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Chlorine in PDB 6f10: Glic Mutant D88N

Protein crystallography data

The structure of Glic Mutant D88N, PDB code: 6f10 was solved by H.D.Hu, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.370, 134.810, 160.680, 90.00, 103.12, 90.00
R / Rfree (%) 20.7 / 22.3

Other elements in 6f10:

The structure of Glic Mutant D88N also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Glic Mutant D88N (pdb code 6f10). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Glic Mutant D88N, PDB code: 6f10:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6f10

Go back to Chlorine Binding Sites List in 6f10
Chlorine binding site 1 out of 7 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:0.6
occ:1.00
 N A:PHE78 3.3 0.2 1.0
N A:ARG85 3.5 0.3 1.0
CD1 A:PHE78 3.6 0.2 1.0
CB A:PHE78 3.8 1.0 1.0
CD A:ARG85 3.9 0.6 1.0
CG2 A:VAL81 3.9 98.6 1.0
CA A:ARG77 4.1 97.8 1.0
CB A:ARG85 4.1 99.0 1.0
CA A:ALA84 4.1 0.5 1.0
CA A:PHE78 4.1 0.8 1.0
NH1 A:ARG85 4.2 98.1 1.0
C A:ARG77 4.2 0.9 1.0
O A:PHE78 4.2 0.2 1.0
CG A:PHE78 4.2 0.0 1.0
CG A:ARG85 4.3 0.4 1.0
C A:ALA84 4.3 0.1 1.0
CB A:ARG77 4.3 93.2 1.0
CA A:ARG85 4.4 1.0 1.0
CB A:ALA84 4.6 0.5 1.0
C A:PHE78 4.6 0.2 1.0
CE1 A:PHE78 4.7 0.7 1.0
CG A:ARG77 4.8 99.4 1.0
NE A:ARG85 4.9 0.7 1.0
CZ A:ARG85 5.0 0.6 1.0
CB A:VAL81 5.0 98.1 1.0

Chlorine binding site 2 out of 7 in 6f10

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Chlorine binding site 2 out of 7 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:0.2
occ:1.00
 ND2 A:ASN139 3.1 0.8 1.0
N A:LEU180 3.4 0.3 1.0
CA A:ARG179 3.8 0.6 1.0
CG A:ASN139 4.0 0.1 1.0
CB A:LEU180 4.0 0.8 1.0
OD1 A:ASN139 4.0 0.1 1.0
C A:ARG179 4.1 0.8 1.0
CD A:ARG179 4.2 0.9 1.0
CA A:LEU180 4.3 1.0 1.0
CB A:SER134 4.4 0.2 1.0
CB A:ARG179 4.6 0.8 1.0
O A:ASP178 4.7 0.1 1.0
N A:ARG179 4.8 0.6 1.0
CG A:ARG179 4.9 1.0 1.0
OG A:SER134 5.0 0.5 1.0

Chlorine binding site 3 out of 7 in 6f10

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Chlorine binding site 3 out of 7 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:1.0
occ:1.00
 N A:ALA175 3.6 0.6 1.0
CA A:PHE174 4.0 0.1 1.0
CB A:PHE174 4.2 0.7 1.0
CB A:ALA175 4.2 0.6 1.0
C A:PHE174 4.3 0.5 1.0
CA A:ALA175 4.5 0.5 1.0
O A:ALA175 5.0 0.5 1.0

Chlorine binding site 4 out of 7 in 6f10

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Chlorine binding site 4 out of 7 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:0.6
occ:1.00
 N B:PHE78 3.3 0.6 1.0
CD2 B:PHE78 3.6 0.7 1.0
N B:ARG85 3.7 0.0 1.0
CB B:PHE78 3.7 0.3 1.0
CG2 B:VAL81 3.9 0.2 1.0
CD B:ARG85 3.9 0.6 1.0
CA B:PHE78 4.0 0.4 1.0
CA B:ARG77 4.1 0.3 1.0
NH1 B:ARG85 4.1 0.7 1.0
CB B:ARG85 4.1 0.5 1.0
O B:PHE78 4.1 0.1 1.0
C B:ARG77 4.2 0.7 1.0
CG B:PHE78 4.2 0.5 1.0
CA B:ALA84 4.3 0.0 1.0
CG B:ARG85 4.3 0.9 1.0
CB B:ARG77 4.4 98.7 1.0
C B:ALA84 4.5 0.5 1.0
CA B:ARG85 4.5 0.9 1.0
C B:PHE78 4.6 0.7 1.0
CE2 B:PHE78 4.7 0.2 1.0
CB B:ALA84 4.9 0.7 1.0
NE B:ARG85 4.9 0.2 1.0
CG B:ARG77 4.9 0.2 1.0
CZ B:ARG85 5.0 0.9 1.0
CB B:VAL81 5.0 0.4 1.0
CG1 B:VAL81 5.0 99.2 1.0

