Atomistry » Chlorine » PDB 1vq4-1wbn » 1w5u
Atomistry »
  Chlorine »
    PDB 1vq4-1wbn »
      1w5u »

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

Protein crystallography data

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

Other elements in 1w5u:

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

Rubidium (Rb) 14 atoms

Chlorine Binding Sites:

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 1w5u

Go back to Chlorine Binding Sites List in 1w5u
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 1w5u

Go back to Chlorine Binding Sites List in 1w5u
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 1w5u

Go back to Chlorine Binding Sites List in 1w5u
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 1w5u

Go back to Chlorine Binding Sites List in 1w5u
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 1w5u

Go back to Chlorine Binding Sites List in 1w5u
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 1w5u

Go back to Chlorine Binding Sites List in 1w5u
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 1w5u

Go back to Chlorine Binding Sites List in 1w5u
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 1w5u

Go back to Chlorine Binding Sites List in 1w5u
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 1w5u

Go back to Chlorine Binding Sites List in 1w5u
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 1w5u

Go back to Chlorine Binding Sites List in 1w5u
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

Reference:

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
Page generated: Sat Dec 12 08:53:27 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy