Fluorine in PDB 5avy: Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min, PDB code: 5avy was solved by H.Ogawa, F.Cornelius, A.Hirata, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.94 / 3.45
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	220.590, 50.671, 163.924, 90.00, 103.63, 90.00
R / Rfree (%)	30.8 / 30.5

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Potassium	(K)	1 atom
Thallium	(Tl)	3 atoms

The binding sites of Fluorine atom in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min (pdb code 5avy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min, PDB code: 5avy:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:0.9 occ:1.00 F1 A:MF42001 0.0 0.9 1.0 MG A:MF42001 2.0 0.5 1.0 OD2 A:ASP376 2.4 0.4 1.0 NZ A:LYS698 2.7 0.1 1.0 ND2 A:ASN720 2.9 0.3 1.0 N A:GLY618 3.1 0.9 1.0 F2 A:MF42001 3.2 0.1 1.0 F4 A:MF42001 3.2 0.9 1.0 F3 A:MF42001 3.3 0.1 1.0 O A:THR219 3.4 0.3 1.0 CE A:LYS698 3.6 0.7 1.0 CG A:ASP376 3.6 0.5 1.0 CA A:THR617 3.7 0.5 1.0 C A:THR617 3.9 0.5 1.0 OG1 A:THR617 3.9 0.7 1.0 CG A:ASN720 4.0 0.4 1.0 CA A:GLY618 4.0 0.4 1.0 OD1 A:ASN720 4.2 0.4 1.0 OD1 A:ASP721 4.3 1.0 1.0 OD1 A:ASP376 4.3 0.8 1.0 CB A:THR617 4.3 0.4 1.0 O A:VAL616 4.3 0.7 1.0 C A:THR219 4.3 0.7 1.0 CA A:GLY220 4.4 0.0 1.0 CB A:ASP376 4.6 0.2 1.0 MG A:MG2002 4.6 0.6 1.0 N A:GLY220 4.7 0.1 1.0 N A:THR617 4.8 0.9 1.0 CD A:LYS698 4.9 0.7 1.0 N A:ASP619 4.9 0.5 1.0 C A:GLY618 5.0 0.0 1.0 CA A:ASP376 5.0 0.4 1.0

Fluorine binding site 2 out of 4 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:0.1 occ:1.00 F2 A:MF42001 0.0 0.1 1.0 MG A:MG2002 1.9 0.6 1.0 MG A:MF42001 2.0 0.5 1.0 OD2 A:ASP376 2.6 0.4 1.0 OD1 A:ASP376 2.7 0.8 1.0 O A:THR378 2.9 0.3 1.0 CG A:ASP376 3.1 0.5 1.0 F4 A:MF42001 3.2 0.9 1.0 F1 A:MF42001 3.2 0.9 1.0 CB A:THR378 3.2 0.4 1.0 F3 A:MF42001 3.4 0.1 1.0 N A:THR378 3.5 0.1 1.0 O A:GLY220 3.5 0.1 1.0 CA A:THR378 3.6 0.4 1.0 C A:THR378 3.6 0.6 1.0 CA A:GLY220 3.7 0.0 1.0 OD2 A:ASP717 3.8 0.9 1.0 C A:GLY220 4.0 0.3 1.0 OG1 A:THR378 4.1 0.8 1.0 CG2 A:THR378 4.2 0.5 1.0 C A:LYS377 4.5 0.3 1.0 O A:THR219 4.5 0.3 1.0 CB A:ASP376 4.6 0.2 1.0 N A:LYS377 4.6 0.8 1.0 OE1 A:GLU221 4.7 0.5 1.0 OD1 A:ASN720 4.8 0.4 1.0 CG A:ASP717 4.9 0.0 1.0 N A:GLY220 4.9 0.1 1.0 N A:GLY379 4.9 1.0 1.0 ND2 A:ASN720 4.9 0.3 1.0 OD2 A:ASP721 5.0 0.2 1.0

