
|
1.0
|
|
H
|
C:GLN690
|
3.8
|
0.5
|
1.0
|
|
OD2
|
C:ASP626
|
3.8
|
0.0
|
1.0
|
|
O
|
C:TYR686
|
3.8
|
0.7
|
1.0
|
|
N
|
C:HIS627
|
4.0
|
88.7
|
1.0
|
|
C
|
C:GLY687
|
4.0
|
0.4
|
1.0
|
|
N
|
C:LEU688
|
4.0
|
94.8
|
1.0
|
|
CA
|
C:HIS627
|
4.2
|
95.4
|
1.0
|
|
H
|
C:LEU688
|
4.2
|
0.4
|
1.0
|
|
O
|
C:GLY687
|
4.2
|
1.0
|
1.0
|
|
HE21
|
C:GLN690
|
4.3
|
90.6
|
1.0
|
|
CB
|
C:HIS627
|
4.3
|
96.1
|
1.0
|
|
CA
|
C:LEU688
|
4.3
|
99.5
|
1.0
|
|
CA
|
C:GLY687
|
4.4
|
0.7
|
1.0
|
|
N
|
C:ALA689
|
4.4
|
0.1
|
1.0
|
|
CA
|
C:ALA689
|
4.4
|
0.8
|
1.0
|
|
HA
|
C:PRO628
|
4.4
|
0.2
|
1.0
|
|
N
|
C:GLN690
|
4.5
|
0.4
|
1.0
|
|
CG
|
C:GLN690
|
4.5
|
86.3
|
1.0
|
|
HG3
|
C:GLN690
|
4.6
|
0.6
|
1.0
|
|
HA
|
C:LEU688
|
4.7
|
0.4
|
1.0
|
|
N
|
C:PRO628
|
4.7
|
0.6
|
1.0
|
|
CG
|
C:GLU684
|
4.8
|
93.2
|
1.0
|
|
HB2
|
C:HIS627
|
4.8
|
0.3
|
1.0
|
|
C
|
C:TYR686
|
4.8
|
0.8
|
1.0
|
|
HA
|
C:ASP626
|
4.9
|
0.7
|
1.0
|
|
CA
|
C:PRO628
|
4.9
|
0.7
|
1.0
|
|
CB
|
C:ASP626
|
4.9
|
98.3
|
1.0
|
|
C
|
C:ALA689
|
4.9
|
0.1
|
1.0
|
|
HB2
|
C:GLU684
|
4.9
|
0.1
|
1.0
|
|
C
|
C:ASP626
|
5.0
|
95.2
|
1.0
|
|
HB3
|
C:GLU684
|
5.0
|
0.1
|
1.0
|
|
Sodium binding site 4 out
of 6 in 6cl5
Go back to
Sodium Binding Sites List in 6cl5
Sodium binding site 4 out
of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na803
b:84.6
occ:1.00
|
O
|
D:LEU688
|
2.2
|
63.6
|
1.0
|
|
O
|
D:HIS627
|
2.4
|
60.0
|
1.0
|
|
OE1
|
D:GLN690
|
2.5
|
58.3
|
1.0
|
|
OD1
|
D:ASP626
|
2.5
|
78.2
|
1.0
|
|
OE1
|
D:GLU684
|
2.5
|
78.9
|
1.0
|
|
H
|
D:HIS627
|
3.0
|
67.2
|
1.0
|
|
HE22
|
D:GLN690
|
3.1
|
76.3
|
1.0
|
|
CD
|
D:GLN690
|
3.1
|
67.1
|
1.0
|
|
HB3
|
D:HIS627
|
3.1
|
68.3
|
1.0
|
|
O
|
D:HOH1114
|
3.1
|
61.5
|
1.0
|
|
NE2
|
D:GLN690
|
3.3
|
63.5
|
1.0
|
|
HA
|
D:ALA689
|
3.3
|
79.5
|
1.0
|
|
C
|
D:LEU688
|
3.3
|
61.7
|
1.0
|
|
O
|
D:HOH1060
|
3.4
|
73.8
|
1.0
|
|
C
|
D:HIS627
|
3.4
|
63.4
|
1.0
|
|
CD
|
D:GLU684
|
3.4
|
80.6
|
1.0
|
|
H
|
D:GLN690
