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Chlorine in PDB 6ivp: Crystal Structure of A Membrane Protein P262A

Protein crystallography data

The structure of Crystal Structure of A Membrane Protein P262A, PDB code: 6ivp 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) 50.01 / 3.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.482, 162.411, 161.790, 90.00, 90.00, 90.00
R / Rfree (%) 26.6 / 31.5

Other elements in 6ivp:

The structure of Crystal Structure of A Membrane Protein P262A also contains other interesting chemical elements:

Zinc (Zn) 14 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of A Membrane Protein P262A (pdb code 6ivp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of A Membrane Protein P262A, PDB code: 6ivp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 6ivp

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Chlorine binding site 1 out of 10 in the Crystal Structure of A Membrane Protein P262A


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 P262A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:0.8
occ:1.00
 ZN A:ZN303 2.4 0.7 1.0
ND1 A:HIS108 3.2 0.2 1.0
NH1 A:ARG112 3.5 0.7 1.0
O A:HIS108 3.5 0.6 1.0
CB A:HIS108 3.6 0.3 1.0
CB A:HIS111 3.6 0.5 1.0
ND1 A:HIS111 3.8 0.1 1.0
CG A:HIS108 3.9 0.9 1.0
CA A:HIS108 3.9 0.8 1.0
C A:HIS108 4.1 0.1 1.0
CG A:HIS111 4.1 0.2 1.0
CB A:THR287 4.2 0.1 1.0
CG A:ARG112 4.2 0.1 1.0
CG2 A:THR287 4.2 0.2 1.0
CZ A:ARG112 4.2 0.7 1.0
CE1 A:HIS108 4.3 0.9 1.0
N A:GLY288 4.5 0.7 1.0
N A:ARG112 4.7 1.0 1.0
NE A:ARG112 4.8 0.4 1.0
CD A:ARG112 4.8 0.5 1.0
CA A:THR287 4.8 0.9 1.0
NH2 A:ARG112 4.9 1.0 1.0
CE1 A:HIS111 4.9 0.5 1.0
O A:GLN289 4.9 0.4 1.0
CA A:HIS111 5.0 0.4 1.0

Chlorine binding site 2 out of 10 in 6ivp

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Chlorine binding site 2 out of 10 in the Crystal Structure of A Membrane Protein P262A


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 P262A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:0.5
occ:1.00
 ZN A:ZN302 2.3 0.1 1.0
NE2 A:HIS194 3.2 0.0 1.0
OG1 B:THR95 3.2 0.1 1.0
CD2 A:HIS194 3.6 0.5 1.0
CE B:LYS188 3.6 0.5 1.0
CD B:LYS188 3.7 0.3 1.0
OE1 B:GLU191 3.7 0.9 1.0
OE2 B:GLU191 3.8 0.8 1.0
CD B:GLU191 4.1 0.7 1.0
CG2 B:ILE91 4.1 0.8 1.0
CA B:ALA92 4.2 0.8 1.0
CB B:THR95 4.2 0.2 1.0
O B:ILE91 4.2 0.3 1.0
CG2 B:THR95 4.2 0.6 1.0
CB A:ASP190 4.4 0.4 1.0
CE1 A:HIS194 4.4 0.9 1.0
O A:ASP190 4.4 0.2 1.0
NZ B:LYS188 4.4 0.1 1.0
OD1 A:ASP190 4.5 0.7 1.0
C B:ILE91 4.5 1.0 1.0
N B:ALA92 4.5 0.8 1.0
CG A:ASP190 4.6 0.0 1.0
CA A:ASP190 4.8 0.4 1.0
CB B:ALA92 4.8 0.2 1.0
CG A:HIS194 4.8 0.8 1.0
C A:ASP190 5.0 0.4 1.0

Chlorine binding site 3 out of 10 in 6ivp

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Chlorine binding site 3 out of 10 in the Crystal Structure of A Membrane Protein P262A


