Chlorine in PDB 8xx8: Structure of Glycilhalorhodopsin From Salinarimonas Soli

Protein crystallography data

The structure of Structure of Glycilhalorhodopsin From Salinarimonas Soli, PDB code: 8xx8 was solved by K.Suzuki, T.Ishizuka, M.Konno, K.Inoue, T.Murata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.19 / 2.63
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 90.22, 126.18, 97.61, 90, 104.77, 90
R / Rfree (%) 20.9 / 24.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Glycilhalorhodopsin From Salinarimonas Soli (pdb code 8xx8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of Glycilhalorhodopsin From Salinarimonas Soli, PDB code: 8xx8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8xx8

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Chlorine binding site 1 out of 6 in the Structure of Glycilhalorhodopsin From Salinarimonas Soli


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Glycilhalorhodopsin From Salinarimonas Soli within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:40.6
occ:1.00
 OG1 A:THR83 3.0 40.9 1.0
O A:HOH404 3.1 42.2 1.0
OG1 A:THR87 3.3 40.7 1.0
CG2 A:THR87 3.4 35.7 1.0
CB A:THR83 3.4 43.3 1.0
CD1 A:TRP84 3.5 38.3 1.0
C A:THR83 3.6 40.8 1.0
N A:TRP84 3.7 37.4 1.0
O A:THR83 3.8 37.9 1.0
CE A:LYS221 3.8 35.7 1.0
CG2 A:THR57 3.8 44.9 1.0
NZ A:LYS221 3.9 37.4 1.0
CB A:THR87 3.9 40.4 1.0
CA A:ALA54 4.0 39.6 1.0
CA A:THR83 4.2 38.7 1.0
CA A:TRP84 4.2 36.4 1.0
CB A:ALA54 4.2 38.8 1.0
NE1 A:TRP84 4.2 38.4 1.0
N A:ALA54 4.3 39.4 1.0
CG A:TRP84 4.6 38.8 1.0
O A:ARG80 4.6 38.1 1.0
CG2 A:ILE53 4.7 35.9 1.0
CB A:THR57 4.7 40.0 1.0
CG2 A:THR83 4.7 40.3 1.0
C A:ILE53 4.7 42.1 1.0
O A:ILE53 4.8 43.5 1.0
CD A:LYS221 4.8 44.7 1.0
CB A:TRP84 5.0 39.3 1.0

Chlorine binding site 2 out of 6 in 8xx8

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Chlorine binding site 2 out of 6 in the Structure of Glycilhalorhodopsin From Salinarimonas Soli


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Glycilhalorhodopsin From Salinarimonas Soli within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:43.6
occ:1.00
 OG1 B:THR87 3.0 41.4 1.0
OG1 B:THR83 3.1 46.0 1.0
O B:HOH406 3.1 40.5 1.0
CG2 B:THR87 3.4 43.9 1.0
CB B:THR83 3.5 43.1 1.0
CE B:LYS221 3.6 43.6 1.0
O B:THR83 3.6 39.2 1.0
C B:THR83 3.6 38.4 1.0
CB B:THR87 3.8 42.9 1.0
CD1 B:TRP84 3.8 45.0 1.0
N B:TRP84 3.8 38.8 1.0
NZ B:LYS221 3.9 44.9 1.0
CA B:ALA54 4.0 39.5 1.0
CG2 B:THR57 4.0 38.3 1.0
CB B:ALA54 4.1 38.5 1.0
CA B:THR83 4.2 39.4 1.0
N B:ALA54 4.2 40.9 1.0
CA B:TRP84 4.3 42.1 1.0
NE1 B:TRP84 4.5 41.0 1.0
CG2 B:ILE53 4.6 34.8 1.0
C B:ILE53 4.6 39.2 1.0
O B:ILE53 4.6 35.0 1.0
CD B:LYS221 4.7 40.1 1.0
CG2 B:THR83 4.8 35.7 1.0
O B:ARG80 4.8 38.6 1.0
CB B:THR57 4.8 42.2 1.0
CG B:TRP84 4.8 41.9 1.0

Chlorine binding site 3 out of 6 in 8xx8

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Chlorine binding site 3 out of 6 in the Structure of Glycilhalorhodopsin From Salinarimonas Soli


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Glycilhalorhodopsin From Salinarimonas Soli within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl305

b:42.1
occ:1.00
 OG1 D:THR83 3.0 43.2 1.0
O D:HOH408 3.1 44.1 1.0
OG1 D:THR87 3.3 39.3 1.0
CG2 D:THR87 3.4 33.8 1.0
CB D:THR83 3.5 45.5 1.0
C D:THR83 3.7 39.1 1.0
O D:THR83 3.7 39.0 1.0
CE D:LYS221 3.7 42.5 1.0
CD1 D:TRP84 3.8 38.2 1.0
N D:TRP84 3.9 40.9 1.0
CA D:ALA54 3.9 37.2 1.0
CG2 D:THR57 3.9 42.3 1.0
CB D:THR87 3.9 38.1 1.0
CB D:ALA54 4.1 35.0 1.0
NZ D:LYS221 4.1 38.1 1.0
N D:ALA54 4.2 35.3 1.0
CA D:THR83 4.2 38.9 1.0
CA D:TRP84 4.3 40.4 1.0
NE1 D:TRP84 4.6 35.5 1.0
CG2 D:ILE53 4.6 39.3 1.0
C D:ILE53 4.6 35.0 1.0
O D:ILE53 4.7 37.0 1.0
O D:ARG80 4.7 36.9 1.0
CB D:THR57 4.7 37.5 1.0
CG2 D:THR83 4.8 39.0 1.0
CD D:LYS221 4.8 37.8 1.0
CG D:TRP84 4.9 38.9 1.0