|
3.5
|
59.9
|
1.0
|
|
CG
|
D:ASP626
|
3.6
|
66.9
|
1.0
|
|
N
|
D:HIS627
|
3.6
|
56.3
|
1.0
|
|
OE2
|
D:GLU684
|
3.7
|
80.1
|
1.0
|
|
CB
|
D:HIS627
|
3.8
|
57.2
|
1.0
|
|
CA
|
D:HIS627
|
3.8
|
56.8
|
1.0
|
|
OD2
|
D:ASP626
|
4.0
|
70.0
|
1.0
|
|
CA
|
D:ALA689
|
4.0
|
66.2
|
1.0
|
|
HE21
|
D:GLN690
|
4.0
|
76.3
|
1.0
|
|
N
|
D:GLN690
|
4.0
|
50.2
|
1.0
|
|
H
|
D:LEU688
|
4.1
|
91.9
|
1.0
|
|
N
|
D:ALA689
|
4.1
|
54.0
|
1.0
|
|
N
|
D:LEU688
|
4.2
|
76.5
|
1.0
|
|
HB2
|
D:HIS627
|
4.2
|
68.3
|
1.0
|
|
HG3
|
D:GLN690
|
4.2
|
73.7
|
1.0
|
|
CG
|
D:GLN690
|
4.2
|
61.4
|
1.0
|
|
C
|
D:ALA689
|
4.4
|
64.7
|
1.0
|
|
CA
|
D:LEU688
|
4.4
|
62.2
|
1.0
|
|
HA
|
D:PRO628
|
4.6
|
81.4
|
1.0
|
|
N
|
D:PRO628
|
4.6
|
67.3
|
1.0
|
|
H
|
D:GLY629
|
4.6
|
95.4
|
1.0
|
|
HB2
|
D:GLN690
|
4.6
|
71.2
|
1.0
|
|
HA
|
D:ASP626
|
4.7
|
81.5
|
1.0
|
|
C
|
D:ASP626
|
4.7
|
59.8
|
1.0
|
|
C
|
D:GLY687
|
4.7
|
86.0
|
1.0
|
|
HA2
|
D:GLY687
|
4.7
|
96.3
|
1.0
|
|
HA
|
D:HIS627
|
4.8
|
68.2
|
1.0
|
|
HB3
|
D:GLU684
|
4.8
|
89.3
|
1.0
|
|
CG
|
D:GLU684
|
4.8
|
75.0
|
1.0
|
|
HA
|
D:LEU688
|
4.8
|
74.7
|
1.0
|
|
CB
|
D:GLN690
|
4.9
|
59.3
|
1.0
|
|
CB
|
D:ASP626
|
4.9
|
72.3
|
1.0
|
|
H
|
D:ALA689
|
4.9
|
64.9
|
1.0
|
|
HB2
|
D:GLU684
|
5.0
|
89.3
|
1.0
|
|
HG2
|
D:GLN690
|
5.0
|
73.7
|
1.0
|
|
Sodium binding site 5 out
of 6 in 6cl5
Go back to
Sodium Binding Sites List in 6cl5
Sodium binding site 5 out
of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na801
b:0.4
occ:1.00
|
O
|
E:LEU688
|
2.1
|
0.3
|
1.0
|
|
O
|
E:HIS627
|
2.2
|
82.6
|
1.0
|
|
OE1
|
E:GLU684
|
2.5
|
0.2
|
1.0
|
|
OD1
|
E:ASP626
|
2.5
|
0.6
|
1.0
|
|
OE1
|
E:GLN690
|
2.5
|
82.3
|
1.0
|
|
HB3
|
E:HIS627
|
2.8
|
95.2
|
1.0
|
|
H
|
E:HIS627
|
3.0
|
97.1
|
1.0
|
|
HA
|
E:ALA689
|
3.0
|
0.5
|
1.0
|
|
C
|
E:HIS627
|
3.2
|
98.8
|
1.0
|
|
C
|
E:LEU688
|
3.2
|
0.0
|
1.0
|
|
HE22
|
E:GLN690
|
3.3
|
97.3
|
1.0
|
|
CD
|
E:GLN690
|
3.3
|
88.8
|
1.0
|
|
CD
|
E:GLU684
