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Caesium 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 (Cl) 6 atoms

Caesium Binding Sites:

The binding sites of Caesium atom in the Gramicidin Cscl Complex (pdb code 1c4d). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 8 binding sites of Caesium where determined in the Gramicidin Cscl Complex, PDB code: 1c4d:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Caesium binding site 1 out of 8 in 1c4d

Go back to Caesium Binding Sites List in 1c4d
Caesium binding site 1 out of 8 in the Gramicidin Cscl Complex


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Gramicidin Cscl Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs116

b:53.0
occ:1.00
 O A:MOH133 2.4 14.5 1.0
C A:MOH133 2.7 14.2 1.0
O A:ALA5 2.8 10.8 1.0
O B:TRP9 2.9 17.3 1.0
C A:ALA5 3.2 23.9 1.0
CA B:DLE10 3.2 30.1 1.0
C B:TRP9 3.4 26.1 1.0
CA A:DVA6 3.4 18.6 1.0
N A:VAL7 3.5 16.7 1.0
CG2 A:DVA6 3.5 21.5 1.0
C B:DLE10 3.5 33.4 1.0
N B:TRP11 3.5 28.5 1.0
N A:DVA6 3.5 20.0 1.0
N A:ALA5 3.6 38.6 1.0
N B:DLE10 3.6 24.7 1.0
C A:DVA6 3.6 22.7 1.0
O B:DLE12 3.9 34.1 1.0
N B:DLE12 4.0 26.3 1.0
CB A:DVA6 4.0 15.2 1.0
CB B:DLE10 4.0 23.4 1.0
CA A:ALA5 4.2 25.2 1.0
N B:TRP9 4.2 19.5 1.0
N A:DVA8 4.2 26.7 1.0
C B:DLE12 4.2 37.0 1.0
CA A:VAL7 4.2 22.7 1.0
O B:DLE10 4.2 17.3 1.0
C B:TRP11 4.2 25.9 1.0
C A:VAL7 4.3 20.0 1.0
CA B:TRP11 4.3 23.5 1.0
O A:DVA8 4.4 10.8 1.0
CA B:TRP9 4.4 20.4 1.0
O A:DVA6 4.5 9.4 1.0
C A:DLE4 4.5 30.6 1.0
CA B:DLE12 4.6 25.0 1.0
C A:DVA8 4.6 16.5 1.0
N B:TRP13 4.7 34.6 1.0
CL A:CL120 4.7 7.7 1.0
CA A:DLE4 4.7 23.2 1.0
O B:DLE14 4.7 9.6 1.0
O B:VAL7 4.8 15.7 1.0
CA A:DVA8 4.9 14.6 1.0
CA B:TRP13 4.9 15.4 1.0
O B:TRP11 4.9 6.9 1.0
O A:VAL7 5.0 15.4 1.0

Caesium binding site 2 out of 8 in 1c4d

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Caesium binding site 2 out of 8 in the Gramicidin Cscl Complex


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Gramicidin Cscl Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs117

b:45.4
occ:0.50
 CD2 A:DLE14 3.2 19.8 1.0
CD1 C:DLE14 3.2 23.6 1.0
C D:MOH121 3.6 17.9 1.0
CN B:FVA1 3.7 24.2 1.0
CG A:DLE14 3.7 22.0 1.0
CG C:DLE14 4.0 23.1 1.0
CD2 C:DLE14 4.0 31.1 1.0
O1 B:FVA1 4.1 12.2 1.0
CB A:DLE14 4.1 31.7 1.0
CZ3 A:TRP15 4.2 21.4 1.0
CE3 A:TRP15 4.2 15.1 1.0
O D:MOH121 4.4 17.6 1.0
CA A:DLE14 4.7 29.4 1.0
N B:FVA1 4.7 24.8 1.0

Caesium binding site 3 out of 8 in 1c4d

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Caesium binding site 3 out of 8 in the Gramicidin Cscl Complex


