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Caesium in PDB 1av2: Gramicidin A/Cscl Complex, Active As A Dimer

Protein crystallography data

The structure of Gramicidin A/Cscl Complex, Active As A Dimer, PDB code: 1av2 was solved by B.M.Burkhart, N.Li, D.A.Langs, W.L.Duax, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 31.060, 31.880, 52.110, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18.6

Other elements in 1av2:

The structure of Gramicidin A/Cscl Complex, Active As A Dimer also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Caesium Binding Sites:

The binding sites of Caesium atom in the Gramicidin A/Cscl Complex, Active As A Dimer (pdb code 1av2). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 7 binding sites of Caesium where determined in the Gramicidin A/Cscl Complex, Active As A Dimer, PDB code: 1av2:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Caesium binding site 1 out of 7 in 1av2

Go back to Caesium Binding Sites List in 1av2
Caesium binding site 1 out of 7 in the Gramicidin A/Cscl Complex, Active As A Dimer


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Gramicidin A/Cscl Complex, Active As A Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs17

b:21.0
occ:0.14
O B:HOH2001 1.6 22.7 0.7
CS B:CS17 1.9 35.7 0.1
N A:DLE14 3.4 14.6 1.0
O B:GLY2 3.5 16.8 1.0
C A:DLE14 3.6 16.0 1.0
O B:ALA5 3.6 20.1 1.0
N A:TRP15 3.7 16.2 1.0
O B:HOH2004 3.7 22.6 0.9
C B:ALA5 3.7 16.2 1.0
O B:DLE4 3.8 20.6 1.0
H A:TRP15 3.8 19.4 1.0
HA B:DVA6 3.8 19.3 1.0
O A:DLE12 3.8 19.6 1.0
O A:DLE14 3.9 17.6 1.0
HA A:TRP13 3.9 17.2 1.0
C B:DLE4 3.9 16.6 1.0
O A:TRP15 3.9 19.2 1.0
CA A:DLE14 3.9 15.1 1.0
C A:TRP13 3.9 13.8 1.0
HA A:DLE14 4.0 18.1 1.0
C A:TRP15 4.0 19.1 1.0
N B:DVA6 4.0 16.4 1.0
N B:DLE4 4.1 15.8 1.0
N B:ALA5 4.2 17.0 1.0
HA B:ALA3 4.2 19.3 1.0
CA A:TRP13 4.3 14.4 1.0
H B:VAL7 4.3 18.4 1.0
C A:DLE12 4.3 14.5 1.0
CA B:DVA6 4.3 16.1 1.0
O B:VAL7 4.4 17.1 1.0
CA A:TRP15 4.4 17.6 1.0
CA B:ALA5 4.4 17.7 1.0
H B:DVA6 4.4 19.6 1.0
HA B:ALA5 4.4 21.3 1.0
C B:ALA3 4.4 15.0 1.0
N A:TRP13 4.5 13.5 1.0
C B:GLY2 4.5 15.2 1.0
CA B:DLE4 4.5 16.8 1.0
O B:HOH2002 4.5 18.6 0.7
N A:ETA16 4.5 21.4 1.0
HA1 A:ETA16 4.5 31.4 1.0
H B:ALA5 4.6 20.4 1.0
HA2 A:ETA16 4.6 31.4 1.0
HA A:TRP15 4.6 21.1 1.0
N B:VAL7 4.6 15.3 1.0
HA B:DLE4 4.6 20.1 1.0
C B:DVA6 4.7 15.3 1.0
H B:GLY2 4.7 18.5 1.0
O A:TRP13 4.7 15.5 1.0
CA B:ALA3 4.8 16.1 1.0
CA A:ETA16 4.8 26.2 1.0
HN1 A:ETA16 4.9 25.6 1.0
N B:ALA3 5.0 15.2 1.0
N A:DLE12 5.0 14.1 1.0
H A:TRP13 5.0 16.2 1.0

Caesium binding site 2 out of 7 in 1av2

Go back to Caesium Binding Sites List in 1av2
Caesium binding site 2 out of 7 in the Gramicidin A/Cscl Complex, Active As A Dimer


