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Chlorine in PDB 6ivl: Crystal Structure of A Membrane Protein L259A

Protein crystallography data

The structure of Crystal Structure of A Membrane Protein L259A, PDB code: 6ivl was solved by A.Kittredge, F.Fukuda, Y.Zhang, T.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.80 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.350, 160.539, 161.878, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 24.4

Other elements in 6ivl:

The structure of Crystal Structure of A Membrane Protein L259A also contains other interesting chemical elements:

Zinc (Zn) 16 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of A Membrane Protein L259A (pdb code 6ivl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of A Membrane Protein L259A, PDB code: 6ivl:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 6ivl

Go back to Chlorine Binding Sites List in 6ivl
Chlorine binding site 1 out of 6 in the Crystal Structure of A Membrane Protein L259A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of A Membrane Protein L259A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:0.7
occ:1.00
 ZN A:ZN302 2.6 0.9 1.0
CB A:HIS108 3.2 96.7 1.0
ND1 A:HIS108 3.4 0.0 1.0
CG A:HIS108 3.7 0.5 1.0
O A:HIS108 3.7 99.4 1.0
CB A:HIS111 3.7 92.8 1.0
CG A:ARG112 3.7 0.5 1.0
CA A:HIS108 3.8 90.4 1.0
ND1 A:HIS111 4.0 91.2 1.0
NH1 A:ARG112 4.1 0.9 1.0
C A:HIS108 4.2 99.2 1.0
O A:HOH402 4.2 91.7 1.0
CD A:ARG112 4.3 0.1 1.0
O A:THR287 4.3 0.1 1.0
CG A:HIS111 4.4 93.6 1.0
CB A:THR287 4.5 93.4 1.0
N A:ARG112 4.6 82.7 1.0
CZ A:ARG112 4.6 0.6 1.0
CE1 A:HIS108 4.6 0.9 1.0
CG2 A:THR287 4.6 76.3 1.0
NE A:ARG112 4.7 0.9 1.0
CB A:ARG112 4.9 0.6 1.0
CD2 A:HIS108 5.0 0.5 1.0
CA A:HIS111 5.0 88.7 1.0

Chlorine binding site 2 out of 6 in 6ivl

Go back to Chlorine Binding Sites List in 6ivl
Chlorine binding site 2 out of 6 in the Crystal Structure of A Membrane Protein L259A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of A Membrane Protein L259A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl305

b:83.8
occ:1.00
 ZN C:ZN301 2.1 90.3 1.0
OE1 C:GLU191 3.3 78.9 1.0
OG1 C:THR95 3.3 83.1 1.0
NZ C:LYS188 3.3 85.0 1.0
NE2 D:HIS194 3.4 69.7 1.0
CE C:LYS188 3.4 78.1 1.0
CD C:LYS188 3.4 75.0 1.0
O C:HOH403 3.5 73.2 1.0
OD1 D:ASP190 3.6 97.2 1.0
CG D:ASP190 3.9 89.9 1.0
CD2 D:HIS194 3.9 72.2 1.0
CG2 C:THR95 3.9 68.0 1.0
CB D:ASP190 4.0 76.0 1.0
CB C:THR95 4.1 73.5 1.0
CD C:GLU191 4.2 82.0 1.0
OE2 C:GLU191 4.2 86.6 1.0
CG2 C:ILE91 4.3 71.0 1.0
CE1 D:HIS194 4.3 73.3 1.0
CA D:ASP190 4.4 72.1 1.0
O C:ILE91 4.5 69.9 1.0
CA C:ALA92 4.5 60.5 1.0
OD2 D:ASP190 4.7 95.0 1.0
O D:ASP190 4.8 67.8 1.0
CG C:LYS188 4.8 73.9 1.0
C C:ILE91 4.9 73.5 1.0
C D:ASP190 4.9 74.1 1.0
N C:ALA92 5.0 72.3 1.0

Chlorine binding site 3 out of 6 in 6ivl

Go back to Chlorine Binding Sites List in 6ivl
Chlorine binding site 3 out of 6 in the Crystal Structure of A Membrane Protein L259A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of A Membrane Protein L259A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl304

b:0.9
occ:1.00
 ZN D:ZN301 2.3 0.5 1.0
CE1 D:HIS108 3.3 0.0 1.0
CD D:ARG101 3.4 0.8 1.0
CG D:ARG101 3.6 0.4 1.0
NE D:ARG101 3.6 1.0 1.0
ND1 D:HIS108 3.8 0.5 1.0
ND1 D:HIS111 3.8 0.2 1.0
CL D:CL305 4.1 0.2 1.0
CZ D:ARG101 4.1 0.9 1.0
CA D:THR287 4.2 0.0 1.0
CE1 D:HIS111 4.2 0.6 1.0
O D:THR287 4.2 0.9 1.0
NH2 D:ARG101 4.3 0.0 1.0
NE2 D:HIS108 4.3 0.1 1.0
C D:THR287 4.4 0.3 1.0
O D:MET286 4.5 0.6 1.0
CG2 D:THR287 4.7 0.8 1.0
CB D:THR287 4.8 0.2 1.0
NH1 D:ARG101 4.9 0.5 1.0
CG D:HIS108 4.9 0.5 1.0

