Chlorine in PDB 1c4d: Gramicidin Cscl Complex
Protein crystallography data
The structure of Gramicidin Cscl Complex, PDB code: 1c4d
was solved by
B.A.Wallace,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
5.00 /
2.00
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
32.118,
52.103,
31.174,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
23.2 /
n/a
|
Other elements in 1c4d:
The structure of Gramicidin Cscl Complex also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Gramicidin Cscl Complex
(pdb code 1c4d). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Gramicidin Cscl Complex, PDB code: 1c4d:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 1c4d
Go back to
Chlorine Binding Sites List in 1c4d
Chlorine binding site 1 out
of 6 in the Gramicidin Cscl Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Gramicidin Cscl Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl119
b:9.9
occ:1.00
|
C
|
A:MOH133
|
2.8
|
14.2
|
1.0
|
|
N
|
B:VAL7
|
2.9
|
25.6
|
1.0
|
|
O
|
A:TRP9
|
3.1
|
7.5
|
1.0
|
|
O
|
B:ALA5
|
3.2
|
30.3
|
1.0
|
|
C
|
A:TRP9
|
3.3
|
16.2
|
1.0
|
|
O
|
A:MOH133
|
3.4
|
14.5
|
1.0
|
|
C
|
B:VAL7
|
3.4
|
19.0
|
1.0
|
|
N
|
A:DLE10
|
3.4
|
6.2
|
1.0
|
|
N
|
A:TRP9
|
3.4
|
17.3
|
1.0
|
|
CA
|
B:VAL7
|
3.5
|
24.3
|
1.0
|
|
C
|
B:DVA6
|
3.5
|
30.8
|
1.0
|
|
N
|
B:DVA8
|
3.5
|
23.3
|
1.0
|
|
C
|
B:ALA5
|
3.7
|
26.9
|
1.0
|
|
C
|
A:DLE10
|
3.8
|
23.5
|
1.0
|
|
O
|
A:VAL7
|
3.8
|
15.4
|
1.0
|
|
CA
|
A:DLE10
|
3.9
|
8.1
|
1.0
|
|
CA
|
A:TRP9
|
3.9
|
13.7
|
1.0
|
|
CA
|
B:DVA6
|
3.9
|
28.8
|
1.0
|
|
N
|
A:TRP11
|
4.0
|
31.2
|
1.0
|
|
O
|
B:VAL7
|
4.0
|
15.7
|
1.0
|
|
N
|
B:DVA6
|
4.0
|
24.6
|
1.0
|
|
C
|
A:DVA8
|
4.1
|
16.5
|
1.0
|
|
CA
|
A:DVA8
|
4.2
|
14.6
|
1.0
|
|
C
|
B:DVA8
|
4.2
|
21.9
|
1.0
|
|
O
|
A:DLE10
|
4.2
|
9.2
|
1.0
|
|
O
|
A:DLE12
|
4.3
|
20.3
|
1.0
|
|
CA
|
B:DVA8
|
4.3
|
19.1
|
1.0
|
|
O
|
B:DVA6
|
4.4
|
24.6
|
1.0
|
|
C
|
A:VAL7
|
4.5
|
20.0
|
1.0
|
|
N
|
B:ALA5
|
4.5
|
12.6
|
1.0
|
|
O
|
B:DVA8
|
4.6
|
26.2
|
1.0
|
|
N
|
A:DLE12
|
4.6
|
38.5
|
1.0
|
|
CA
|
B:ALA5
|
4.6
|
12.4
|
1.0
|
|
