Fluorine in PDB 5aw6: Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min

The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min, PDB code: 5aw6 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)	14.98 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	220.606, 50.591, 163.163, 90.00, 104.60, 90.00
R / Rfree (%)	28 / 27.1

The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min also contains other interesting chemical elements:

Rubidium	(Rb)	3 atoms
Magnesium	(Mg)	2 atoms
Potassium	(K)	3 atoms

The binding sites of Fluorine atom in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min (pdb code 5aw6). 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: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min, PDB code: 5aw6:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 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: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:66.2 occ:1.00 F1 A:MF42001 0.0 66.2 1.0 MG A:MF42001 2.0 66.8 1.0 OD1 A:ASP376 2.4 59.7 1.0 NZ A:LYS698 2.7 62.5 1.0 ND2 A:ASN720 2.9 62.7 1.0 N A:GLY618 3.1 59.2 1.0 F2 A:MF42001 3.2 65.5 1.0 F4 A:MF42001 3.2 64.2 1.0 F3 A:MF42001 3.3 67.4 1.0 O A:THR219 3.4 62.7 1.0 CE A:LYS698 3.6 63.0 1.0 CG A:ASP376 3.6 60.8 1.0 CA A:THR617 3.7 58.8 1.0 C A:THR617 3.9 58.9 1.0 OG1 A:THR617 3.9 59.0 1.0 CG A:ASN720 4.0 63.7 1.0 CA A:GLY618 4.0 59.7 1.0 OD1 A:ASN720 4.2 63.8 1.0 OD1 A:ASP721 4.3 66.3 1.0 CB A:THR617 4.3 58.7 1.0 OD2 A:ASP376 4.3 60.2 1.0 O A:VAL616 4.3 60.0 1.0 C A:THR219 4.3 63.1 1.0 CA A:GLY220 4.4 62.4 1.0 CB A:ASP376 4.6 60.5 1.0 MG A:MG2002 4.6 60.9 1.0 N A:GLY220 4.8 62.5 1.0 N A:THR617 4.8 59.2 1.0 CD A:LYS698 4.9 63.1 1.0 N A:ASP619 4.9 60.8 1.0 C A:GLY618 5.0 60.3 1.0 CA A:ASP376 5.0 60.7 1.0

Fluorine binding site 2 out of 4 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 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: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:65.5 occ:1.00 F2 A:MF42001 0.0 65.5 1.0 MG A:MG2002 1.9 60.9 1.0 MG A:MF42001 2.0 66.8 1.0 OD1 A:ASP376 2.6 59.7 1.0 OD2 A:ASP376 2.7 60.2 1.0 O A:THR378 2.9 59.6 1.0 CG A:ASP376 3.1 60.8 1.0 F4 A:MF42001 3.2 64.2 1.0 F1 A:MF42001 3.2 66.2 1.0 CB A:THR378 3.2 59.8 1.0 F3 A:MF42001 3.4 67.4 1.0 N A:THR378 3.5 59.4 1.0 O A:GLY220 3.5 62.4 1.0 CA A:THR378 3.6 59.7 1.0 C A:THR378 3.6 60.0 1.0 CA A:GLY220 3.7 62.4 1.0 OD1 A:ASP717 3.8 64.2 1.0 C A:GLY220 4.0 62.6 1.0 OG1 A:THR378 4.1 60.1 1.0 CG2 A:THR378 4.2 57.8 1.0 C A:LYS377 4.5 59.6 1.0 O A:THR219 4.5 62.7 1.0 CB A:ASP376 4.6 60.5 1.0 N A:LYS377 4.6 60.1 1.0 OE1 A:GLU221 4.7 65.8 1.0 OD1 A:ASN720 4.8 63.8 1.0 CG A:ASP717 4.9 63.4 1.0 N A:GLY220 4.9 62.5 1.0 N A:GLY379 4.9 60.3 1.0 ND2 A:ASN720 4.9 62.7 1.0 OD2 A:ASP721 5.0 65.6 1.0