Fluorine binding site 3 out of 4 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:0.1 occ:1.00 F3 A:MF42001 0.0 0.1 1.0 MG A:MF42001 2.0 0.5 1.0 OE1 A:GLU221 2.4 0.5 1.0 O A:THR219 2.6 0.3 1.0 CD A:GLU221 3.3 0.8 1.0 F1 A:MF42001 3.3 0.9 1.0 F4 A:MF42001 3.3 0.9 1.0 N A:ASP619 3.3 0.5 1.0 OG1 A:THR617 3.3 0.7 1.0 CG A:GLU221 3.4 0.2 1.0 F2 A:MF42001 3.4 0.1 1.0 N A:GLY618 3.7 0.9 1.0 C A:GLY220 3.7 0.3 1.0 C A:THR219 3.7 0.7 1.0 OG1 A:THR378 3.8 0.8 1.0 CB A:ASP619 3.8 1.0 1.0 C A:GLY618 3.8 0.0 1.0 CA A:GLY220 3.9 0.0 1.0 CA A:GLY618 3.9 0.4 1.0 CA A:ASP619 4.0 0.2 1.0 O A:GLY220 4.0 0.1 1.0 N A:GLU221 4.0 0.8 1.0 CB A:THR378 4.0 0.4 1.0 N A:GLY220 4.3 0.1 1.0 OE2 A:GLU221 4.4 0.3 1.0 OD2 A:ASP376 4.5 0.4 1.0 CB A:GLU221 4.5 0.8 1.0 CG A:ASP619 4.6 0.6 1.0 CB A:THR617 4.6 0.4 1.0 CA A:GLU221 4.6 0.6 1.0 O A:GLY618 4.6 0.5 1.0 C A:THR617 4.7 0.5 1.0 N A:THR378 4.9 0.1 1.0 CA A:THR219 4.9 0.0 1.0 CA A:THR617 4.9 0.5 1.0 CG2 A:THR378 5.0 0.5 1.0

Fluorine binding site 4 out of 4 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:0.9 occ:1.00 F4 A:MF42001 0.0 0.9 1.0 MG A:MF42001 2.0 0.5 1.0 OD2 A:ASP376 2.5 0.4 1.0 OG1 A:THR617 2.6 0.7 1.0 N A:LYS377 2.6 0.8 1.0 N A:THR378 2.8 0.1 1.0 CB A:THR617 3.0 0.4 1.0 CB A:LYS377 3.1 0.2 1.0 F2 A:MF42001 3.2 0.1 1.0 CA A:LYS377 3.2 0.3 1.0 F1 A:MF42001 3.2 0.9 1.0 F3 A:MF42001 3.3 0.1 1.0 CG A:ASP376 3.3 0.5 1.0 C A:LYS377 3.5 0.3 1.0 CA A:THR617 3.7 0.5 1.0 C A:ASP376 3.8 0.2 1.0 OD1 A:ASP376 3.9 0.8 1.0 OG1 A:THR378 3.9 0.8 1.0 CA A:THR378 4.0 0.4 1.0 CB A:THR378 4.0 0.4 1.0 CA A:ASP376 4.1 0.4 1.0 CG A:LYS377 4.2 0.8 1.0 N A:GLY618 4.3 0.9 1.0 CB A:ASP376 4.3 0.2 1.0 CG2 A:THR617 4.4 0.2 1.0 O A:VAL616 4.5 0.7 1.0 C A:THR617 4.5 0.5 1.0 OE1 A:GLU221 4.5 0.5 1.0 MG A:MG2002 4.6 0.6 1.0 CE A:LYS377 4.6 0.5 1.0 O A:LYS377 4.7 0.3 1.0 N A:THR617 4.8 0.9 1.0 NZ A:LYS698 4.8 0.1 1.0 O A:THR378 4.8 0.3 1.0 O A:ASP376 4.9 0.2 1.0 CD A:LYS377 4.9 0.2 1.0 C A:THR378 4.9 0.6 1.0 N A:ASP619 4.9 0.5 1.0 C A:VAL616 5.0 0.3 1.0

H.Ogawa, F.Cornelius, A.Hirata, C.Toyoshima. Sequential Substitution of K(+) Bound to Na(+),K(+)-Atpase Visualized By X-Ray Crystallography. Nat Commun V. 6 8004 2015.
ISSN: ESSN 2041-1723
PubMed: 26258479
DOI: 10.1038/NCOMMS9004