|
3.3
|
0.8
|
1.0
|
|
N
|
E:HIS627
|
3.5
|
81.2
|
1.0
|
|
OE2
|
E:GLU684
|
3.5
|
1.0
|
1.0
|
|
CB
|
E:HIS627
|
3.6
|
79.7
|
1.0
|
|
CG
|
E:ASP626
|
3.6
|
0.0
|
1.0
|
|
CA
|
E:HIS627
|
3.6
|
89.4
|
1.0
|
|
NE2
|
E:GLN690
|
3.6
|
81.3
|
1.0
|
|
CA
|
E:ALA689
|
3.8
|
0.2
|
1.0
|
|
H
|
E:GLN690
|
3.9
|
0.2
|
1.0
|
|
N
|
E:ALA689
|
3.9
|
0.7
|
1.0
|
|
OD2
|
E:ASP626
|
4.0
|
0.9
|
1.0
|
|
HB2
|
E:HIS627
|
4.1
|
95.2
|
1.0
|
|
N
|
E:GLN690
|
4.2
|
0.8
|
1.0
|
|
C
|
E:ALA689
|
4.3
|
0.3
|
1.0
|
|
N
|
E:LEU688
|
4.3
|
0.1
|
1.0
|
|
H
|
E:LEU688
|
4.3
|
1.0
|
1.0
|
|
CA
|
E:LEU688
|
4.4
|
0.7
|
1.0
|
|
N
|
E:PRO628
|
4.4
|
84.9
|
1.0
|
|
HE21
|
E:GLN690
|
4.4
|
97.3
|
1.0
|
|
HA
|
E:PRO628
|
4.5
|
1.0
|
1.0
|
|
HA
|
E:HIS627
|
4.6
|
0.3
|
1.0
|
|
C
|
E:ASP626
|
4.6
|
91.8
|
1.0
|
|
CG
|
E:GLN690
|
4.6
|
81.8
|
1.0
|
|
HB2
|
E:GLN690
|
4.6
|
98.1
|
1.0
|
|
HA
|
E:ASP626
|
4.6
|
0.8
|
1.0
|
|
CG
|
E:HIS627
|
4.6
|
81.2
|
1.0
|
|
CG
|
E:GLU684
|
4.7
|
0.9
|
1.0
|
|
HB3
|
E:GLU684
|
4.7
|
0.9
|
1.0
|
|
C
|
E:GLY687
|
4.7
|
0.3
|
1.0
|
|
ND1
|
E:HIS627
|
4.7
|
89.5
|
1.0
|
|
O
|
E:TYR686
|
4.7
|
0.3
|
1.0
|
|
HG3
|
E:GLN690
|
4.8
|
97.8
|
1.0
|
|
CA
|
E:PRO628
|
4.8
|
85.2
|
1.0
|
|
H
|
E:ALA689
|
4.8
|
0.2
|
1.0
|
|
C
|
E:PRO628
|
4.8
|
89.8
|
1.0
|
|
HA
|
E:LEU688
|
4.8
|
0.5
|
1.0
|
|
CB
|
E:ASP626
|
4.8
|
0.3
|
1.0
|
|
HA2
|
E:GLY687
|
4.8
|
0.1
|
1.0
|
|
CA
|
E:ASP626
|
4.9
|
0.3
|
1.0
|
|
HG2
|
E:GLU684
|
5.0
|
0.7
|
1.0
|
|
Sodium binding site 6 out
of 6 in 6cl5
Go back to
Sodium Binding Sites List in 6cl5
Sodium binding site 6 out
of 6 in the Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Structure of P. Aeruginosa R1 Pyocin Fiber PALES_06171 Comprising C- Terminal Residues 323-701 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na801
b:75.5
occ:1.00
|
OE1
|
F:GLN690
|
2.3
|
98.1
|
1.0
|
|
O
|
F:HIS627
|
2.3
|
0.5
|
1.0
|
|
O
|
F:LEU688
|
2.4
|
84.3
|
1.0
|
|
OD1
|
F:ASP626
|
2.5
|
95.7
|