N
|
B:TRP9
|
4.7
|
19.5
|
1.0
|
|
N
|
A:DVA8
|
4.7
|
26.7
|
1.0
|
|
O
|
B:HOH2005
|
4.7
|
2.3
|
1.0
|
|
CA
|
A:TRP11
|
4.8
|
31.7
|
1.0
|
|
C
|
A:DLE12
|
4.8
|
36.8
|
1.0
|
|
CG2
|
A:DVA8
|
4.9
|
29.1
|
1.0
|
|
N
|
B:DLE10
|
4.9
|
24.7
|
1.0
|
|
C
|
A:TRP11
|
5.0
|
30.6
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 1c4d
Go back to
Chlorine Binding Sites List in 1c4d
Chlorine binding site 2 out
of 6 in the Gramicidin Cscl Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Gramicidin Cscl Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl120
b:7.7
occ:1.00
|
N
|
A:ALA3
|
3.0
|
25.4
|
1.0
|
|
N
|
A:DLE4
|
3.1
|
15.0
|
1.0
|
|
C
|
A:ALA3
|
3.1
|
22.4
|
1.0
|
|
O
|
B:DLE14
|
3.4
|
9.6
|
1.0
|
|
N
|
B:TRP13
|
3.4
|
34.6
|
1.0
|
|
O
|
A:FVA1
|
3.5
|
11.0
|
1.0
|
|
CA
|
A:ALA3
|
3.5
|
17.4
|
1.0
|
|
C
|
B:TRP13
|
3.6
|
20.7
|
1.0
|
|
C
|
B:DLE14
|
3.6
|
16.1
|
1.0
|
|
N
|
B:DLE14
|
3.6
|
15.3
|
1.0
|
|
O
|
A:ALA3
|
3.6
|
14.3
|
1.0
|
|
CA
|
A:DLE4
|
3.6
|
23.2
|
1.0
|
|
C
|
A:DLE4
|
3.6
|
30.6
|
1.0
|
|
O
|
B:TRP13
|
3.6
|
15.4
|
1.0
|
|
C
|
A:FVA1
|
3.8
|
26.2
|
1.0
|
|
O
|
B:TRP11
|
3.9
|
6.9
|
1.0
|
|
CA
|
B:TRP13
|
3.9
|
15.4
|
1.0
|
|
C
|
A:GLY2
|
4.0
|
34.0
|
1.0
|
|
CA
|
B:DLE14
|
4.1
|
22.8
|
1.0
|
|
N
|
A:ALA5
|
4.1
|
38.6
|
1.0
|
|
CA
|
A:GLY2
|
4.1
|
18.5
|
1.0
|
|
O
|
A:DLE4
|
4.1
|
21.9
|
1.0
|
|
N
|
A:GLY2
|
4.1
|
28.8
|
1.0
|
|
C
|
B:DLE12
|
4.1
|
37.0
|
1.0
|
|
N
|
B:TRP15
|
4.2
|
24.0
|
1.0
|
|
CA
|
B:DLE12
|
4.3
|
25.0
|
1.0
|
|
N
|
B:ETA16
|
4.5
|
16.9
|
1.0
|
|
C
|
B:TRP11
|
4.5
|
25.9
|
1.0
|
|
CA
|
B:TRP15
|
4.6
|
19.9
|
1.0
|
|
O
|
B:ETA16
|
4.6
|
21.7
|
1.0
|
|
N
|
A:FVA1
|
4.7
|
15.7
|
1.0
|
|
C
|
B:TRP15
|
4.7
|
12.7
|
1.0
|
|
CS
|
A:CS116
|
4.7
|
53.0
|
1.0
|
|
CA
|
A:FVA1
|
4.7
|
21.9
|
1.0
|
|
N
|
B:DLE12
|
4.7
|
26.3
|
1.0
|
|
CA
|
A:ALA5
|
4.8
|
25.2
|
1.0
|
|
CB
|
B:ETA16
|
4.9
|
4.0
|
1.0
|
|
CB
|
A:ALA3
|
4.9
|
19.5
|
1.0
|
|
N
|
A:DVA6
|
4.9
|
20.0
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 1c4d
Go back to
Chlorine Binding Sites List in 1c4d
Chlorine binding site 3 out