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 P262A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:0.0
occ:1.00
 ZN B:ZN301 2.8 0.4 1.0
CG2 B:ILE39 3.7 0.3 1.0
O B:ILE39 4.2 0.2 1.0
CZ B:TYR236 4.3 0.4 1.0
CE2 B:TYR236 4.4 0.0 1.0
CE1 B:TYR236 4.6 0.9 1.0
O B:HIS235 4.6 0.3 1.0
C B:HIS235 4.7 0.9 1.0
OH B:TYR236 4.7 0.7 1.0
CB B:HIS235 4.7 0.7 1.0
CD2 B:TYR236 4.7 0.0 1.0
ND1 B:HIS235 4.8 0.2 1.0
CA B:HIS235 4.8 0.7 1.0
CD1 B:TYR236 4.9 0.3 1.0
CB B:ILE39 4.9 0.4 1.0
C B:ILE39 4.9 0.5 1.0
CG B:TYR236 4.9 0.9 1.0
CA B:ILE39 5.0 0.6 1.0

Chlorine binding site 4 out of 10 in 6ivp

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Chlorine binding site 4 out of 10 in the Crystal Structure of A Membrane Protein P262A


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 P262A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:0.2
occ:1.00
 ZN B:ZN302 2.3 0.2 1.0
O B:GLY288 3.2 0.6 1.0
ND1 B:HIS108 3.4 0.7 1.0
O B:HIS108 3.6 0.2 1.0
NH1 B:ARG112 3.7 0.9 1.0
CB B:HIS111 3.7 0.5 1.0
ND1 B:HIS111 4.0 0.4 1.0
CB B:HIS108 4.0 0.9 1.0
C B:GLY288 4.0 0.2 1.0
CA B:HIS108 4.1 0.8 1.0
CG B:HIS108 4.1 0.1 1.0
CG B:HIS111 4.2 0.4 1.0
CG B:ARG112 4.3 0.3 1.0
C B:HIS108 4.3 0.3 1.0
CZ B:ARG112 4.4 0.7 1.0
CE1 B:HIS108 4.5 0.8 1.0
NE2 B:HIS290 4.6 0.8 1.0
CA B:GLY288 4.6 0.7 1.0
CD2 B:HIS290 4.7 0.8 1.0
N B:ARG112 4.8 0.3 1.0
N B:GLN289 4.8 0.7 1.0
CD B:ARG112 4.9 0.2 1.0
NE B:ARG112 4.9 0.0 1.0

Chlorine binding site 5 out of 10 in 6ivp

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Chlorine binding site 5 out of 10 in the Crystal Structure of A Membrane Protein P262A


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 P262A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl303

b:0.1
occ:1.00
 ZN C:ZN301 2.3 0.2 1.0
OG1 C:THR95 3.0 0.8 1.0
OE1 C:GLU191 3.2 0.2 1.0
NE2 D:HIS194 3.3 1.0 1.0
NZ C:LYS188 3.6 0.8 1.0
CD C:LYS188 3.7 0.2 1.0
CG2 C:THR95 3.7 0.6 1.0
CG2 C:ILE91 3.7 0.3 1.0
CD2 D:HIS194 3.7 1.0 1.0
CB C:THR95 3.8 0.1 1.0
CA C:ALA92 3.9 0.9 1.0
O C:ILE91 4.1 0.5 1.0
CE C:LYS188 4.1 0.5 1.0
N C:ALA92 4.2 0.4 1.0
C C:ILE91 4.2 1.0 1.0
CD C:GLU191 4.2 0.6 1.0
CE1 D:HIS194 4.4 0.7 1.0
O C:HOH401 4.5 0.2 1.0
OE2 C:GLU191 4.5 0.7 1.0
CB C:ALA92 4.6 0.4 1.0
CB D:ASP190 4.6 0.9 1.0
OD1 D:ASP190 4.6 0.1 1.0
O D:ASP190 4.6 0.3 1.0
CB C:ILE91 4.7 0.3 1.0
CG D:ASP190 4.8 0.4 1.0
CG D:HIS194 4.9 0.6 1.0
C C:ALA92 4.9 0.8 1.0
O C:ALA92 5.0 0.5 1.0

