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Fluorine in PDB 5nkq: Crystal Structure of A Dual Topology Fluoride Ion Channel.

Protein crystallography data

The structure of Crystal Structure of A Dual Topology Fluoride Ion Channel., PDB code: 5nkq was solved by R.Stockbridge, C.Miller, S.Newstead, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.95 / 2.17
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 40.590, 84.060, 85.960, 109.41, 101.40, 101.37
R / Rfree (%) 21.7 / 24.3

Other elements in 5nkq:

The structure of Crystal Structure of A Dual Topology Fluoride Ion Channel. also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of A Dual Topology Fluoride Ion Channel. (pdb code 5nkq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of A Dual Topology Fluoride Ion Channel., PDB code: 5nkq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5nkq

Go back to Fluorine Binding Sites List in 5nkq
Fluorine binding site 1 out of 8 in the Crystal Structure of A Dual Topology Fluoride Ion Channel.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of A Dual Topology Fluoride Ion Channel. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:42.5
occ:1.00
 OG A:SER108 2.8 38.0 1.0
ND2 A:ASN43 2.8 39.4 1.0
OH A:TYR104 3.0 34.4 1.0
CZ A:TYR104 3.4 35.3 1.0
CD1 A:PHE85 3.6 38.1 1.0
CB A:SER108 3.6 37.1 1.0
CA A:LEU40 3.8 39.0 1.0
CE1 A:TYR104 3.9 31.4 1.0
CG A:ASN43 3.9 38.8 1.0
CG2 A:THR39 3.9 27.8 1.0
O A:THR39 3.9 33.3 1.0
N A:LEU40 4.0 28.3 1.0
CD1 A:LEU40 4.0 38.6 1.0
CB A:PHE85 4.0 36.8 1.0
C A:THR39 4.1 31.8 1.0
CB A:ASN43 4.1 27.7 1.0
CE2 A:TYR104 4.2 35.5 1.0
CG A:PHE85 4.2 35.7 1.0
CB A:LEU40 4.3 37.5 1.0
CE1 A:PHE85 4.5 38.3 1.0
CB A:THR39 4.6 30.9 1.0
CA A:SER108 4.6 39.3 1.0
CA A:PHE85 4.8 32.5 1.0
CG A:LEU40 4.8 39.6 1.0
CD1 A:TYR104 4.9 30.0 1.0
C A:LEU40 4.9 38.1 1.0
CA A:THR39 5.0 32.3 1.0
OD1 A:ASN43 5.0 35.5 1.0
OE2 A:GLU88 5.0 42.2 1.0

Fluorine binding site 2 out of 8 in 5nkq

Go back to Fluorine Binding Sites List in 5nkq
Fluorine binding site 2 out of 8 in the Crystal Structure of A Dual Topology Fluoride Ion Channel.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of A Dual Topology Fluoride Ion Channel. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:37.3
occ:0.90
 OG B:SER112 2.5 51.1 1.0
O B:ASN43 3.0 33.0 1.0
C A:PHE82 3.2 32.5 1.0
N A:SER83 3.2 29.6 1.0
O A:PHE82 3.2 35.7 1.0
CA A:SER83 3.3 26.9 1.0
CA B:GLY47 3.4 31.8 1.0
CD1 A:PHE82 3.5 45.6 1.0
N B:GLY47 3.5 32.2 1.0
CB A:PHE82 3.5 37.9 1.0
CB B:SER112 3.5 44.0 1.0
CG A:PHE82 3.9 40.2 1.0
CG2 B:THR80 3.9 28.5 1.0
C B:ASN43 3.9 32.8 1.0
CA A:PHE82 4.0 38.1 1.0
CB A:SER83 4.0 29.2 1.0
CB A:SER86 4.0 26.9 1.0
CA B:ASN43 4.2 26.2 1.0
C B:GLY46 4.3 30.2 1.0
CB B:ASN43 4.4 26.3 1.0
CE1 A:PHE82 4.5 48.6 1.0
CB B:THR80 4.5 26.5 1.0
C A:SER83 4.6 31.8 1.0
OG A:SER86 4.6 36.2 1.0
CA B:SER112 4.7 38.3 1.0
O B:GLY46 4.8 28.6 1.0
C B:GLY47 4.9 33.7 1.0
O A:SER83 4.9 32.9 1.0