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Gramicidin A/Cscl Complex, Active As A Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cs18

b:19.8
occ:0.38
O B:HOH2003 0.8 18.0 0.5
O B:HOH2002 2.5 18.6 0.7
O B:HOH2006 3.0 25.3 1.0
O B:HOH2004 3.3 22.6 0.9
HA A:DLE10 3.4 20.4 1.0
HA B:DLE10 3.4 21.2 1.0
H A:TRP11 3.5 17.9 1.0
O B:TRP11 3.5 18.4 1.0
O B:DVA8 3.6 16.4 1.0
O A:DVA8 3.6 17.9 1.0
N B:DLE10 3.7 15.3 1.0
N A:DLE10 3.7 15.6 1.0
N A:TRP11 3.7 14.9 1.0
C B:DLE10 3.7 15.1 1.0
H B:TRP11 3.8 17.7 1.0
C A:DLE10 3.8 14.7 1.0
N B:TRP11 3.8 14.8 1.0
C B:TRP9 3.8 14.3 1.0
CA A:DLE10 3.8 17.0 1.0
CA B:DLE10 3.8 17.6 1.0
C A:TRP9 3.8 15.9 1.0
O A:TRP11 3.9 17.8 1.0
O B:TRP9 4.0 16.6 1.0
O A:TRP9 4.0 19.0 1.0
C B:TRP11 4.0 15.5 1.0
C A:DVA8 4.1 14.6 1.0
C B:DVA8 4.1 13.9 1.0
H B:DVA8 4.2 16.9 1.0
H A:DVA8 4.2 15.5 1.0
O B:DLE10 4.2 16.9 1.0
C A:TRP11 4.3 13.9 1.0
HA B:DLE12 4.3 21.8 1.0
O A:DLE10 4.3 18.9 1.0
N A:TRP9 4.4 14.7 1.0
N B:TRP9 4.5 14.5 1.0
CA B:TRP11 4.5 15.4 1.0
N A:DVA8 4.5 12.9 1.0
HA B:TRP9 4.5 17.0 1.0
CA B:TRP9 4.5 14.1 1.0
CA A:TRP9 4.6 15.6 1.0
HA A:TRP9 4.6 18.8 1.0
HA A:VAL7 4.6 16.2 1.0
N B:DVA8 4.6 14.1 1.0
CA A:TRP11 4.6 15.2 1.0
N B:DLE12 4.8 15.1 1.0
HA B:VAL7 4.8 19.2 1.0
HA A:DLE12 4.8 19.4 1.0
O A:DVA6 4.9 16.2 1.0
O B:DVA6 4.9 18.0 1.0
CA A:DVA8 4.9 14.7 1.0
H A:TRP9 4.9 17.6 1.0
HA B:TRP11 4.9 18.4 1.0
N A:DLE12 4.9 14.1 1.0
H B:TRP9 5.0 17.4 1.0

Caesium binding site 3 out of 7 in 1av2

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Caesium binding site 3 out of 7 in the Gramicidin A/Cscl Complex, Active As A Dimer


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Gramicidin A/Cscl Complex, Active As A Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs17

b:35.7
occ:0.15
CS A:CS17 1.9 21.0 0.1
O B:ALA5 3.3 20.1 1.0
HA1 A:ETA16 3.3 31.4 1.0
O B:GLY2 3.4 16.8 1.0
O B:HOH2001 3.5 22.7 0.7
N A:ETA16 3.7 21.4 1.0
C A:TRP15 3.8 19.1 1.0
O A:DLE14 3.8 17.6 1.0
C B:ALA3 3.9 15.0 1.0
CA A:ETA16 3.9 26.2 1.0
N B:DLE4 3.9 15.8 1.0
HA B:DLE4 3.9 20.1 1.0
HN1 A:ETA16 3.9 25.6 1.0
O B:ALA3 4.0 17.0 1.0
C B:ALA5 4.0 16.2 1.0
C B:GLY2 4.0 15.2 1.0
HA2 A:ETA16 4.0 31.4 1.0
C B:DLE4 4.0 16.6 1.0
N B:ALA5 4.0 17.0 1.0
H B:ALA5 4.1 20.4 1.0
H B:GLY2 4.1 18.5 1.0
C A:DLE14 4.1 16.0 1.0
O A:TRP15 4.1 19.2 1.0
CA B:DLE4 4.2 16.8 1.0
HA A:TRP15 4.2 21.1 1.0
N A:TRP15 4.2 16.2 1.0
HA B:DVA6 4.3 19.3 1.0
CA A:TRP15 4.3 17.6 1.0
HA B:ALA3 4.4 19.3 1.0
N B:ALA3 4.4 15.2 1.0
O B:DLE4 4.5 20.6 1.0
CA B:ALA3 4.5 16.1 1.0
N B:GLY2 4.5 15.4 1.0
N A:DLE14 4.5 14.6 1.0
H A:TRP15 4.6 19.4 1.0
O1 B:FVA1 4.6 27.3 1.0
CA B:ALA5 4.6 17.7 1.0
N B:DVA6 4.7 16.4 1.0
CL B:CL19 4.7 44.6 0.5
O A:DLE12 4.8 19.6 1.0
HA B:FVA1 4.8 22.9 1.0
CA B:GLY2 4.9 16.0 1.0
HA A:TRP13 4.9 17.2 1.0
CA A:DLE14 4.9 15.1 1.0
CA B:DVA6 5.0 16.1 1.0