Chlorine binding site 4 out of 6 in 8xx8

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Chlorine binding site 4 out of 6 in the Structure of Glycilhalorhodopsin From Salinarimonas Soli


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Glycilhalorhodopsin From Salinarimonas Soli within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl302

b:43.1
occ:1.00
 OG1 E:THR83 3.0 48.6 1.0
O E:HOH405 3.1 42.9 1.0
OG1 E:THR87 3.3 48.5 1.0
CG2 E:THR87 3.4 42.6 1.0
CB E:THR83 3.5 47.7 1.0
C E:THR83 3.7 44.4 1.0
CE E:LYS221 3.7 45.9 1.0
O E:THR83 3.8 43.2 1.0
CD1 E:TRP84 3.8 42.5 1.0
CG2 E:THR57 3.8 44.5 1.0
N E:TRP84 3.9 45.6 1.0
CA E:ALA54 3.9 39.9 1.0
CB E:THR87 4.0 43.9 1.0
CB E:ALA54 4.1 44.0 1.0
NZ E:LYS221 4.1 48.9 1.0
CA E:THR83 4.2 42.7 1.0
N E:ALA54 4.3 40.1 1.0
CA E:TRP84 4.3 41.4 1.0
NE1 E:TRP84 4.5 48.1 1.0
O E:ILE53 4.6 38.2 1.0
C E:ILE53 4.6 38.9 1.0
CG2 E:ILE53 4.6 38.4 1.0
O E:ARG80 4.7 42.8 1.0
CB E:THR57 4.7 43.8 1.0
CG2 E:THR83 4.7 46.2 1.0
CD E:LYS221 4.8 46.6 1.0
CG E:TRP84 4.8 44.4 1.0

Chlorine binding site 5 out of 6 in 8xx8

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Chlorine binding site 5 out of 6 in the Structure of Glycilhalorhodopsin From Salinarimonas Soli


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Glycilhalorhodopsin From Salinarimonas Soli within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl305

b:44.2
occ:1.00
 OG1 F:THR83 3.0 44.4 1.0
O F:HOH406 3.1 39.1 1.0
OG1 F:THR87 3.2 45.2 1.0
CG2 F:THR87 3.5 36.1 1.0
CB F:THR83 3.5 43.8 1.0
C F:THR83 3.6 38.9 1.0
O F:THR83 3.6 38.3 1.0
CD1 F:TRP84 3.6 47.1 1.0
CE F:LYS221 3.7 48.9 1.0
N F:TRP84 3.7 40.8 1.0
CB F:THR87 3.9 42.7 1.0
CG2 F:THR57 3.9 40.8 1.0
CA F:ALA54 4.0 37.9 1.0
CB F:ALA54 4.0 41.0 1.0
NZ F:LYS221 4.0 44.0 1.0
CA F:THR83 4.2 40.5 1.0
CA F:TRP84 4.2 42.9 1.0
N F:ALA54 4.3 41.5 1.0
NE1 F:TRP84 4.3 45.7 1.0
CG2 F:ILE53 4.6 36.9 1.0
O F:ARG80 4.7 42.4 1.0
CG F:TRP84 4.7 46.8 1.0
CB F:THR57 4.7 43.9 1.0
C F:ILE53 4.8 43.8 1.0
CD F:LYS221 4.8 42.3 1.0
O F:ILE53 4.8 41.3 1.0
CG2 F:THR83 4.8 36.3 1.0

Chlorine binding site 6 out of 6 in 8xx8

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Chlorine binding site 6 out of 6 in the Structure of Glycilhalorhodopsin From Salinarimonas Soli


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Glycilhalorhodopsin From Salinarimonas Soli within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:43.0
occ:1.00
 OG1 C:THR87 3.0 41.3 1.0
O C:HOH406 3.1 41.9 1.0
OG1 C:THR83 3.2 46.7 1.0
CG2 C:THR87 3.4 38.4 1.0
CB C:THR83 3.5 40.8 1.0
O C:THR83 3.6 37.0 1.0
CE C:LYS221 3.6 46.4 1.0
C C:THR83 3.6 36.9 1.0
CD1 C:TRP84 3.7 43.5 1.0
CB C:THR87 3.7 42.1 1.0
N C:TRP84 3.8 42.3 1.0
NZ C:LYS221 3.8 45.2 1.0
CG2 C:THR57 4.0 46.5 1.0
CA C:ALA54 4.0 35.9 1.0
CB C:ALA54 4.1 36.7 1.0
CA C:THR83 4.2 38.0 1.0
CA C:TRP84 4.2 42.2 1.0
N C:ALA54 4.3 39.2 1.0
NE1 C:TRP84 4.4 44.0 1.0
O C:ILE53 4.6 38.2 1.0
C C:ILE53 4.6 39.2 1.0
CG2 C:ILE53 4.7 36.2 1.0
O C:ARG80 4.7 40.0 1.0
CD C:LYS221 4.7 38.7 1.0
CG C:TRP84 4.7 42.5 1.0
CG2 C:THR83 4.8 43.0 1.0
CB C:THR57 4.9 38.3 1.0

Reference:

T.Ishizuka, K.Suzuki, M.Konno, K.Shibata, Y.Kawasaki, H.Akiyama, T.Murata, K.Inoue. Light-Driven Anion-Pumping Rhodopsin with Unique Cytoplasmic Anion-Release Mechanism. J.Biol.Chem. 07797 2024.
ISSN: ESSN 1083-351X
PubMed: 39305959
DOI: 10.1016/J.JBC.2024.107797
Page generated: Thu Oct 31 18:08:52 2024

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