Fluorine binding site 3 out of 8 in 5nkq

Go back to Fluorine Binding Sites List in 5nkq
Fluorine binding site 3 out of 8 in the Crystal Structure of A Dual Topology Fluoride Ion Channel.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of A Dual Topology Fluoride Ion Channel. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:33.0
occ:1.00
 OG B:SER108 2.7 34.1 1.0
ND2 B:ASN43 2.8 33.0 1.0
OH B:TYR104 3.1 33.3 1.0
CB B:SER108 3.5 38.0 1.0
CZ B:TYR104 3.6 33.9 1.0
CA B:LEU40 3.6 34.6 1.0
CG B:ASN43 3.8 33.4 1.0
O B:THR39 3.9 30.6 1.0
CD1 B:PHE85 3.9 39.9 1.0
CD1 B:LEU40 3.9 38.4 1.0
CE1 B:TYR104 3.9 37.9 1.0
N B:LEU40 3.9 34.0 1.0
CG2 B:THR39 3.9 26.3 1.0
C B:THR39 4.0 34.0 1.0
CB B:ASN43 4.0 26.3 1.0
CB B:PHE85 4.1 35.4 1.0
CB B:LEU40 4.3 35.1 1.0
CG B:PHE85 4.4 40.6 1.0
CE2 B:TYR104 4.4 30.9 1.0
CA B:SER108 4.4 39.4 1.0
CB B:THR39 4.6 38.0 1.0
CG B:LEU40 4.7 35.3 1.0
CE1 B:PHE85 4.8 41.7 1.0
C B:LEU40 4.8 31.3 1.0
CD1 B:TYR104 4.9 37.9 1.0
O B:LEU40 4.9 34.5 1.0
OD1 B:ASN43 4.9 30.9 1.0
CE2 A:PHE82 5.0 45.5 1.0
CA B:THR39 5.0 34.9 1.0
CA B:PHE85 5.0 33.8 1.0

Fluorine binding site 4 out of 8 in 5nkq

Go back to Fluorine Binding Sites List in 5nkq
Fluorine binding site 4 out of 8 in the Crystal Structure of A Dual Topology Fluoride Ion Channel.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of A Dual Topology Fluoride Ion Channel. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:51.5
occ:1.00
 OG A:SER112 2.8 42.8 1.0
O A:ASN43 2.9 34.7 1.0
N B:SER83 3.1 27.0 1.0
C B:PHE82 3.1 38.5 1.0
CB B:PHE82 3.3 31.7 1.0
O B:PHE82 3.3 27.0 1.0
CD1 B:PHE82 3.3 36.0 1.0
CA B:SER83 3.3 28.5 1.0
N A:GLY47 3.5 28.7 1.0
CG2 A:THR80 3.7 27.3 1.0
CA A:GLY47 3.7 27.7 1.0
CG B:PHE82 3.7 34.5 1.0
C A:ASN43 3.8 30.7 1.0
CA B:PHE82 3.8 34.1 1.0
CB A:SER112 3.9 39.9 1.0
CB B:SER83 4.0 31.2 1.0
CA A:ASN43 4.0 34.7 1.0
CB A:ASN43 4.2 27.7 1.0
CB A:THR80 4.2 29.6 1.0
C A:GLY46 4.2 31.9 1.0
CB B:SER86 4.4 27.3 1.0
CE1 B:PHE82 4.4 36.9 1.0
OD1 A:ASN43 4.6 35.5 1.0
C B:SER83 4.7 33.4 1.0
CG A:ASN43 4.7 38.8 1.0
N B:PHE82 4.8 32.2 1.0
OG1 A:THR80 4.8 31.0 1.0
O A:GLY46 4.8 30.4 1.0
CA A:GLY46 4.9 27.7 1.0
OG B:SER83 4.9 32.6 1.0
CA A:SER112 4.9 37.3 1.0
N A:LEU44 5.0 32.4 1.0
CD2 B:PHE82 5.0 36.5 1.0
OG B:SER86 5.0 30.7 1.0