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Gramicidin Cscl Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs118

b:57.9
occ:0.50
 NE1 D:TRP13 2.4 16.4 1.0
CD1 D:TRP13 2.6 20.3 1.0
CB A:VAL7 2.6 25.4 1.0
C C:MOH120 2.7 28.6 1.0
CG2 A:VAL7 2.7 17.7 1.0
CG1 A:VAL7 3.0 14.9 1.0
O C:MOH120 3.0 28.5 1.0
CE2 D:TRP13 3.6 23.3 1.0
CG D:TRP13 3.8 17.2 1.0
CA A:VAL7 4.1 22.7 1.0
CB B:TRP13 4.1 10.0 1.0
CD2 D:TRP13 4.2 23.0 1.0
CG2 C:VAL7 4.4 5.4 1.0
CD1 B:TRP13 4.4 32.9 1.0
CG B:TRP13 4.5 14.7 1.0
CZ2 D:TRP13 4.5 22.0 1.0
O A:DVA6 4.5 9.4 1.0
O C:HOH2007 4.5 7.2 1.0
O C:HOH2005 4.7 1.9 1.0
O D:HOH2001 4.7 1.9 1.0
CG1 C:VAL7 4.7 10.9 1.0
N A:VAL7 4.7 16.7 1.0
CB D:TRP13 4.8 26.0 1.0
CG1 B:VAL7 4.9 28.4 1.0
C A:DVA6 4.9 22.7 1.0

Caesium binding site 4 out of 8 in 1c4d

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Caesium binding site 4 out of 8 in the Gramicidin Cscl Complex


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Gramicidin Cscl Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs116

b:47.2
occ:1.00
 O B:HOH2003 2.3 1.9 1.0
N B:DLE4 2.7 19.4 1.0
O A:HOH2001 3.0 14.8 1.0
C B:ALA3 3.1 15.6 1.0
O B:ALA3 3.1 22.1 1.0
O A:DLE14 3.2 22.9 1.0
C B:DLE4 3.3 16.3 1.0
N B:ALA5 3.4 12.6 1.0
C A:DLE14 3.4 31.5 1.0
CA B:DLE4 3.4 16.6 1.0
N B:ALA3 3.5 32.7 1.0
N A:DLE14 3.5 21.7 1.0
CA B:ALA3 3.5 15.3 1.0
O B:DLE4 3.6 13.1 1.0
C A:TRP13 3.8 28.3 1.0
CA A:DLE14 3.9 29.4 1.0
N A:TRP13 3.9 27.9 1.0
N A:TRP15 4.0 27.6 1.0
O A:TRP11 4.0 18.2 1.0
CA B:ALA5 4.2 12.4 1.0
O A:TRP13 4.2 10.1 1.0
N A:ETA16 4.2 10.7 1.0
CA A:TRP13 4.3 26.8 1.0
O B:FVA1 4.3 21.3 1.0
N B:DVA6 4.3 24.6 1.0
C A:DLE12 4.4 36.8 1.0
C B:FVA1 4.4 31.4 1.0
CA A:TRP15 4.5 16.3 1.0
C A:TRP11 4.5 30.6 1.0
C B:ALA5 4.5 26.9 1.0
C A:TRP15 4.6 15.5 1.0
C B:GLY2 4.6 26.2 1.0
N B:GLY2 4.7 29.2 1.0
CA A:DLE12 4.7 36.8 1.0
CB A:ETA16 4.8 10.5 1.0
N A:DLE12 4.8 38.5 1.0
CB B:DLE4 4.8 17.7 1.0
N B:FVA1 4.9 24.8 1.0
CA B:GLY2 4.9 27.8 1.0
O B:DVA6 4.9 24.6 1.0
CA A:ETA16 4.9 18.2 1.0
CL B:CL117 5.0 2.3 1.0

Caesium binding site 5 out of 8 in 1c4d

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Caesium binding site 5 out of 8 in the Gramicidin Cscl Complex


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of Gramicidin Cscl Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cs116

b:48.8
occ:1.00
 N C:TRP13 3.2 22.8 1.0
CL D:CL119 3.2 1.9 1.0
C C:DLE12 3.3 27.8 1.0
N C:DLE14 3.3 3.8 1.0
CA C:DLE12 3.4 32.2 1.0
O C:TRP11 3.4 10.5 1.0
C C:TRP13 3.5 17.8 1.0
O C:DLE14 3.5 21.8 1.0
N D:ALA5 3.6 16.6 1.0
N D:DVA6 3.7 15.2 1.0
CA C:TRP13 3.7 17.9 1.0
C C:TRP11 3.8 23.1 1.0
C C:DLE14 3.8 25.3 1.0
C D:DLE4 3.8 16.0 1.0
O D:DVA6 3.8 9.8 1.0
N D:DLE4 3.9 23.8 1.0
N C:DLE12 3.9 30.6 1.0
O C:TRP13 3.9 5.7 1.0
CA C:DLE14 4.0 23.4 1.0
O C:DLE12 4.0 28.8 1.0
O D:ALA3 4.0 16.5 1.0
C D:ALA3 4.0 27.4 1.0
CA D:DLE4 4.0 23.8 1.0
C D:DVA6 4.2 24.3 1.0
CA D:ALA5 4.2 19.7 1.0
N D:ALA3 4.2 29.3 1.0
O D:FVA1 4.2 24.4 1.0
C D:ALA5 4.2 22.5 1.0
CB C:DLE12 4.3 27.9 1.0
O D:DLE4 4.4 10.3 1.0
CA D:DVA6 4.4 21.3 1.0
N C:TRP15 4.6 28.2 1.0
C D:FVA1 4.6 29.6 1.0
CA D:ALA3 4.7 24.9 1.0
O1 D:FVA1 4.7 23.8 1.0
N C:TRP11 4.7 27.7 1.0
O C:HOH2003 4.8 28.0 1.0
CA C:TRP11 4.8 23.9 1.0
N D:VAL7 4.9 21.9 1.0
N D:GLY2 5.0 25.4 1.0