Chlorine binding site 4 out of 6 in 6ivl

Go back to Chlorine Binding Sites List in 6ivl
Chlorine binding site 4 out of 6 in the Crystal Structure of A Membrane Protein L259A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of A Membrane Protein L259A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl305

b:0.2
occ:1.00
 ZN D:ZN301 2.1 0.5 1.0
ND1 D:HIS108 2.9 0.5 1.0
CB D:HIS108 3.3 0.9 1.0
CG D:HIS108 3.3 0.5 1.0
CB D:HIS111 3.3 0.3 1.0
ND1 D:HIS111 3.4 0.2 1.0
CA D:HIS108 3.6 0.4 1.0
O D:HIS108 3.7 0.1 1.0
CG D:HIS111 3.7 0.7 1.0
CE1 D:HIS108 3.9 0.0 1.0
CL D:CL304 4.1 0.9 1.0
C D:HIS108 4.1 0.4 1.0
CD2 D:HIS108 4.3 0.0 1.0
O D:THR287 4.4 0.9 1.0
CG D:ARG112 4.4 0.1 1.0
CE1 D:HIS111 4.5 0.6 1.0
NE2 D:HIS108 4.6 0.1 1.0
N D:ARG112 4.6 0.3 1.0
CA D:HIS111 4.6 0.9 1.0
CG2 D:THR287 4.7 0.8 1.0
NH1 D:ARG112 4.7 0.2 1.0
CB D:THR287 4.8 0.2 1.0
C D:HIS111 4.9 0.2 1.0
N D:HIS108 4.9 0.5 1.0
CD2 D:HIS111 5.0 96.9 1.0

Chlorine binding site 5 out of 6 in 6ivl

Go back to Chlorine Binding Sites List in 6ivl
Chlorine binding site 5 out of 6 in the Crystal Structure of A Membrane Protein L259A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of A Membrane Protein L259A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl304

b:81.4
occ:1.00
 ZN E:ZN302 2.1 88.5 1.0
ND1 E:HIS108 3.1 91.0 1.0
CE1 E:HIS108 3.2 90.7 1.0
ND1 E:HIS111 3.4 86.0 1.0
NE E:ARG101 3.7 85.5 1.0
CD E:ARG101 3.7 84.7 1.0
CZ E:ARG101 3.8 86.7 1.0
CE1 E:HIS111 3.9 84.4 1.0
NH2 E:ARG101 3.9 85.8 1.0
CG E:ARG101 4.1 83.2 1.0
CL E:CL305 4.1 91.1 1.0
O E:THR287 4.2 93.0 1.0
CA E:THR287 4.3 86.8 1.0
CG E:HIS108 4.4 82.4 1.0
NE2 E:HIS108 4.4 92.7 1.0
NH1 E:ARG101 4.4 97.5 1.0
CG E:HIS111 4.5 77.1 1.0
C E:THR287 4.5 92.2 1.0
CB E:THR287 4.7 90.8 1.0
CG2 E:THR287 4.7 78.9 1.0
O E:MET286 4.7 89.9 1.0
O E:PRO105 4.8 79.2 1.0
CB E:HIS111 4.9 78.1 1.0
NE2 E:HIS111 5.0 85.1 1.0

Chlorine binding site 6 out of 6 in 6ivl

Go back to Chlorine Binding Sites List in 6ivl
Chlorine binding site 6 out of 6 in the Crystal Structure of A Membrane Protein L259A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of A Membrane Protein L259A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl305

b:91.1
occ:1.00
 ZN E:ZN302 2.4 88.5 1.0
O E:HIS108 3.4 89.5 1.0
CB E:HIS108 3.4 79.4 1.0
CB E:HIS111 3.7 78.1 1.0
CA E:HIS108 3.8 82.6 1.0
NE E:ARG112 3.8 0.9 1.0
O E:THR287 3.8 93.0 1.0
ND1 E:HIS108 3.8 91.0 1.0
CG E:ARG112 3.9 0.2 1.0
CG E:HIS108 3.9 82.4 1.0
C E:HIS108 4.0 87.0 1.0
CB E:THR287 4.1 90.8 1.0
CL E:CL304 4.1 81.4 1.0
ND1 E:HIS111 4.2 86.0 1.0
N E:ARG112 4.2 78.5 1.0
CD E:ARG112 4.2 0.7 1.0
CG E:HIS111 4.4 77.1 1.0
CZ E:ARG112 4.5 0.4 1.0
CG2 E:THR287 4.5 78.9 1.0
CB E:ARG112 4.6 98.2 1.0
CA E:ARG112 4.7 83.7 1.0
C E:THR287 4.7 92.2 1.0
NH2 E:ARG112 4.8 0.2 1.0
C E:HIS111 4.8 86.1 1.0
CA E:THR287 4.8 86.8 1.0
CA E:HIS111 4.9 81.3 1.0
NE2 E:GLN289 4.9 98.7 1.0
CE1 E:HIS108 4.9 90.7 1.0

Reference:

C.Ji, A.Kittredge, A.Hopiavuori, N.Ward, S.Chen, Y.Fukuda, Y.Zhang, T.Yang. Dual CA2+-Dependent Gates in Human BESTROPHIN1 Underlie Disease-Causing Mechanisms of Gain-of-Function Mutations. Commun Biol V. 2 240 2019.
ISSN: ESSN 2399-3642
PubMed: 31263784
DOI: 10.1038/S42003-019-0433-3
Page generated: Sun Jul 28 01:48:44 2024

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