Chlorine binding site 5 out of 7 in 6f10

Go back to Chlorine Binding Sites List in 6f10
Chlorine binding site 5 out of 7 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:0.9
occ:1.00
 N C:PHE78 3.3 0.9 1.0
N C:ARG85 3.5 0.9 1.0
CD2 C:PHE78 3.7 0.2 1.0
CB C:PHE78 3.8 0.5 1.0
CG2 C:VAL81 3.9 0.3 1.0
CD C:ARG85 3.9 0.8 1.0
CB C:ARG85 4.0 0.9 1.0
CA C:ARG77 4.1 1.0 1.0
CA C:PHE78 4.1 0.8 1.0
CA C:ALA84 4.1 0.5 1.0
NH1 C:ARG85 4.2 0.4 1.0
O C:PHE78 4.2 0.4 1.0
C C:ARG77 4.2 0.4 1.0
CG C:ARG85 4.3 0.4 1.0
CG C:PHE78 4.3 0.3 1.0
CB C:ARG77 4.3 0.8 1.0
C C:ALA84 4.4 0.7 1.0
CA C:ARG85 4.4 0.9 1.0
C C:PHE78 4.7 0.6 1.0
CB C:ALA84 4.7 0.4 1.0
CE2 C:PHE78 4.8 0.7 1.0
CG C:ARG77 4.8 0.6 1.0
NE C:ARG85 4.9 0.4 1.0
CB C:VAL81 4.9 1.0 1.0
CG1 C:VAL81 5.0 0.4 1.0
CZ C:ARG85 5.0 0.8 1.0

Chlorine binding site 6 out of 7 in 6f10

Go back to Chlorine Binding Sites List in 6f10
Chlorine binding site 6 out of 7 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:0.6
occ:1.00
 N D:PHE78 3.3 0.6 1.0
N D:ARG85 3.6 0.4 1.0
CD1 D:PHE78 3.6 0.8 1.0
CB D:PHE78 3.8 0.6 1.0
CD D:ARG85 3.9 0.9 1.0
CG2 D:VAL81 3.9 96.4 1.0
CA D:PHE78 4.1 0.1 1.0
CA D:ARG77 4.1 97.7 1.0
CB D:ARG85 4.1 0.8 1.0
NH1 D:ARG85 4.1 0.9 1.0
CA D:ALA84 4.2 1.0 1.0
C D:ARG77 4.2 0.1 1.0
O D:PHE78 4.2 0.2 1.0
CG D:PHE78 4.2 0.2 1.0
CG D:ARG85 4.3 0.3 1.0
CB D:ARG77 4.4 95.8 1.0
C D:ALA84 4.4 0.0 1.0
CA D:ARG85 4.5 0.6 1.0
C D:PHE78 4.6 0.3 1.0
CB D:ALA84 4.7 0.7 1.0
CE1 D:PHE78 4.7 0.4 1.0
CG D:ARG77 4.8 0.2 1.0
NE D:ARG85 4.8 0.5 1.0
CZ D:ARG85 4.9 1.0 1.0
CB D:VAL81 5.0 96.7 1.0

Chlorine binding site 7 out of 7 in 6f10

Go back to Chlorine Binding Sites List in 6f10
Chlorine binding site 7 out of 7 in the Glic Mutant D88N


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Glic Mutant D88N within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl402

b:0.3
occ:1.00
 N E:PHE78 3.3 0.8 1.0
CD1 E:PHE78 3.6 0.2 1.0
N E:ARG85 3.6 0.5 1.0
CB E:PHE78 3.7 0.7 1.0
CD E:ARG85 3.9 0.7 1.0
CG2 E:VAL81 3.9 0.6 1.0
CA E:PHE78 4.0 0.3 1.0
CA E:ARG77 4.0 0.0 1.0
CB E:ARG85 4.1 0.7 1.0
C E:ARG77 4.1 0.9 1.0
CG E:PHE78 4.1 0.6 1.0
O E:PHE78 4.2 0.4 1.0
NH1 E:ARG85 4.2 0.2 1.0
CA E:ALA84 4.2 0.9 1.0
CG E:ARG85 4.3 0.1 1.0
CB E:ARG77 4.3 0.4 1.0
C E:ALA84 4.4 0.2 1.0
CA E:ARG85 4.5 1.0 1.0
C E:PHE78 4.6 0.9 1.0
CE1 E:PHE78 4.7 0.6 1.0
CB E:ALA84 4.8 0.5 1.0
CG E:ARG77 4.8 0.7 1.0
NE E:ARG85 4.9 1.0 1.0
CG1 E:VAL81 5.0 0.6 1.0
CB E:VAL81 5.0 0.3 1.0

Reference:

A.Nemecz, H.Hu, Z.Fourati, C.Van Renterghem, M.Delarue, P.J.Corringer. Full Mutational Mapping of Titratable Residues Helps to Identify Proton-Sensors Involved in the Control of Channel Gating in the Gloeobacter Violaceus Pentameric Ligand-Gated Ion Channel. Plos Biol. V. 15 04470 2017.
ISSN: ESSN 1545-7885
PubMed: 29281623
DOI: 10.1371/JOURNAL.PBIO.2004470
Page generated: Sat Jul 27 22:48:09 2024

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