Caesium binding site 6 out of 8 in 1c4d

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Caesium binding site 6 out of 8 in the Gramicidin Cscl Complex


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of Gramicidin Cscl Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cs116

b:57.5
occ:1.00
 O D:MOH132 2.2 1.9 1.0
C D:MOH132 2.9 3.2 1.0
O D:DLE12 3.0 21.1 1.0
C D:DLE12 3.0 30.2 1.0
CA D:DLE12 3.1 21.0 1.0
N D:DLE12 3.2 31.0 1.0
N C:ALA5 3.3 26.3 1.0
N D:TRP13 3.3 29.1 1.0
C D:TRP11 3.3 26.2 1.0
O D:TRP11 3.5 28.3 1.0
O D:DLE14 3.6 5.5 1.0
O C:ALA3 3.7 13.4 1.0
N D:TRP11 3.7 19.8 1.0
N D:DLE14 3.8 3.7 1.0
C C:ALA5 3.8 22.4 1.0
C C:DLE4 3.9 25.6 1.0
O C:DVA6 4.0 15.8 1.0
N C:DVA6 4.0 22.4 1.0
CA D:TRP13 4.0 18.3 1.0
CA C:ALA5 4.1 23.1 1.0
CA C:DLE4 4.1 9.9 1.0
O C:ALA5 4.1 33.4 1.0
CA D:TRP11 4.1 23.8 1.0
N C:DLE4 4.1 26.1 1.0
C C:ALA3 4.1 28.1 1.0
C C:DVA6 4.2 15.9 1.0
C D:TRP13 4.2 24.7 1.0
O D:HOH2001 4.3 1.9 1.0
C D:DLE14 4.3 15.8 1.0
C D:DLE10 4.4 24.4 1.0
CG D:DLE10 4.4 16.1 1.0
CB D:DLE12 4.4 6.1 1.0
CA C:DVA6 4.6 22.5 1.0
O D:TRP9 4.6 15.5 1.0
CA D:DLE10 4.6 20.7 1.0
N C:VAL7 4.7 7.2 1.0
CA D:DLE14 4.7 14.4 1.0
CL C:CL118 4.7 9.8 1.0
N C:ALA3 4.8 38.6 1.0
N C:DVA8 4.8 24.4 1.0
O C:DLE4 4.9 18.9 1.0
CD1 D:DLE10 5.0 14.9 1.0
CA C:VAL7 5.0 15.6 1.0

Caesium binding site 7 out of 8 in 1c4d

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Caesium binding site 7 out of 8 in the Gramicidin Cscl Complex


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of Gramicidin Cscl Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cs117

b:50.0
occ:0.50
 CD2 D:DLE4 4.1 22.7 1.0
CD1 D:DLE4 4.7 17.2 1.0

Caesium binding site 8 out of 8 in 1c4d

Go back to Caesium Binding Sites List in 1c4d
Caesium binding site 8 out of 8 in the Gramicidin Cscl Complex


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 8 of Gramicidin Cscl Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cs118

b:56.3
occ:0.50
 CB D:DLE10 2.8 19.7 1.0
CD1 D:DLE10 3.5 14.9 1.0
CD2 C:DLE10 3.5 21.1 1.0
CG D:DLE10 3.6 16.1 1.0
CD2 C:DLE4 3.6 18.6 1.0
CG C:DLE10 3.7 31.0 1.0
CD2 D:DLE10 3.7 4.0 1.0
CD1 C:DLE10 3.8 25.4 1.0
CA D:DLE10 4.2 20.7 1.0
N D:DLE10 4.7 13.0 1.0
CG C:DLE4 4.9 30.3 1.0
C D:DLE10 5.0 24.4 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: Tue Jul 30 20:09:00 2024

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