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Chlorine in PDB 3d32: Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide

Protein crystallography data

The structure of Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide, PDB code: 3d32 was solved by O.H.Weiergraeber, T.Stangler, D.Willbold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.17 / 1.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 129.287, 35.415, 58.209, 90.00, 100.59, 90.00
R / Rfree (%) 17.7 / 19.5

Other elements in 3d32:

The structure of Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide (pdb code 3d32). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide, PDB code: 3d32:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 3d32

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Chlorine binding site 1 out of 8 in the Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl121

b:11.9
occ:1.00
OG1 A:THR89 3.0 4.8 1.0
O A:HOH128 3.3 8.4 1.0
O A:HOH223 3.3 29.1 1.0
CB A:THR89 3.6 5.3 1.0
N A:SER90 3.7 4.7 1.0
C A:THR89 3.7 5.2 1.0
O A:THR89 3.8 5.6 1.0
CA A:SER90 3.9 5.3 1.0
CB A:SER90 4.0 5.6 1.0
CA A:THR89 4.3 4.9 1.0
O A:HOH136 4.6 17.9 1.0
CG2 A:THR89 5.0 6.9 1.0
OG A:SER90 5.0 8.0 1.0

Chlorine binding site 2 out of 8 in 3d32

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Chlorine binding site 2 out of 8 in the Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl122

b:20.0
occ:1.00
O A:HOH148 3.0 15.1 1.0
N A:ASP47 3.1 10.2 0.5
NE A:ARG69 3.1 10.2 1.0
N A:ASP47 3.2 10.0 0.5
CG A:ASP47 3.4 11.8 0.5
OD2 A:ASP47 3.4 13.1 0.5
NH2 A:ARG69 3.5 11.8 1.0
CB A:ASP47 3.5 10.3 0.5
CA A:LEU46 3.8 10.7 1.0
CZ A:ARG69 3.8 11.5 1.0
CD2 A:LEU46 3.9 9.4 1.0
CA A:ASP47 3.9 10.3 0.5
CG A:ARG69 4.0 10.2 1.0
C A:LEU46 4.0 10.8 1.0
OD1 A:ASP47 4.0 13.3 0.5
CB A:ASP47 4.1 9.7 0.5
CD A:ARG69 4.2 9.2 1.0
CA A:ASP47 4.2 9.7 0.5
CB A:LEU46 4.3 10.1 1.0
O A:ASP45 4.5 14.8 1.0
CG2 A:ILE70 4.6 13.7 1.0
CG A:LEU46 4.7 9.4 1.0
O C:HOH266 4.9 14.4 1.0
N A:LEU46 4.9 11.3 1.0
N A:LYS48 5.0 8.4 1.0

Chlorine binding site 3 out of 8 in 3d32

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Chlorine binding site 3 out of 8 in the Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl123

b:20.4
occ:1.00
O A:HOH213 3.1 27.6 1.0
N A:LYS49 3.1 7.0 1.0
N A:LYS50 3.4 7.6 0.5
N A:LYS50 3.4 7.4 0.5
CA A:LYS48 3.9 8.2 1.0
CB A:LYS48 3.9 8.3 1.0
CB A:LYS50 3.9 7.5 0.5
CA A:LYS49 4.0 7.9 1.0
C A:LYS48 4.0 7.3 1.0
NZ A:LYS50 4.0 10.1 0.5
CB A:LYS50 4.1 8.0 0.5
CB A:LYS49 4.1 7.7 1.0
C A:LYS49 4.2 7.9 1.0
CA A:LYS50 4.2 7.7 0.5
CA A:LYS50 4.3 7.9 0.5
CE A:LYS48 4.5 17.6 1.0
CG A:LYS48 4.5 11.0 1.0
O A:LYS50 4.6 7.3 0.5
O A:LYS50 4.7 7.3 0.5
CG A:LYS49 4.8 8.9 1.0
O A:HOH230 4.9 32.7 1.0
C A:LYS50 5.0 7.6 0.5
C A:LYS50 5.0 7.5 0.5

Chlorine binding site 4 out of 8 in 3d32

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Chlorine binding site 4 out of 8 in the Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl124

b:24.1
occ:1.00
O A:HOH228 2.9 27.3 1.0
O A:HOH168 3.0 22.3 1.0
N A:ASP29 3.4 10.0 1.0
CA A:TYR27 3.5 9.8 1.0
C A:TYR27 3.5 9.8 1.0
NE A:ARG30 3.7 10.4 1.0
CB A:TYR27 3.7 9.8 1.0
N A:PRO28 3.8 9.7 1.0
CG A:ARG30 3.9 10.2 1.0
CB A:ASP29 3.9 10.0 1.0
CA A:ASP29 3.9 9.9 1.0
CD A:PRO28 4.0 9.2 1.0
O A:TYR27 4.0 10.6 1.0
N A:ARG30 4.0 9.0 1.0
C A:ASP29 4.1 9.3 1.0
CD1 A:TYR27 4.2 12.5 1.0
CD A:ARG30 4.3 11.6 1.0
CG A:TYR27 4.4 10.8 1.0
C A:PRO28 4.5 10.6 1.0
CZ A:ARG30 4.5 9.5 1.0
NH2 A:ARG30 4.5 10.2 1.0
CB A:ARG30 4.6 9.5 1.0
OD2 A:ASP29 4.6 15.9 1.0
CG A:ASP29 4.7 13.2 1.0
CA A:PRO28 4.7 10.3 1.0
CG A:PRO28 4.7 11.1 1.0
O A:ASP29 4.8 8.9 1.0
N A:TYR27 4.9 9.6 1.0
CA A:ARG30 4.9 8.7 1.0

