Chlorine in PDB 1w5u: Gramicidin D From Bacillus Brevis (Ethanol Solvate)

The structure of Gramicidin D From Bacillus Brevis (Ethanol Solvate), PDB code: 1w5u was solved by M.L.Glowka, A.Olczak, J.Bojarska, M.Szczesio, W.L.Duax, B.M.Burkhart, W.A.Pangborn, D.A.Langs, Z.Wawrzak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	30.060, 31.300, 51.691, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.5

The structure of Gramicidin D From Bacillus Brevis (Ethanol Solvate) also contains other interesting chemical elements:

Rubidium

(Rb)

14 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Gramicidin D From Bacillus Brevis (Ethanol Solvate) (pdb code 1w5u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Gramicidin D From Bacillus Brevis (Ethanol Solvate), PDB code: 1w5u:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1019 b:14.0 occ:0.15 CL A:CL1019 0.0 14.0 0.1 CL A:CL1019 1.1 16.0 0.3 CL A:CL1019 2.3 10.5 0.2 CL A:CL1019 2.7 64.7 0.3 NE1 A:TRP13 3.2 11.6 1.0 CD1 A:TRP13 3.9 9.2 1.0 CE2 A:TRP13 4.3 11.3 1.0 CZ3 B:TRP9 4.4 22.3 1.0 CD1 A:DLE14 4.6 18.6 1.0 CZ2 A:TRP13 4.8 12.1 1.0 CH2 B:TRP9 4.9 24.4 1.0

Chlorine binding site 2 out of 12 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1019 b:64.7 occ:0.32 CL A:CL1019 0.0 64.7 0.3 CL A:CL1019 2.1 16.0 0.3 CL A:CL1019 2.7 14.0 0.1 CL A:CL1019 4.7 10.5 0.2

Chlorine binding site 3 out of 12 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1019 b:16.0 occ:0.34 CL A:CL1019 0.0 16.0 0.3 CL A:CL1019 1.1 14.0 0.1 CL A:CL1019 2.1 64.7 0.3 CL A:CL1019 3.3 10.5 0.2 NE1 A:TRP13 3.4 11.6 1.0 CE2 A:TRP13 4.2 11.3 1.0 CD1 A:TRP13 4.3 9.2 1.0 CZ2 A:TRP13 4.4 12.1 1.0

Chlorine binding site 4 out of 12 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1019 b:10.5 occ:0.16 CL A:CL1019 0.0 10.5 0.2 CZ3 B:TRP9 2.3 22.3 1.0 CL A:CL1019 2.3 14.0 0.1 CH2 B:TRP9 2.7 24.4 1.0 CL A:CL1019 3.3 16.0 0.3 CE3 B:TRP9 3.3 19.7 1.0 CD1 A:TRP13 3.8 9.2 1.0 CZ2 B:TRP9 3.9 20.8 1.0 NE1 A:TRP13 3.9 11.6 1.0 CD2 B:TRP9 4.4 17.2 1.0 CD1 A:DLE14 4.4 18.6 1.0 CE2 B:TRP9 4.6 18.9 1.0 CL A:CL1019 4.7 64.7 0.3

Chlorine binding site 5 out of 12 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1020 b:39.6 occ:0.36 O A:ETA16 2.2 28.2 0.5 CB A:ETA16 2.2 22.4 0.5 NE1 A:TRP15 2.4 31.6 1.0 CE2 A:TRP15 2.6 31.2 1.0 CD1 A:TRP15 2.7 29.4 1.0 CD2 A:TRP15 2.9 28.7 1.0 CG A:TRP15 3.0 26.2 1.0 CA A:ETA16 3.1 21.0 0.5 CZ2 A:TRP15 3.3 33.4 1.0 CA A:ETA16 3.4 20.9 0.5 N A:ETA16 3.5 18.5 1.0 CE3 A:TRP15 3.9 29.3 1.0 C A:TRP15 3.9 15.7 1.0 CH2 A:TRP15 4.0 33.9 1.0 O A:TRP15 4.1 16.4 1.0 CB A:TRP15 4.1 20.5 1.0 CZ3 A:TRP15 4.3 31.5 1.0 CB A:ETA16 4.4 21.6 0.5 CA A:TRP15 4.6 13.8 1.0 O A:ETA16 4.7 23.0 0.5 O A:HOH2007 4.9 13.1 0.2

Chlorine binding site 6 out of 12 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1019 b:35.5 occ:0.12 CL B:CL1019 0.0 35.5 0.1 CL B:CL1019 2.6 10.0 0.1 NE1 B:TYR11 2.9 14.2 0.8 CE2 B:TYR11 3.2 13.6 0.2 CD1 A:DLE4 3.4 15.7 0.4 CD1 B:TYR11 3.5 12.0 0.8 CG A:DLE4 3.8 14.2 0.4 CE2 B:TYR11 4.0 14.2 0.8 CD2 B:TYR11 4.0 12.6 0.2 OH B:TYR11 4.1 18.2 0.2 CZ B:TYR11 4.1 14.4 0.2 CD2 A:DLE4 4.2 13.8 0.4 CZ2 D:TRP13 4.4 18.4 0.5 CZ2 B:TYR11 4.6 15.9 0.8 CZ2 D:TRP13 4.6 20.4 0.5 NE1 D:TRP13 4.6 18.4 0.5 NE1 D:TRP13 4.6 17.8 0.5 CG B:TYR11 4.8 11.3 0.8 CD2 D:DLE12 4.8 24.1 1.0 CE2 D:TRP13 4.9 17.7 0.5 CB A:ALA5 5.0 15.6 1.0 CB A:DLE4 5.0 13.7 0.6 CE2 D:TRP13 5.0 17.8 0.5