Caesium binding site 4 out of 7 in 1av2

Go back to Caesium Binding Sites List in 1av2
Caesium binding site 4 out of 7 in the Gramicidin A/Cscl Complex, Active As A Dimer


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Gramicidin A/Cscl Complex, Active As A Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cs18

b:20.1
occ:0.35
O B:HOH2008 0.3 19.2 0.5
O A:HOH2001 2.7 29.3 0.7
O B:HOH2006 3.2 25.3 1.0
O B:TRP15 3.4 18.1 1.0
HA A:DVA6 3.6 17.8 1.0
N B:DLE14 3.6 16.7 1.0
O A:VAL7 3.6 16.8 1.0
O B:DLE12 3.6 19.9 1.0
H A:VAL7 3.6 17.4 1.0
O A:ALA5 3.6 16.7 1.0
HA B:DLE14 3.7 21.5 1.0
C A:ALA5 3.7 15.3 1.0
O A:DLE4 3.7 23.1 1.0
C B:DLE14 3.7 15.7 1.0
N A:DVA6 3.8 14.2 1.0
N B:TRP15 3.8 15.7 1.0
C B:TRP13 3.9 16.6 1.0
H B:TRP15 3.9 18.8 1.0
CA B:DLE14 3.9 17.9 1.0
N A:VAL7 3.9 14.5 1.0
C B:TRP15 4.0 18.0 1.0
CA A:DVA6 4.0 14.8 1.0
C A:DLE4 4.1 14.8 1.0
O B:DLE14 4.1 17.1 1.0
C B:DLE12 4.1 15.8 1.0
C A:DVA6 4.1 13.8 1.0
H A:DVA6 4.2 17.0 1.0
O A:GLY2 4.2 21.4 1.0
HA B:TRP13 4.2 21.4 1.0
C A:VAL7 4.3 12.7 1.0
O B:TRP13 4.3 18.2 1.0
HA2 B:ETA16 4.4 23.9 0.5
HA A:ALA5 4.4 18.4 1.0
CA B:TRP13 4.4 17.8 1.0
CA A:ALA5 4.4 15.3 1.0
N A:DLE4 4.4 15.4 1.0
N B:TRP13 4.5 16.3 1.0
N A:ALA5 4.5 14.5 1.0
CA B:TRP15 4.5 16.6 1.0
HA1 B:ETA16 4.6 23.9 0.5
HA A:ALA3 4.6 17.4 1.0
N B:ETA16 4.7 19.0 0.5
CA A:VAL7 4.7 13.5 1.0
C B:MOH511 4.7 46.8 0.5
N B:ETA16 4.7 18.9 0.5
CA A:DLE4 4.8 15.5 1.0
HB2 B:ETA16 4.9 26.5 0.5
N B:DLE12 4.9 15.1 1.0
O B:DLE10 4.9 16.9 1.0
HA B:TRP15 4.9 19.9 1.0
O A:DVA6 4.9 16.2 1.0
HA A:DVA8 5.0 17.6 1.0
C A:ALA3 5.0 14.2 1.0

Caesium binding site 5 out of 7 in 1av2

Go back to Caesium Binding Sites List in 1av2
Caesium binding site 5 out of 7 in the Gramicidin A/Cscl Complex, Active As A Dimer