of 6 in the Gramicidin Cscl Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Gramicidin Cscl Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl117
b:2.3
occ:1.00
|
O
|
A:HOH2003
|
2.5
|
1.9
|
1.0
|
|
O
|
B:HOH2003
|
2.7
|
1.9
|
1.0
|
|
N
|
B:GLY2
|
3.1
|
29.2
|
1.0
|
|
CA
|
B:FVA1
|
3.5
|
17.4
|
1.0
|
|
C
|
B:GLY2
|
3.5
|
26.2
|
1.0
|
|
C
|
B:FVA1
|
3.6
|
31.4
|
1.0
|
|
N
|
B:ALA3
|
3.7
|
32.7
|
1.0
|
|
CA
|
B:ALA3
|
3.9
|
15.3
|
1.0
|
|
O
|
B:GLY2
|
3.9
|
29.3
|
1.0
|
|
CA
|
A:ETA16
|
4.0
|
18.2
|
1.0
|
|
CA
|
B:GLY2
|
4.0
|
27.8
|
1.0
|
|
O
|
B:HOH2002
|
4.0
|
8.1
|
1.0
|
|
O
|
A:ETA16
|
4.1
|
14.1
|
1.0
|
|
N
|
B:FVA1
|
4.1
|
24.8
|
1.0
|
|
O
|
A:TRP15
|
4.3
|
11.5
|
1.0
|
|
N
|
A:ETA16
|
4.4
|
10.7
|
1.0
|
|
CB
|
B:ALA3
|
4.4
|
17.9
|
1.0
|
|
CB
|
A:ETA16
|
4.5
|
10.5
|
1.0
|
|
C
|
A:TRP15
|
4.5
|
15.5
|
1.0
|
|
CG1
|
B:FVA1
|
4.5
|
14.6
|
1.0
|
|
O1
|
B:FVA1
|
4.6
|
12.2
|
1.0
|
|
CB
|
B:FVA1
|
4.6
|
16.5
|
1.0
|
|
O
|
B:FVA1
|
4.7
|
21.3
|
1.0
|
|
CN
|
B:FVA1
|
4.8
|
24.2
|
1.0
|
|
O
|
B:HOH2001
|
4.9
|
27.3
|
1.0
|
|
CS
|
B:CS116
|
5.0
|
47.2
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 1c4d
Go back to
Chlorine Binding Sites List in 1c4d
Chlorine binding site 4 out
of 6 in the Gramicidin Cscl Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Gramicidin Cscl Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl117
b:9.4
occ:1.00
|
N
|
C:TRP9
|
3.1
|
18.9
|
1.0
|
|
N
|
C:DLE10
|
3.2
|
12.0
|
1.0
|
|
CG2
|
C:DVA8
|
3.3
|
14.2
|
1.0
|
|
O
|
D:VAL7
|
3.3
|
11.5
|
1.0
|
|
O
|
C:VAL7
|
3.3
|
14.0
|
1.0
|
|
CA
|
C:DVA8
|
3.4
|
19.5
|
1.0
|
|
C
|
C:DVA8
|
3.4
|
18.9
|
1.0
|
|
C
|
C:TRP9
|
3.5
|
27.5
|
1.0
|
|
C
|
D:VAL7
|
3.5
|
26.3
|
1.0
|
|
C
|
C:VAL7
|
3.6
|
19.2
|
1.0
|
|
CA
|
C:TRP9
|
3.7
|
25.7
|
1.0
|
|
N
|
D:DVA8
|
3.7
|
35.3
|
1.0
|
|
CA
|
D:DVA8
|
3.7
|
29.8
|
1.0
|
|
N
|
D:TRP9
|
3.7
|
17.0
|
1.0
|
|
N
|
C:DVA8
|
3.7
|
24.4
|
1.0
|
|
N
|
D:VAL7
|
3.9
|
21.9
|
1.0
|
|
N
|
D:DLE10
|
3.9
|
13.0
|
1.0
|
|
CA
|
C:DLE10
|
4.0
|
6.3
|
1.0
|
|
C
|
D:DVA8
|
4.0
|
23.5
|
1.0
|
|
C
|
C:DLE10
|
4.0
|
23.3
|
1.0
|
|
O
|
D:DLE10
