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

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5 Min, PDB code: 5avt 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)	14.99 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	221.468, 50.933, 164.123, 90.00, 104.52, 90.00
R / Rfree (%)	26.8 / 25.4

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5 Min also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Potassium	(K)	2 atoms
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 5 Min (pdb code 5avt). 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 5 Min, PDB code: 5avt:
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 5 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:58.7 occ:1.00 F1 A:MF42001 0.0 58.7 1.0 MG A:MF42001 2.0 59.3 1.0 OD2 A:ASP376 2.4 52.2 1.0 NZ A:LYS698 2.7 55.0 1.0 ND2 A:ASN720 2.9 55.2 1.0 N A:GLY618 3.1 51.8 1.0 F2 A:MF42001 3.2 58.0 1.0 F4 A:MF42001 3.2 56.7 1.0 F3 A:MF42001 3.3 59.9 1.0 O A:THR219 3.4 55.2 1.0 CE A:LYS698 3.6 55.6 1.0 CG A:ASP376 3.6 53.4 1.0 CA A:THR617 3.7 51.3 1.0 C A:THR617 3.9 51.4 1.0 OG1 A:THR617 3.9 51.5 1.0 CG A:ASN720 4.0 56.2 1.0 CA A:GLY618 4.0 52.2 1.0 OD1 A:ASN720 4.2 56.3 1.0 OD1 A:ASP721 4.3 58.8 1.0 CB A:THR617 4.3 51.2 1.0 OD1 A:ASP376 4.3 52.7 1.0 O A:VAL616 4.3 52.6 1.0 C A:THR219 4.3 55.6 1.0 CA A:GLY220 4.4 54.9 1.0 CB A:ASP376 4.6 53.1 1.0 MG A:MG2002 4.6 53.5 1.0 N A:GLY220 4.7 55.0 1.0 N A:THR617 4.8 51.7 1.0 CD A:LYS698 4.9 55.6 1.0 N A:ASP619 4.9 53.3 1.0 C A:GLY618 5.0 52.9 1.0 CA A:ASP376 5.0 53.3 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 5 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:58.0 occ:1.00 F2 A:MF42001 0.0 58.0 1.0 MG A:MG2002 1.9 53.5 1.0 MG A:MF42001 2.0 59.3 1.0 OD2 A:ASP376 2.6 52.2 1.0 OD1 A:ASP376 2.7 52.7 1.0 O A:THR378 2.9 52.2 1.0 CG A:ASP376 3.0 53.4 1.0 F4 A:MF42001 3.2 56.7 1.0 F1 A:MF42001 3.2 58.7 1.0 CB A:THR378 3.2 52.3 1.0 F3 A:MF42001 3.4 59.9 1.0 N A:THR378 3.5 52.0 1.0 O A:GLY220 3.5 55.0 1.0 CA A:THR378 3.6 52.2 1.0 C A:THR378 3.6 52.5 1.0 CA A:GLY220 3.7 54.9 1.0 OD2 A:ASP717 3.8 56.8 1.0 C A:GLY220 4.0 55.2 1.0 OG1 A:THR378 4.1 52.6 1.0 CG2 A:THR378 4.2 50.4 1.0 C A:LYS377 4.5 52.1 1.0 O A:THR219 4.5 55.2 1.0 CB A:ASP376 4.6 53.1 1.0 N A:LYS377 4.6 52.6 1.0 OE1 A:GLU221 4.7 58.3 1.0 OD1 A:ASN720 