Chlorine binding site 6 out of 10 in 6ivp

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Chlorine binding site 6 out of 10 in the Crystal Structure of A Membrane Protein P262A


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 P262A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl304

b:0.8
occ:1.00
 ZN C:ZN302 2.4 0.5 1.0
ND1 C:HIS111 3.2 0.2 1.0
ND1 C:HIS108 3.2 0.1 1.0
CE1 C:HIS108 3.4 0.9 1.0
CG C:HIS111 3.5 0.2 1.0
NE C:ARG101 3.5 0.1 1.0
CA C:THR287 3.7 0.8 1.0
CG2 C:THR287 3.7 0.8 1.0
O C:THR287 3.7 0.6 1.0
CB C:HIS111 3.7 0.4 1.0
CD C:ARG101 3.8 0.6 1.0
CE1 C:HIS111 3.9 0.0 1.0
CB C:THR287 3.9 0.3 1.0
CZ C:ARG101 4.1 0.5 1.0
CG C:ARG101 4.1 0.5 1.0
C C:THR287 4.1 0.3 1.0
CD2 C:HIS111 4.3 0.3 1.0
NH1 C:ARG101 4.4 0.9 1.0
NE2 C:HIS111 4.5 0.8 1.0
CG C:HIS108 4.6 0.6 1.0
O C:MET286 4.7 0.7 1.0
NE2 C:HIS108 4.7 0.8 1.0
NH2 C:ARG101 4.8 0.7 1.0
N C:THR287 4.8 0.8 1.0

Chlorine binding site 7 out of 10 in 6ivp

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Chlorine binding site 7 out of 10 in the Crystal Structure of A Membrane Protein P262A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of A Membrane Protein P262A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl304

b:0.9
occ:1.00
 ZN B:ZN305 2.4 0.4 1.0
NZ D:LYS188 3.1 0.4 1.0
NE2 B:HIS194 3.1 0.5 1.0
OE1 D:GLU191 3.2 0.2 1.0
OG1 D:THR95 3.4 1.0 1.0
CD2 B:HIS194 3.5 0.6 1.0
CG2 D:ILE91 3.7 0.9 1.0
CG2 D:THR95 3.7 0.1 1.0
CD D:LYS188 3.9 0.3 1.0
CE D:LYS188 4.0 0.6 1.0
CD D:GLU191 4.0 0.4 1.0
OE2 D:GLU191 4.0 0.8 1.0
CB D:THR95 4.0 0.3 1.0
CE1 B:HIS194 4.1 0.1 1.0
O B:ASP190 4.3 0.5 1.0
CB B:ASP190 4.3 0.3 1.0
CA D:ALA92 4.3 0.3 1.0
O D:ILE91 4.4 0.2 1.0
C D:ILE91 4.5 0.9 1.0
N D:ALA92 4.5 0.7 1.0
OD1 B:ASP190 4.6 0.1 1.0
CG B:ASP190 4.6 0.4 1.0
CG B:HIS194 4.6 0.0 1.0
CA B:ASP190 4.8 0.6 1.0
CB D:ILE91 4.8 0.7 1.0
C B:ASP190 4.9 0.5 1.0
CB D:ALA92 4.9 0.4 1.0
ND1 B:HIS194 4.9 0.2 1.0