|
4.1
|
23.3
|
1.0
|
|
CB
|
C:DVA8
|
4.1
|
12.6
|
1.0
|
|
O
|
C:DLE10
|
4.1
|
13.0
|
1.0
|
|
O
|
C:TRP9
|
4.2
|
42.8
|
1.0
|
|
C
|
D:TRP9
|
4.2
|
16.8
|
1.0
|
|
C
|
D:DLE10
|
4.2
|
24.4
|
1.0
|
|
CA
|
D:VAL7
|
4.2
|
26.9
|
1.0
|
|
O
|
C:DVA8
|
4.3
|
7.2
|
1.0
|
|
CA
|
D:DLE10
|
4.3
|
20.7
|
1.0
|
|
CA
|
D:TRP9
|
4.4
|
8.0
|
1.0
|
|
N
|
C:VAL7
|
4.5
|
7.2
|
1.0
|
|
CB
|
D:DVA8
|
4.5
|
27.6
|
1.0
|
|
CA
|
C:VAL7
|
4.6
|
15.6
|
1.0
|
|
O
|
D:ALA5
|
4.8
|
10.7
|
1.0
|
|
N
|
C:TRP11
|
4.8
|
27.7
|
1.0
|
|
O
|
D:DVA8
|
4.8
|
19.1
|
1.0
|
|
O
|
C:ALA5
|
4.8
|
33.4
|
1.0
|
|
O
|
D:TRP9
|
4.8
|
15.5
|
1.0
|
|
C
|
D:DVA6
|
4.9
|
24.3
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 1c4d
Go back to
Chlorine Binding Sites List in 1c4d
Chlorine binding site 5 out
of 6 in the Gramicidin Cscl Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Gramicidin Cscl Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl118
b:9.8
occ:1.00
|
O
|
D:MOH132
|
2.6
|
1.9
|
1.0
|
|
C
|
D:MOH132
|
2.8
|
3.2
|
1.0
|
|
N
|
C:ALA3
|
2.9
|
38.6
|
1.0
|
|
N
|
D:ETA16
|
3.1
|
22.4
|
1.0
|
|
C
|
D:TRP15
|
3.1
|
8.0
|
1.0
|
|
N
|
C:DLE4
|
3.3
|
26.1
|
1.0
|
|
O
|
D:ETA16
|
3.3
|
14.4
|
1.0
|
|
N
|
C:GLY2
|
3.3
|
14.7
|
1.0
|
|
CA
|
C:ALA3
|
3.4
|
24.5
|
1.0
|
|
CA
|
D:TRP15
|
3.4
|
20.2
|
1.0
|
|
C
|
C:GLY2
|
3.4
|
34.5
|
1.0
|
|
C
|
C:FVA1
|
3.5
|
18.8
|
1.0
|
|
N
|
D:TRP15
|
3.5
|
15.0
|
1.0
|
|
CA
|
D:ETA16
|
3.6
|
4.8
|
1.0
|
|
C
|
C:ALA3
|
3.7
|
28.1
|
1.0
|
|
CA
|
C:GLY2
|
3.8
|
21.0
|
1.0
|
|
O
|
D:TRP15
|
3.8
|
7.1
|
1.0
|
|
C
|
D:DLE14
|
3.9
|
15.8
|
1.0
|
|
CA
|
C:FVA1
|
4.0
|
9.0
|
1.0
|
|
O
|
C:FVA1
|
4.0
|
7.2
|
1.0
|
|
N
|
C:FVA1
|
4.1
|
23.2
|
1.0
|
|
O
|
C:GLY2
|
4.1
|
37.0
|
1.0
|
|
CB
|
D:ETA16
|
4.1
|
1.8
|
1.0
|
|
CA
|
C:DLE4
|
4.2
|
9.9
|
1.0
|
|
O
|
D:DLE14
|
4.3
|
5.5
|
1.0
|
|
O
|
D:TRP13
|
4.3
|
23.1
|
1.0
|
|
CN
|
C:FVA1
|
4.4
|
24.9
|
1.0
|
|
C
|
C:DLE4
|
4.4
|
25.6
|
1.0
|
|
O
|
C:ALA3
|
4.6
|
13.4
|
1.0
|
|
O
|
C:DLE4
|
4.6
|
18.9
|
1.0
|
|
C
|
D:TRP13
|
4.7
|
24.7
|
1.0
|
|
CB
|
C:ALA3
|
4.7
|
22.5
|
1.0
|
|
CS
|
D:CS116
|
4.7
|
