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Chlorine in PDB 6f11: Glic Mutant D86A

Protein crystallography data

The structure of Glic Mutant D86A, PDB code: 6f11 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 / 2.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 181.820, 133.790, 160.160, 90.00, 102.29, 90.00
R / Rfree (%) 19.5 / 21.6

Other elements in 6f11:

The structure of Glic Mutant D86A also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Glic Mutant D86A (pdb code 6f11). 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 D86A, PDB code: 6f11:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6f11

Go back to Chlorine Binding Sites List in 6f11
Chlorine binding site 1 out of 7 in the Glic Mutant D86A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Glic Mutant D86A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:78.2
occ:1.00
 N A:PHE78 3.3 73.3 1.0
N A:ARG85 3.6 84.1 1.0
CD1 A:PHE78 3.6 85.1 1.0
CB A:PHE78 3.7 75.3 1.0
CD A:ARG85 3.9 76.7 1.0
CG2 A:VAL81 3.9 77.7 1.0
CA A:PHE78 4.1 73.2 1.0
CA A:ARG77 4.1 66.4 1.0
CB A:ARG85 4.1 76.8 1.0
O A:PHE78 4.1 76.5 1.0
NH1 A:ARG85 4.2 85.9 1.0
CG A:PHE78 4.2 79.0 1.0
C A:ARG77 4.2 73.6 1.0
CA A:ALA84 4.2 87.3 1.0
CG A:ARG85 4.3 76.5 1.0
CB A:ARG77 4.4 66.1 1.0
C A:ALA84 4.4 91.0 1.0
CA A:ARG85 4.5 81.8 1.0
C A:PHE78 4.6 75.5 1.0
CB A:ALA84 4.7 88.9 1.0
CE1 A:PHE78 4.7 87.6 1.0
NE A:ARG85 4.9 74.9 1.0
CG A:ARG77 4.9 72.9 1.0
CZ A:ARG85 5.0 95.2 1.0
CB A:VAL81 5.0 77.0 1.0

Chlorine binding site 2 out of 7 in 6f11

Go back to Chlorine Binding Sites List in 6f11
Chlorine binding site 2 out of 7 in the Glic Mutant D86A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Glic Mutant D86A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:0.1
occ:1.00
 ND2 A:ASN139 3.1 0.6 1.0
N A:LEU180 3.3 70.5 1.0
CA A:ARG179 3.8 69.5 1.0
CG A:ASN139 3.9 0.3 1.0
CB A:LEU180 3.9 69.8 1.0
OD1 A:ASN139 4.0 76.0 1.0
C A:ARG179 4.0 72.0 1.0
CA A:LEU180 4.3 69.3 1.0
CD A:ARG179 4.3 83.8 1.0
CB A:SER134 4.5 76.9 1.0
CB A:ARG179 4.5 66.1 1.0
O A:ASP178 4.7 82.3 1.0
N A:ARG179 4.7 71.6 1.0
CG A:ARG179 4.9 72.7 1.0
OG A:SER134 5.0 87.7 1.0

Chlorine binding site 3 out of 7 in 6f11

Go back to Chlorine Binding Sites List in 6f11
Chlorine binding site 3 out of 7 in the Glic Mutant D86A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Glic Mutant D86A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:0.3
occ:1.00
 N A:ALA175 3.6 71.2 1.0
CB A:ALA175 4.1 73.5 1.0
CA A:PHE174 4.1 66.9 1.0
CB A:PHE174 4.3 66.6 1.0
C A:PHE174 4.4 73.3 1.0
CA A:ALA175 4.5 71.3 1.0
O A:ALA175 5.0 76.2 1.0

Chlorine binding site 4 out of 7 in 6f11

Go back to Chlorine Binding Sites List in 6f11
Chlorine binding site 4 out of 7 in the Glic Mutant D86A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Glic Mutant D86A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:87.0
occ:1.00
 N B:PHE78 3.2 70.7 1.0
CD2 B:PHE78 3.6 82.6 1.0
CB B:PHE78 3.7 74.4 1.0
N B:ARG85 3.8 91.0 1.0
CD B:ARG85 3.8 90.8 1.0
CG2 B:VAL81 3.9 71.2 1.0
CA B:PHE78 4.0 71.9 1.0
NH1 B:ARG85 4.1 80.8 1.0
CA B:ARG77 4.1 65.6 1.0
CG B:PHE78 4.1 78.3 1.0
O B:PHE78 4.1 77.6 1.0
C B:ARG77 4.1 70.0 1.0
CB B:ARG85 4.1 84.8 1.0
CG B:ARG85 4.3 84.8 1.0
CA B:ALA84 4.4 94.8 1.0
CB B:ARG77 4.4 63.6 1.0
C B:PHE78 4.5 76.5 1.0
CA B:ARG85 4.6 88.2 1.0
C B:ALA84 4.6 98.6 1.0
CE2 B:PHE78 4.7 86.7 1.0
NE B:ARG85 4.8 89.0 1.0
CB B:ALA84 4.9 96.6 1.0
CZ B:ARG85 4.9 97.4 1.0
CG B:ARG77 4.9 71.2 1.0