1.0
|
|
O
|
F:HOH1025
|
2.6
|
60.4
|
1.0
|
|
OE1
|
F:GLU684
|
2.9
|
92.3
|
1.0
|
|
O
|
F:HOH1117
|
3.1
|
66.2
|
1.0
|
|
H
|
F:HIS627
|
3.2
|
0.8
|
1.0
|
|
HA
|
F:ALA689
|
3.2
|
0.9
|
1.0
|
|
H
|
F:GLN690
|
3.3
|
0.6
|
1.0
|
|
CD
|
F:GLN690
|
3.3
|
98.2
|
1.0
|
|
HB3
|
F:HIS627
|
3.3
|
0.1
|
1.0
|
|
C
|
F:HIS627
|
3.4
|
1.0
|
1.0
|
|
C
|
F:LEU688
|
3.5
|
87.7
|
1.0
|
|
CG
|
F:ASP626
|
3.5
|
0.1
|
1.0
|
|
HE22
|
F:GLN690
|
3.5
|
0.6
|
1.0
|
|
N
|
F:HIS627
|
3.7
|
93.9
|
1.0
|
|
NE2
|
F:GLN690
|
3.8
|
87.9
|
1.0
|
|
CD
|
F:GLU684
|
3.8
|
87.4
|
1.0
|
|
OD2
|
F:ASP626
|
3.8
|
0.7
|
1.0
|
|
OE2
|
F:GLU684
|
3.9
|
96.3
|
1.0
|
|
CA
|
F:HIS627
|
4.0
|
0.8
|
1.0
|
|
CA
|
F:ALA689
|
4.0
|
0.0
|
1.0
|
|
N
|
F:GLN690
|
4.1
|
0.1
|
1.0
|
|
CB
|
F:HIS627
|
4.1
|
85.0
|
1.0
|
|
N
|
F:ALA689
|
4.2
|
0.2
|
1.0
|
|
HA
|
F:PRO628
|
4.4
|
0.6
|
1.0
|
|
N
|
F:LEU688
|
4.4
|
89.1
|
1.0
|
|
HA2
|
F:GLY687
|
4.4
|
0.1
|
1.0
|
|
C
|
F:GLY687
|
4.4
|
84.8
|
1.0
|
|
CA
|
F:LEU688
|
4.5
|
96.3
|
1.0
|
|
CG
|
F:GLN690
|
4.5
|
94.0
|
1.0
|
|
O
|
F:TYR686
|
4.5
|
0.9
|
1.0
|
|
N
|
F:PRO628
|
4.5
|
0.1
|
1.0
|
|
C
|
F:ALA689
|
4.5
|
0.6
|
1.0
|
|
O
|
F:GLY687
|
4.5
|
98.2
|
1.0
|
|
HB2
|
F:HIS627
|
4.6
|
0.1
|
1.0
|
|
HG3
|
F:GLN690
|
4.6
|
0.9
|
1.0
|
|
HE21
|
F:GLN690
|
4.6
|
0.6
|
1.0
|
|
H
|
F:LEU688
|
4.7
|
1.0
|
1.0
|
|
HA
|
F:ASP626
|
4.7
|
1.0
|
1.0
|
|
HB2
|
F:GLN690
|
4.7
|
0.7
|
1.0
|
|
C
|
F:ASP626
|
4.8
|
94.9
|
1.0
|
|
CA
|
F:PRO628
|
4.8
|
0.1
|
1.0
|
|
HA
|
F:LEU688
|
4.8
|
0.6
|
1.0
|
|
CB
|
F:ASP626
|
4.8
|
0.8
|
1.0
|
|
C
|
F:PRO628
|
4.9
|
0.1
|
1.0
|
|
HA
|
F:HIS627
|
4.9
|
1.0
|
1.0
|
|
H
|
F:ALA689
|
5.0
|
0.4
|
1.0
|
|
CA
|
F:GLY687
|
5.0
|
84.5
|
1.0
|
|
Reference:
S.A.Buth,
M.M.Shneider,
D.Scholl,
P.G.Leiman.
Structure and Analysis of R1 and R2 Pyocin Receptor-Binding Fibers. Viruses V. 10 2018.
ISSN: ISSN 1999-4915
PubMed: 30110933
DOI: 10.3390/V10080427
Page generated: Tue Oct 8 06:35:45 2024
|