Fluorine binding site 5 out of 8 in 5nkq

Go back to Fluorine Binding Sites List in 5nkq
Fluorine binding site 5 out of 8 in the Crystal Structure of A Dual Topology Fluoride Ion Channel.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of A Dual Topology Fluoride Ion Channel. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F202

b:39.1
occ:1.00
 OG C:SER112 2.5 36.5 1.0
O C:ASN43 2.8 36.3 1.0
N C:GLY47 3.3 35.7 1.0
CA C:GLY47 3.3 34.9 1.0
N D:SER83 3.3 31.3 1.0
C D:PHE82 3.4 32.7 1.0
CA D:SER83 3.4 34.4 1.0
O D:PHE82 3.4 27.4 1.0
CB C:SER112 3.6 34.9 1.0
CD1 D:PHE82 3.6 31.9 1.0
CB D:PHE82 3.6 32.9 1.0
C C:ASN43 3.8 35.0 1.0
CG2 C:THR80 3.9 27.5 1.0
CG D:PHE82 4.0 32.8 1.0
CB D:SER83 4.0 34.3 1.0
C C:GLY46 4.1 34.5 1.0
CB D:SER86 4.1 34.9 1.0
CA D:PHE82 4.1 30.9 1.0
CA C:ASN43 4.2 38.6 1.0
CB C:ASN43 4.4 27.5 1.0
CB C:THR80 4.6 31.2 1.0
CE1 D:PHE82 4.6 34.8 1.0
CA C:SER112 4.6 35.1 1.0
OG D:SER86 4.6 38.8 1.0
O C:GLY46 4.7 36.6 1.0
C D:SER83 4.7 38.8 1.0
C C:GLY47 4.8 35.5 1.0
CA C:GLY46 4.8 34.4 1.0
OD1 C:ASN43 5.0 29.9 1.0
N C:LEU44 5.0 35.7 1.0

Fluorine binding site 6 out of 8 in 5nkq

Go back to Fluorine Binding Sites List in 5nkq
Fluorine binding site 6 out of 8 in the Crystal Structure of A Dual Topology Fluoride Ion Channel.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of A Dual Topology Fluoride Ion Channel. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F203

b:26.4
occ:0.65
 OG D:SER112 2.5 45.3 1.0
O D:ASN43 3.0 33.7 1.0
C C:PHE82 3.1 30.0 1.0
O C:PHE82 3.1 30.1 1.0
N C:SER83 3.2 26.5 1.0
CA C:SER83 3.3 28.6 1.0
CD1 C:PHE82 3.4 35.8 1.0
CB C:PHE82 3.5 32.8 1.0
CA D:GLY47 3.5 32.4 1.0
N D:GLY47 3.6 32.5 1.0
CB D:SER112 3.6 41.2 1.0
CG C:PHE82 3.9 34.0 1.0
CA C:PHE82 3.9 34.0 1.0
CG2 D:THR80 4.0 26.5 1.0
CB C:SER83 4.0 28.7 1.0
C D:ASN43 4.0 29.5 1.0
CB C:SER86 4.0 32.8 1.0
CA D:ASN43 4.3 31.4 1.0
C D:GLY46 4.3 31.8 1.0
CB D:ASN43 4.4 31.4 1.0
CB D:THR80 4.5 27.9 1.0
CE1 C:PHE82 4.5 33.6 1.0
C C:SER83 4.5 30.9 1.0
OG C:SER86 4.6 37.3 1.0
CA D:SER112 4.7 38.3 1.0
O D:GLY46 4.8 32.1 1.0
O C:SER83 4.9 29.4 1.0
OD1 D:ASN43 4.9 31.7 1.0
N C:PHE82 5.0 36.3 1.0