Chlorine binding site 5 out of 8 in 3d32

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Chlorine binding site 5 out of 8 in the Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl120

b:15.8
occ:1.00
OG B:SER90 3.0 12.8 0.5
OG1 B:THR89 3.0 9.3 1.0
O B:HOH320 3.1 26.5 1.0
O B:HOH264 3.2 11.1 1.0
N B:SER90 3.6 8.2 0.5
N B:SER90 3.6 9.0 0.5
CB B:THR89 3.6 8.9 1.0
C B:THR89 3.7 8.7 1.0
CA B:SER90 3.8 7.5 0.5
CA B:SER90 3.8 9.3 0.5
O B:THR89 3.8 9.0 1.0
CB B:SER90 3.9 9.4 0.5
CB B:SER90 4.1 7.5 0.5
CA B:THR89 4.3 9.0 1.0
O B:HOH310 4.3 23.4 1.0
O B:HOH361 4.7 28.6 1.0
CG2 B:THR89 5.0 10.5 1.0

Chlorine binding site 6 out of 8 in 3d32

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Chlorine binding site 6 out of 8 in the Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl121

b:18.8
occ:1.00
NE B:ARG69 3.0 8.5 1.0
N B:ASP47 3.1 9.2 1.0
O B:HOH267 3.2 13.1 1.0
CG B:ASP47 3.4 12.8 1.0
NH2 B:ARG69 3.5 9.5 1.0
OD2 B:ASP47 3.6 14.6 1.0
CZ B:ARG69 3.7 8.9 1.0
OD1 B:ASP47 3.7 13.9 1.0
CA B:LEU46 3.7 9.2 1.0
CG B:ARG69 3.7 11.3 1.0
CB B:ASP47 3.7 10.1 1.0
CD2 B:LEU46 3.9 9.8 1.0
C B:LEU46 3.9 9.2 1.0
CD B:ARG69 4.0 8.9 1.0
CA B:ASP47 4.0 10.0 1.0
CB B:LEU46 4.2 8.9 1.0
CG2 B:ILE70 4.3 16.1 1.0
O B:ASP45 4.6 11.6 1.0
CG B:LEU46 4.7 9.5 1.0
O D:HOH289 4.9 11.2 1.0
N B:LEU46 5.0 9.5 1.0
N B:LYS48 5.0 9.1 0.5
N B:LYS48 5.0 9.3 0.5

Chlorine binding site 7 out of 8 in 3d32

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Chlorine binding site 7 out of 8 in the Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl122

b:16.1
occ:1.00
O B:HOH300 3.0 23.6 1.0
N B:LYS49 3.2 7.7 1.0
N B:LYS50 3.4 7.4 1.0
CB B:LYS48 3.7 9.5 0.5
CA B:LYS48 3.8 9.1 0.5
CA B:LYS48 3.8 8.7 0.5
CD B:LYS48 3.9 8.4 0.5
CB B:LYS48 3.9 8.7 0.5
CB B:LYS50 3.9 9.8 1.0
C B:LYS48 4.0 8.5 0.5
C B:LYS48 4.0 8.3 0.5
CG B:LYS48 4.1 10.1 0.5
CA B:LYS49 4.1 7.7 1.0
C B:LYS49 4.3 7.1 1.0
CA B:LYS50 4.3 7.8 1.0
CB B:LYS49 4.5 8.0 1.0
CG B:LYS48 4.5 9.1 0.5
O B:LYS50 4.6 7.7 1.0
O B:HOH378 4.8 32.6 1.0
O B:HOH375 4.9 34.0 1.0
C B:LYS50 5.0 7.5 1.0

Chlorine binding site 8 out of 8 in 3d32

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Chlorine binding site 8 out of 8 in the Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Complex of Gaba(A) Receptor-Associated Protein (Gabarap) with A Synthetic Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl123

b:13.9
occ:1.00
NZ B:LYS49 3.1 6.9 1.0
CA B:TYR7 3.5 9.9 1.0
NE2 B:HIS11 3.5 9.5 1.0
CE B:LYS49 3.6 7.4 1.0
CD2 B:TYR7 3.7 9.4 1.0
CD B:LYS49 3.8 8.0 1.0
N B:TYR7 3.9 9.6 1.0
CB B:TYR7 4.0 10.2 1.0
CD2 B:HIS11 4.2 4.7 1.0
C B:VAL6 4.2 9.2 1.0
CG B:TYR7 4.2 9.4 1.0
O B:VAL6 4.2 9.5 1.0
CG1 B:VAL6 4.3 10.2 1.0
CB B:GLU10 4.5 6.8 1.0
CE2 B:TYR7 4.6 10.1 1.0
CE1 B:HIS11 4.7 4.2 1.0
C B:TYR7 4.7 9.5 1.0
OE1 B:GLU36 4.8 7.3 1.0
CG B:GLU10 4.8 8.7 1.0
O B:TYR7 4.8 10.9 1.0
CG B:LYS49 4.9 6.9 1.0
CB B:VAL6 4.9 9.1 1.0
O B:HOH293 5.0 17.3 1.0

Reference:

O.H.Weiergraber, T.Stangler, Y.Thielmann, J.Mohrluder, K.Wiesehan, D.Willbold. Ligand Binding Mode of Gaba(A) Receptor-Associated Protein. J.Mol.Biol. V. 381 1320 2008.
ISSN: ISSN 0022-2836
PubMed: 18638487
DOI: 10.1016/J.JMB.2008.06.086
Page generated: Sat Dec 12 09:37:43 2020

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