Chlorine binding site 8 out of 10 in 6ivp

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Chlorine binding site 8 out of 10 in the Crystal Structure of A Membrane Protein P262A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of A Membrane Protein P262A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl305

b:0.8
occ:1.00
 ZN D:ZN301 2.4 0.4 1.0
ND1 D:HIS108 3.4 0.9 1.0
CE1 D:HIS108 3.5 0.7 1.0
CD D:ARG101 3.6 0.4 1.0
O D:THR287 3.8 0.9 1.0
CA D:THR287 3.8 0.1 1.0
NE D:ARG101 3.8 0.5 1.0
CG D:ARG101 3.8 0.3 1.0
ND1 D:HIS111 3.9 0.3 1.0
CG2 D:THR287 4.1 0.9 1.0
C D:THR287 4.2 0.2 1.0
CL D:CL306 4.2 0.4 1.0
CB D:THR287 4.2 0.0 1.0
CE1 D:HIS111 4.3 0.1 1.0
CZ D:ARG101 4.3 0.4 1.0
O D:MET286 4.3 0.1 1.0
CG D:HIS111 4.6 0.7 1.0
NH2 D:ARG101 4.6 0.5 1.0
CG D:HIS108 4.8 0.7 1.0
NE2 D:HIS108 4.8 0.3 1.0
N D:THR287 4.9 0.3 1.0
NH1 D:ARG101 5.0 0.3 1.0

Chlorine binding site 9 out of 10 in 6ivp

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Chlorine binding site 9 out of 10 in the Crystal Structure of A Membrane Protein P262A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of A Membrane Protein P262A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl306

b:0.4
occ:1.00
 ZN D:ZN301 2.9 0.4 1.0
CB D:HIS111 3.7 0.2 1.0
CG D:ARG112 3.7 0.5 1.0
CB D:THR287 3.7 0.0 1.0
CG2 D:THR287 3.8 0.9 1.0
O D:HIS108 3.9 0.4 1.0
CL D:CL305 4.2 0.8 1.0
N D:ARG112 4.2 0.4 1.0
ND1 D:HIS108 4.2 0.9 1.0
O D:THR287 4.3 0.9 1.0
CB D:HIS108 4.4 0.1 1.0
ND1 D:HIS111 4.5 0.3 1.0
CG D:HIS111 4.5 0.7 1.0
C D:HIS111 4.6 0.6 1.0
CD D:ARG112 4.6 0.6 1.0
CA D:HIS108 4.6 0.1 1.0
OE1 D:GLN289 4.6 0.2 1.0
CA D:ARG112 4.6 0.9 1.0
OG1 D:THR287 4.6 0.2 1.0
C D:HIS108 4.7 0.2 1.0
CA D:THR287 4.7 0.1 1.0
CA D:HIS111 4.7 0.0 1.0
CB D:ARG112 4.8 1.0 1.0
CG D:HIS108 4.8 0.7 1.0
C D:THR287 4.9 0.2 1.0
CD D:GLN289 4.9 0.4 1.0

Chlorine binding site 10 out of 10 in 6ivp

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Chlorine binding site 10 out of 10 in the Crystal Structure of A Membrane Protein P262A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of A Membrane Protein P262A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl302

b:0.8
occ:1.00
 ZN E:ZN301 2.6 0.4 1.0
ND1 E:HIS108 3.2 0.1 1.0
CB E:HIS108 3.6 0.7 1.0
CB E:HIS111 3.6 0.9 1.0
O E:HIS108 3.7 0.4 1.0
CG E:HIS108 3.8 1.0 1.0
CA E:HIS108 3.9 0.7 1.0
ND1 E:HIS111 3.9 0.1 1.0
O E:THR287 3.9 0.7 1.0
CB E:THR287 3.9 0.6 1.0
CG E:HIS111 4.2 0.9 1.0
CG2 E:THR287 4.2 0.1 1.0
C E:HIS108 4.2 0.9 1.0
CE1 E:HIS108 4.3 0.5 1.0
CG E:ARG112 4.3 0.4 1.0
NE E:ARG112 4.5 0.8 1.0
CZ E:ARG112 4.5 0.0 1.0
NH2 E:ARG112 4.5 0.9 1.0
CA E:THR287 4.6 0.1 1.0
C E:THR287 4.6 1.0 1.0
N E:ARG112 4.8 0.6 1.0
OE1 E:GLN289 4.8 0.8 1.0
CA E:HIS111 4.9 0.0 1.0
OG1 E:THR287 5.0 0.3 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 01:49:36 2024

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