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of Gramicidin A/Cscl Complex, Active As A Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cs17

b:23.5
occ:0.37
O D:HOH2002 1.4 24.2 0.8
O D:HOH2001 2.7 35.1 0.7
O D:HOH2004 3.3 22.9 0.9
O D:DLE4 3.4 20.8 1.0
N C:DLE14 3.5 14.4 1.0
H C:TRP15 3.6 18.9 1.0
HA D:DVA6 3.6 20.6 1.0
N C:TRP15 3.6 15.7 1.0
C C:DLE14 3.6 16.2 1.0
O D:ALA5 3.7 18.4 1.0
O C:TRP15 3.7 20.0 1.0
O D:VAL7 3.7 17.5 1.0
O D:GLY2 3.8 17.7 1.0
O C:DLE12 3.8 22.2 1.0
HA C:DLE14 3.8 19.8 1.0
C D:ALA5 3.8 15.6 1.0
H D:VAL7 3.8 17.8 1.0
C C:TRP13 3.9 13.0 1.0
CA C:DLE14 3.9 16.5 1.0
N D:DVA6 3.9 15.6 1.0
C D:DLE4 3.9 16.5 1.0
HA C:TRP13 4.0 17.3 1.0
C C:TRP15 4.0 16.7 1.0
O C:DLE14 4.1 18.7 1.0
CA D:DVA6 4.1 17.1 1.0
N D:VAL7 4.1 14.9 1.0
O D:HOH2005 4.2 22.0 0.8
N D:DLE4 4.3 15.6 1.0
C C:DLE12 4.3 15.9 1.0
H D:DVA6 4.3 18.7 1.0
CA C:TRP13 4.3 14.4 1.0
C D:DVA6 4.3 15.1 1.0
N C:TRP13 4.4 14.4 1.0
CA C:TRP15 4.4 17.7 1.0
N D:ALA5 4.4 17.2 1.0
C D:VAL7 4.4 12.8 1.0
O C:TRP13 4.5 15.1 1.0
HA D:ALA3 4.5 18.5 1.0
CA D:ALA5 4.5 16.8 1.0
HA D:ALA5 4.6 20.2 1.0
O D:HOH2003 4.7 29.1 0.2
N C:ETA16 4.7 20.3 1.0
CA D:DLE4 4.7 17.8 1.0
HA C:TRP15 4.8 21.2 1.0
C D:GLY2 4.8 15.2 1.0
C D:ALA3 4.8 15.8 1.0
H C:TRP13 4.9 17.2 1.0
HA2 C:ETA16 4.9 29.1 1.0
N C:DLE12 4.9 14.2 1.0
HA1 C:ETA16 4.9 29.1 1.0
CA D:VAL7 4.9 15.4 1.0
O C:DLE10 5.0 19.5 1.0
H D:GLY2 5.0 19.2 1.0
H D:ALA5 5.0 20.7 1.0

Caesium binding site 6 out of 7 in 1av2

Go back to Caesium Binding Sites List in 1av2
Caesium binding site 6 out of 7 in the Gramicidin A/Cscl Complex, Active As A Dimer


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of Gramicidin A/Cscl Complex, Active As A Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cs18

b:19.4
occ:0.35
O C:HOH2001 0.2 16.6 0.5
O D:HOH2005 2.5 22.0 0.8
O D:HOH2007 3.0 21.7 1.0
HA D:DLE10 3.3 23.5 1.0
O D:HOH2004 3.3 22.9 0.9
HA C:DLE10 3.6 19.6 1.0
O D:TRP11 3.6 17.7 1.0
O C:DVA8 3.6 16.7 1.0
O D:DVA8 3.6 15.2 1.0
N D:DLE10 3.6 15.9 1.0
N C:DLE10 3.7 14.2 1.0
H C:TRP11 3.7 17.6 1.0
C D:DLE10 3.7 14.8 1.0
CA D:DLE10 3.8 19.6 1.0
C C:TRP9 3.8 14.6 1.0
C D:TRP9 3.8 15.6 1.0
N C:TRP11 3.8 14.7 1.0
H D:TRP11 3.8 17.3 1.0
N D:TRP11 3.9 14.4 1.0
C C:DLE10 3.9 15.8 1.0
O C:TRP11 3.9 18.8 1.0
CA C:DLE10 3.9 16.3 1.0
C C:DVA8 4.0 14.6 1.0
O D:TRP9 4.0 17.0 1.0
H D:DVA8 4.1 16.6 1.0
C D:DVA8 4.1 13.0 1.0
O C:TRP9 4.1 18.3 1.0
C D:TRP11 4.1 15.8 1.0
H C:DVA8 4.1 16.7 1.0
O D:DLE10 4.2 17.9 1.0
C C:TRP11 4.2 14.7 1.0
N C:TRP9 4.2 15.2 1.0
O C:DLE10 4.4 19.5 1.0
CA C:TRP9 4.4 16.2 1.0
HA C:TRP9 4.4 19.5 1.0
N D:TRP9 4.4 14.0 1.0
HA D:TRP9 4.5 17.3 1.0
CA D:TRP9 4.5 14.4 1.0
N D:DVA8 4.5 13.8 1.0
N C:DVA8 4.5 13.9 1.0
HA D:DLE12 4.5 18.2 1.0
CA D:TRP11 4.6 15.1 1.0
HA D:VAL7 4.6 18.5 1.0
CA C:TRP11 4.6 14.9 1.0
H C:TRP9 4.7 18.2 1.0
HA C:VAL7 4.7 16.3 1.0
HA C:DLE12 4.8 19.1 1.0
O C:DVA6 4.8 16.6 1.0
CA C:DVA8 4.8 15.8 1.0
N D:DLE12 4.9 13.5 1.0
CA D:DVA8 4.9 14.3 1.0
N C:DLE12 4.9 14.2 1.0
H D:TRP9 4.9 16.8 1.0
HA C:TRP11 5.0 17.9 1.0
O D:DVA6 5.0 16.5 1.0

