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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:

Caesium (Cs) 8 atoms

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

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