Chlorine binding site 5 out of 7 in 6f11

Go back to Chlorine Binding Sites List in 6f11
Chlorine binding site 5 out of 7 in the Glic Mutant D86A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Glic Mutant D86A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:80.7
occ:1.00
 N C:PHE78 3.3 71.2 1.0
CD2 C:PHE78 3.6 81.6 1.0
N C:ARG85 3.7 85.2 1.0
CB C:PHE78 3.7 72.9 1.0
CD C:ARG85 3.8 77.2 1.0
CG2 C:VAL81 3.9 79.0 1.0
CA C:PHE78 4.1 71.0 1.0
CB C:ARG85 4.1 79.6 1.0
CA C:ARG77 4.1 67.8 1.0
NH1 C:ARG85 4.1 79.8 1.0
CG C:PHE78 4.2 76.6 1.0
O C:PHE78 4.2 77.8 1.0
C C:ARG77 4.2 72.8 1.0
CA C:ALA84 4.3 88.7 1.0
CG C:ARG85 4.3 73.0 1.0
CB C:ARG77 4.4 65.8 1.0
C C:ALA84 4.5 91.8 1.0
CA C:ARG85 4.5 83.2 1.0
C C:PHE78 4.6 75.1 1.0
CE2 C:PHE78 4.7 85.8 1.0
CB C:ALA84 4.8 90.4 1.0
NE C:ARG85 4.8 77.8 1.0
CG C:ARG77 4.9 79.4 1.0
NH1 B:ARG105 4.9 1.0 1.0
CZ C:ARG85 4.9 94.3 1.0
CB C:VAL81 5.0 78.3 1.0

Chlorine binding site 6 out of 7 in 6f11

Go back to Chlorine Binding Sites List in 6f11
Chlorine binding site 6 out of 7 in the Glic Mutant D86A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Glic Mutant D86A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl402

b:82.2
occ:1.00
 N D:PHE78 3.3 68.8 1.0
CD1 D:PHE78 3.6 79.6 1.0
N D:ARG85 3.7 79.7 1.0
CB D:PHE78 3.7 71.1 1.0
CD D:ARG85 3.9 83.7 1.0
CG2 D:VAL81 3.9 69.3 1.0
CA D:PHE78 4.0 69.0 1.0
CA D:ARG77 4.1 62.0 1.0
NH1 D:ARG85 4.1 83.0 1.0
CB D:ARG85 4.1 76.7 1.0
O D:PHE78 4.1 74.8 1.0
C D:ARG77 4.1 68.9 1.0
CG D:PHE78 4.2 74.5 1.0
CA D:ALA84 4.3 85.4 1.0
CG D:ARG85 4.3 79.2 1.0
CB D:ARG77 4.3 58.3 1.0
C D:ALA84 4.5 87.3 1.0
CA D:ARG85 4.5 77.9 1.0
C D:PHE78 4.6 73.0 1.0
CE1 D:PHE78 4.7 81.6 1.0
CB D:ALA84 4.8 87.7 1.0
CG D:ARG77 4.8 61.3 1.0
NE D:ARG85 4.9 93.2 1.0
CZ D:ARG85 5.0 0.4 1.0

Chlorine binding site 7 out of 7 in 6f11

Go back to Chlorine Binding Sites List in 6f11
Chlorine binding site 7 out of 7 in the Glic Mutant D86A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Glic Mutant D86A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl402

b:86.3
occ:1.00
 N E:PHE78 3.2 73.1 1.0
CD1 E:PHE78 3.6 86.3 1.0
CB E:PHE78 3.7 75.9 1.0
N E:ARG85 3.7 86.7 1.0
CG2 E:VAL81 3.9 75.4 1.0
CD E:ARG85 3.9 82.4 1.0
CA E:PHE78 4.0 73.4 1.0
CA E:ARG77 4.0 70.7 1.0
CG E:PHE78 4.1 79.8 1.0
C E:ARG77 4.1 75.0 1.0
O E:PHE78 4.1 76.7 1.0
CB E:ARG85 4.1 81.3 1.0
NH1 E:ARG85 4.2 79.3 1.0
CA E:ALA84 4.3 92.3 1.0
CG E:ARG85 4.3 80.4 1.0
CB E:ARG77 4.3 68.9 1.0
C E:ALA84 4.5 95.0 1.0
CA E:ARG85 4.5 84.3 1.0
C E:PHE78 4.6 75.6 1.0
CE1 E:PHE78 4.7 88.1 1.0
CG E:ARG77 4.8 82.2 1.0
CB E:ALA84 4.8 94.5 1.0
NE E:ARG85 4.9 74.1 1.0
CZ E:ARG85 5.0 95.6 1.0
CB E:VAL81 5.0 74.8 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 22:49:39 2024

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