Fluorine binding site 7 out of 8 in 5nkq

Go back to Fluorine Binding Sites List in 5nkq
Fluorine binding site 7 out of 8 in the Crystal Structure of A Dual Topology Fluoride Ion Channel.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of A Dual Topology Fluoride Ion Channel. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F204

b:34.0
occ:1.00
 OG C:SER108 2.8 33.5 1.0
ND2 C:ASN43 2.8 36.2 1.0
OH C:TYR104 3.1 39.0 1.0
CB C:SER108 3.5 33.2 1.0
CA C:LEU40 3.6 32.2 1.0
CZ C:TYR104 3.6 33.0 1.0
CD1 C:PHE85 3.7 33.5 1.0
O C:THR39 3.8 34.6 1.0
N C:LEU40 3.8 31.4 1.0
CG C:ASN43 3.9 32.6 1.0
C C:THR39 3.9 33.2 1.0
CG2 C:THR39 3.9 27.2 1.0
CD1 C:LEU40 3.9 32.2 1.0
CE1 C:TYR104 4.0 30.8 1.0
CB C:ASN43 4.0 27.5 1.0
CB C:PHE85 4.2 32.5 1.0
CB C:LEU40 4.2 34.2 1.0
CG C:PHE85 4.3 34.4 1.0
CE2 C:TYR104 4.3 30.0 1.0
CA C:SER108 4.5 36.8 1.0
CB C:THR39 4.5 27.4 1.0
CE1 C:PHE85 4.6 31.7 1.0
CG C:LEU40 4.7 35.4 1.0
C C:LEU40 4.8 34.8 1.0
CE2 D:PHE82 4.9 38.8 1.0
CA C:THR39 4.9 34.4 1.0
O C:LEU40 4.9 36.3 1.0
OD1 C:ASN43 5.0 29.9 1.0
CD1 C:TYR104 5.0 28.8 1.0

Fluorine binding site 8 out of 8 in 5nkq

Go back to Fluorine Binding Sites List in 5nkq
Fluorine binding site 8 out of 8 in the Crystal Structure of A Dual Topology Fluoride Ion Channel.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of A Dual Topology Fluoride Ion Channel. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F201

b:27.4
occ:0.65
 OG D:SER108 2.6 31.1 1.0
ND2 D:ASN43 2.7 34.5 1.0
OH D:TYR104 3.3 30.9 1.0
CB D:SER108 3.4 33.7 1.0
CA D:LEU40 3.5 37.8 1.0
CZ D:TYR104 3.7 31.5 1.0
CD1 D:LEU40 3.7 42.3 1.0
O D:THR39 3.8 33.0 1.0
CG D:ASN43 3.8 31.8 1.0
N D:LEU40 3.9 38.4 1.0
CD1 D:PHE85 3.9 36.2 1.0
CB D:ASN43 4.0 31.4 1.0
C D:THR39 4.0 37.6 1.0
CB D:LEU40 4.1 38.0 1.0
CG2 D:THR39 4.1 41.8 1.0
CE1 D:TYR104 4.1 34.6 1.0
CB D:PHE85 4.2 32.0 1.0
CE2 D:TYR104 4.4 30.5 1.0
CA D:SER108 4.4 36.6 1.0
CG D:PHE85 4.4 35.7 1.0
CG D:LEU40 4.6 41.3 1.0
C D:LEU40 4.7 39.1 1.0
CB D:THR39 4.7 44.6 1.0
CE1 D:PHE85 4.7 36.9 1.0
O D:LEU40 4.8 39.5 1.0
OD1 D:ASN43 4.9 31.7 1.0
CE2 C:PHE82 5.0 37.9 1.0

Reference:

R.B.Stockbridge, L.Kolmakova-Partensky, T.Shane, A.Koide, S.Koide, C.Miller, S.Newstead. Crystal Structures of A Double-Barrelled Fluoride Ion Channel. Nature V. 525 548 2015.
ISSN: ESSN 1476-4687
PubMed: 26344196
DOI: 10.1038/NATURE14981
Page generated: Thu Aug 1 12:03:45 2024

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