Chlorine binding site 7 out of 12 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1019 b:10.0 occ:0.05 CL B:CL1019 0.0 10.0 0.1 CZ2 D:TRP13 2.4 18.4 0.5 CL B:CL1019 2.6 35.5 0.1 OH B:TYR11 2.9 18.2 0.2 NE1 D:TRP13 3.1 17.8 0.5 CE2 D:TRP13 3.1 17.7 0.5 NE1 D:TRP13 3.2 18.4 0.5 CH2 D:TRP13 3.5 20.8 0.5 CE2 B:TYR11 3.6 13.6 0.2 NE1 B:TYR11 3.6 14.2 0.8 CZ B:TYR11 3.6 14.4 0.2 CZ2 B:TYR11 3.7 15.9 0.8 CE2 D:TRP13 3.8 17.8 0.5 CZ2 D:TRP13 3.9 20.4 0.5 CE2 B:TYR11 3.9 14.2 0.8 CD1 D:TRP13 4.2 16.5 0.5 CD2 D:TRP13 4.5 16.8 0.5 CD1 D:TRP13 4.6 17.3 0.5 CD2 D:DLE12 4.7 24.1 1.0 CD1 B:TYR11 4.7 12.0 0.8 CZ3 D:TRP13 4.8 20.7 0.5 CD2 B:TYR11 4.8 12.6 0.2 CH2 B:TYR11 4.8 16.0 0.8 CE1 B:TYR11 4.9 13.3 0.2

Chlorine binding site 8 out of 12 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1020 b:10.0 occ:0.28 O B:HOH2006 2.3 82.1 0.8 NE1 B:TRP9 3.2 20.1 1.0 CD1 B:TRP9 3.8 16.7 1.0 CG1 A:VAL7 4.2 11.2 1.0 CG1 A:DVA6 4.3 13.4 0.1 CE2 B:TRP9 4.3 18.9 1.0 CG2 A:DVA6 4.6 16.8 0.9 CZ2 B:TRP9 4.9 20.8 1.0

Chlorine binding site 9 out of 12 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1021 b:24.4 occ:0.18 CH2 B:TRP13 2.4 18.4 0.5 CZ3 B:TRP13 2.7 18.8 0.5 CZ2 B:TRP13 3.6 18.3 0.5 CB A:ALA3 3.9 14.4 1.0 CE3 B:TRP13 4.0 17.1 0.5 NE1 B:TRP13 4.0 17.5 0.5 N A:ALA3 4.1 11.1 1.0 CE2 B:TRP13 4.6 17.2 0.5 CA A:ALA3 4.6 11.5 1.0 CD1 B:TRP13 4.7 16.1 0.5 CA A:GLY2 4.7 12.5 1.0 C A:GLY2 4.8 12.2 1.0 CD2 B:TRP13 4.8 16.0 0.5

Chlorine binding site 10 out of 12 in the Gramicidin D From Bacillus Brevis (Ethanol Solvate)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Gramicidin D From Bacillus Brevis (Ethanol Solvate) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl1019 b:16.9 occ:0.30 CH2 B:TRP13 1.4 19.1 0.5 CZ2 B:TRP13 2.4 18.1 0.5 CZ3 B:TRP13 2.4 17.8 0.5 NE1 D:TYR11 3.1 14.8 0.8 CD2 B:DLE12 3.2 14.5 0.3 NE1 B:TRP13 3.2 16.1 0.5 CD2 C:DLE4 3.3 33.7 1.0 CE1 D:TYR11 3.6 13.9 0.2 CE2 B:TRP13 3.6 16.9 0.5 CE3 B:TRP13 3.6 16.3 0.5 CD1 D:TYR11 3.8 14.0 0.8 CE2 B:TRP13 4.1 17.2 0.5 CD2 B:TRP13 4.1 16.0 0.5 CD2 B:DLE12 4.2 16.4 0.7 CE2 D:TYR11 4.2 14.1 0.8 CD1 B:TRP13 4.2 15.9 0.5 OH D:TYR11 4.2 12.5 0.2 CZ D:TYR11 4.3 14.2 0.2 CZ2 B:TRP13 4.3 18.3 0.5 CD1 D:TYR11 4.3 13.5 0.2 CG C:DLE4 4.5 21.8 1.0 CZ2 D:TYR11 4.6 14.8 0.8 CG B:DLE12 4.7 14.4 0.3 NE1 B:TRP13 4.8 17.5 0.5

M.L.Glowka, A.Olczak, J.Bojarska, M.Szczesio, W.L.Duax, B.M.Burkhart, W.A.Pangborn, D.A.Langs, Z.Wawrzak. Structure of Gramicidin D-Rbcl Complex at Atomic Resolution From Low-Temperature Synchrotron Data: Interactions of Double-Stranded Gramicidin Channel Contents and Cations with Channel Wall Acta Crystallogr.,Sect.D V. 61 433 2005.
ISSN: ISSN 0907-4449
PubMed: 15805598
DOI: 10.1107/S0907444905000399