4.8 56.3 1.0 CG A:ASP717 4.9 55.9 1.0 N A:GLY220 4.9 55.0 1.0 ND2 A:ASN720 4.9 55.2 1.0 N A:GLY379 4.9 52.8 1.0 OD2 A:ASP721 5.0 58.1 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 5 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:59.9 occ:1.00 F3 A:MF42001 0.0 59.9 1.0 MG A:MF42001 2.0 59.3 1.0 OE1 A:GLU221 2.4 58.3 1.0 O A:THR219 2.6 55.2 1.0 CD A:GLU221 3.3 57.6 1.0 F1 A:MF42001 3.3 58.7 1.0 F4 A:MF42001 3.3 56.7 1.0 N A:ASP619 3.3 53.3 1.0 OG1 A:THR617 3.3 51.5 1.0 CG A:GLU221 3.4 57.0 1.0 F2 A:MF42001 3.4 58.0 1.0 N A:GLY618 3.7 51.8 1.0 C A:GLY220 3.7 55.2 1.0 C A:THR219 3.7 55.6 1.0 OG1 A:THR378 3.8 52.6 1.0 CB A:ASP619 3.8 53.8 1.0 C A:GLY618 3.8 52.9 1.0 CA A:GLY220 3.9 54.9 1.0 CA A:GLY618 3.9 52.2 1.0 CA A:ASP619 4.0 54.0 1.0 O A:GLY220 4.0 55.0 1.0 N A:GLU221 4.0 55.7 1.0 CB A:THR378 4.0 52.3 1.0 N A:GLY220 4.3 55.0 1.0 OE2 A:GLU221 4.4 59.1 1.0 OD2 A:ASP376 4.5 52.2 1.0 CB A:GLU221 4.5 56.6 1.0 CG A:ASP619 4.6 54.5 1.0 CB A:THR617 4.6 51.2 1.0 CA A:GLU221 4.6 56.5 1.0 O A:GLY618 4.6 53.4 1.0 C A:THR617 4.7 51.4 1.0 N A:THR378 4.9 52.0 1.0 CA A:THR219 4.9 55.9 1.0 CA A:THR617 4.9 51.3 1.0 CG2 A:THR378 5.0 50.4 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 5 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:56.7 occ:1.00 F4 A:MF42001 0.0 56.7 1.0 MG A:MF42001 2.0 59.3 1.0 OD2 A:ASP376 2.5 52.2 1.0 OG1 A:THR617 2.6 51.5 1.0 N A:LYS377 2.6 52.6 1.0 N A:THR378 2.8 52.0 1.0 CB A:THR617 3.0 51.2 1.0 CB A:LYS377 3.1 52.0 1.0 F2 A:MF42001 3.2 58.0 1.0 CA A:LYS377 3.2 52.2 1.0 F1 A:MF42001 3.2 58.7 1.0 F3 A:MF42001 3.3 59.9 1.0 CG A:ASP376 3.3 53.4 1.0 C A:LYS377 3.5 52.1 1.0 CA A:THR617 3.7 51.3 1.0 C A:ASP376 3.8 53.0 1.0 OD1 A:ASP376 3.9 52.7 1.0 OG1 A:THR378 3.9 52.6 1.0 CA A:THR378 4.0 52.2 1.0 CB A:THR378 4.0 52.3 1.0 CA A:ASP376 4.1 53.3 1.0 CG A:LYS377 4.2 51.6 1.0 N A:GLY618 4.3 51.8 1.0 CB A:ASP376 4.3 53.1 1.0 CG2 A:THR617 4.3 51.0 1.0 O A:VAL616 4.5 52.6 1.0 C A:THR617 4.5 51.4 1.0 OE1 A:GLU221 4.5 58.3 1.0 MG A:MG2002 4.6 53.5 1.0 CE A:LYS377 4.6 53.4 1.0 O A:LYS377 4.7 52.1 1.0 N A:THR617 4.8 51.7 1.0 NZ A:LYS698 4.8 55.0 1.0 O A:THR378 4.8 52.2 1.0 O A:ASP376 4.9 53.1 1.0 CD A:LYS377 4.9 52.0 1.0 C A:THR378 4.9 52.5 1.0 N A:ASP619 4.9 53.3 1.0 C A:VAL616 5.0 52.2 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