Caesium binding site 7 out of 7 in 1av2

Go back to Caesium Binding Sites List in 1av2
Caesium binding site 7 out of 7 in the Gramicidin A/Cscl Complex, Active As A Dimer


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of Gramicidin A/Cscl Complex, Active As A Dimer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cs19

b:31.4
occ:0.22
O D:HOH2009 2.9 24.5 1.0
O C:ALA5 3.4 16.7 1.0
O D:DLE14 3.6 16.5 1.0
O D:HOH2011 3.6 25.8 0.3
HA1 D:ETA16 3.7 33.0 1.0
C D:TRP15 3.8 18.1 1.0
HO D:ETA16 3.8 65.5 1.0
O C:GLY2 3.8 20.0 1.0
N D:ETA16 3.8 21.0 1.0
C D:DLE14 4.0 14.7 1.0
O D:TRP15 4.0 18.3 1.0
HN1 D:ETA16 4.0 25.2 1.0
H C:ALA5 4.0 20.1 1.0
H C:GLY2 4.1 19.5 1.0
C C:ALA3 4.1 14.7 1.0
C C:ALA5 4.1 15.1 1.0
O D:ETA16 4.1 43.6 1.0
CL C:CL20 4.1 45.2 0.5
HA C:DLE4 4.1 18.2 1.0
N C:DLE4 4.1 14.9 1.0
C C:GLY2 4.1 14.6 1.0
N C:ALA5 4.2 16.8 1.0
CA D:ETA16 4.2 27.5 1.0
HA D:TRP15 4.2 19.6 1.0
O C:ALA3 4.2 17.7 1.0
N D:TRP15 4.2 15.5 1.0
CA D:TRP15 4.3 16.4 1.0
C C:DLE4 4.3 15.5 1.0
HA C:DVA6 4.4 18.5 1.0
CA C:DLE4 4.4 15.2 1.0
HA C:ALA3 4.4 18.2 1.0
N C:ALA3 4.5 15.6 1.0
N C:GLY2 4.5 16.2 1.0
N D:DLE14 4.5 13.9 1.0
CA C:ALA3 4.6 15.2 1.0
HA C:FVA1 4.7 21.7 1.0
CB D:ETA16 4.7 32.3 1.0
CA C:ALA5 4.7 15.7 1.0
H D:TRP15 4.8 18.6 1.0
O D:DLE12 4.8 16.5 1.0
N C:DVA6 4.9 14.3 1.0
CA D:DLE14 4.9 15.1 1.0
O D:HOH2010 4.9 56.2 1.0
CA C:GLY2 4.9 16.6 1.0
HA D:TRP13 5.0 18.6 1.0
H C:ALA3 5.0 18.7 1.0
O1 C:FVA1 5.0 24.6 1.0

Reference:

B.M.Burkhart, N.Li, D.A.Langs, W.A.Pangborn, W.L.Duax. The Conducting Form of Gramicidin A Is A Right-Handed Double-Stranded Double Helix. Proc.Natl.Acad.Sci.Usa V. 95 12950 1998.
ISSN: ISSN 0027-8424
PubMed: 9789021
DOI: 10.1073/PNAS.95.22.12950
Page generated: Sun Dec 13 10:55:23 2020

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