57.5
|
1.0
|
|
CA
|
D:DLE14
|
4.8
|
14.4
|
1.0
|
|
N
|
D:DLE14
|
4.8
|
3.7
|
1.0
|
|
CB
|
D:TRP15
|
4.9
|
27.3
|
1.0
|
|
CB
|
C:DLE4
|
4.9
|
22.3
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 1c4d
Go back to
Chlorine Binding Sites List in 1c4d
Chlorine binding site 6 out
of 6 in the Gramicidin Cscl Complex
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Gramicidin Cscl Complex within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl119
b:1.9
occ:1.00
|
O
|
C:HOH2003
|
2.6
|
28.0
|
1.0
|
|
N
|
D:GLY2
|
2.8
|
25.4
|
1.0
|
|
C
|
D:FVA1
|
2.9
|
29.6
|
1.0
|
|
N
|
D:ALA3
|
3.0
|
29.3
|
1.0
|
|
C
|
D:MOH131
|
3.0
|
22.7
|
0.5
|
|
N
|
D:FVA1
|
3.1
|
29.1
|
1.0
|
|
CS
|
C:CS116
|
3.2
|
48.8
|
1.0
|
|
CA
|
D:FVA1
|
3.3
|
13.4
|
1.0
|
|
C
|
D:GLY2
|
3.4
|
26.9
|
1.0
|
|
CA
|
D:GLY2
|
3.5
|
17.1
|
1.0
|
|
O
|
D:FVA1
|
3.6
|
24.4
|
1.0
|
|
O
|
D:MOH131
|
3.6
|
22.0
|
0.5
|
|
CA
|
D:ALA3
|
3.6
|
24.9
|
1.0
|
|
N
|
D:DLE4
|
3.8
|
23.8
|
1.0
|
|
N
|
C:ETA16
|
4.0
|
23.2
|
1.0
|
|
CN
|
D:FVA1
|
4.0
|
19.3
|
1.0
|
|
C
|
D:ALA3
|
4.0
|
27.4
|
1.0
|
|
O
|
C:TRP13
|
4.0
|
5.7
|
1.0
|
|
O
|
C:ETA16
|
4.1
|
2.1
|
1.0
|
|
O1
|
D:FVA1
|
4.1
|
23.8
|
1.0
|
|
CA
|
C:ETA16
|
4.2
|
11.7
|
1.0
|
|
O
|
D:GLY2
|
4.2
|
25.2
|
1.0
|
|
C
|
C:TRP15
|
4.3
|
15.9
|
1.0
|
|
N
|
C:TRP15
|
4.5
|
28.2
|
1.0
|
|
CB
|
C:ETA16
|
4.5
|
13.9
|
1.0
|
|
C
|
C:TRP13
|
4.6
|
17.8
|
1.0
|
|
O
|
C:TRP11
|
4.6
|
10.5
|
1.0
|
|
C
|
C:DLE14
|
4.6
|
25.3
|
1.0
|
|
O
|
C:TRP15
|
4.7
|
10.8
|
1.0
|
|
N
|
C:TRP13
|
4.7
|
22.8
|
1.0
|
|
O
|
D:ALA3
|
4.7
|
16.5
|
1.0
|
|
CA
|
C:TRP15
|
4.8
|
24.0
|
1.0
|
|
N
|
C:DLE14
|
4.8
|
3.8
|
1.0
|
|
CA
|
D:DLE4
|
4.8
|
23.8
|
1.0
|
|
O
|
D:DLE4
|
4.9
|
10.3
|
1.0
|
|
C
|
D:DLE4
|
4.9
|
16.0
|
1.0
|
|
CB
|
D:FVA1
|
4.9
|
10.9
|
1.0
|
|
CA
|
C:DLE14
|
4.9
|
23.4
|
1.0
|
|
O
|
C:DLE14
|
5.0
|
21.8
|
1.0
|
|
Reference:
B.A.Wallace,
K.Ravikumar.
The Gramicidin Pore: Crystal Structure of A Cesium Complex. Science V. 241 182 1988.
ISSN: ISSN 0036-8075
PubMed: 2455344
DOI: 10.1126/SCIENCE.2455344
Page generated: Fri Jul 19 21:11:14 2024
|