Fluorine binding site 3 out of 4 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 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: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:67.4 occ:1.00 F3 A:MF42001 0.0 67.4 1.0 MG A:MF42001 2.0 66.8 1.0 OE1 A:GLU221 2.4 65.8 1.0 O A:THR219 2.6 62.7 1.0 CD A:GLU221 3.3 65.1 1.0 F1 A:MF42001 3.3 66.2 1.0 F4 A:MF42001 3.3 64.2 1.0 N A:ASP619 3.3 60.8 1.0 OG1 A:THR617 3.3 59.0 1.0 CG A:GLU221 3.4 64.5 1.0 F2 A:MF42001 3.4 65.5 1.0 N A:GLY618 3.7 59.2 1.0 C A:GLY220 3.7 62.6 1.0 C A:THR219 3.7 63.1 1.0 OG1 A:THR378 3.8 60.1 1.0 CB A:ASP619 3.8 61.3 1.0 C A:GLY618 3.8 60.3 1.0 CA A:GLY220 3.9 62.4 1.0 CA A:GLY618 3.9 59.7 1.0 CA A:ASP619 4.0 61.5 1.0 O A:GLY220 4.0 62.4 1.0 N A:GLU221 4.0 63.1 1.0 CB A:THR378 4.0 59.8 1.0 N A:GLY220 4.3 62.5 1.0 OE2 A:GLU221 4.4 66.6 1.0 OD1 A:ASP376 4.5 59.7 1.0 CB A:GLU221 4.5 64.1 1.0 CG A:ASP619 4.6 62.0 1.0 CB A:THR617 4.6 58.7 1.0 CA A:GLU221 4.6 63.9 1.0 O A:GLY618 4.6 60.8 1.0 C A:THR617 4.7 58.9 1.0 N A:THR378 4.9 59.4 1.0 CA A:THR219 4.9 63.3 1.0 CA A:THR617 4.9 58.8 1.0 CG2 A:THR378 5.0 57.8 1.0

Fluorine binding site 4 out of 4 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 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: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:F2001 b:64.2 occ:1.00 F4 A:MF42001 0.0 64.2 1.0 MG A:MF42001 2.0 66.8 1.0 OD1 A:ASP376 2.5 59.7 1.0 OG1 A:THR617 2.6 59.0 1.0 N A:LYS377 2.6 60.1 1.0 N A:THR378 2.8 59.4 1.0 CB A:THR617 3.0 58.7 1.0 CB A:LYS377 3.1 59.5 1.0 F2 A:MF42001 3.2 65.5 1.0 CA A:LYS377 3.2 59.6 1.0 F1 A:MF42001 3.2 66.2 1.0 F3 A:MF42001 3.3 67.4 1.0 CG A:ASP376 3.3 60.8 1.0 C A:LYS377 3.5 59.6 1.0 CA A:THR617 3.7 58.8 1.0 C A:ASP376 3.8 60.5 1.0 OG1 A:THR378 3.9 60.1 1.0 OD2 A:ASP376 3.9 60.2 1.0 CA A:THR378 4.0 59.7 1.0 CB A:THR378 4.0 59.8 1.0 CA A:ASP376 4.1 60.7 1.0 CG A:LYS377 4.2 59.1 1.0 N A:GLY618 4.3 59.2 1.0 CB A:ASP376 4.3 60.5 1.0 CG2 A:THR617 4.3 58.5 1.0 O A:VAL616 4.5 60.0 1.0 C A:THR617 4.5 58.9 1.0 OE1 A:GLU221 4.5 65.8 1.0 MG A:MG2002 4.6 60.9 1.0 CE A:LYS377 4.6 60.8 1.0 O A:LYS377 4.7 59.6 1.0 N A:THR617 4.8 59.2 1.0 NZ A:LYS698 4.8 62.5 1.0 O A:THR378 4.8 59.6 1.0 O A:ASP376 4.9 60.6 1.0 CD A:LYS377 4.9 59.5 1.0 C A:THR378 4.9 60.0 1.0 N A:ASP619 4.9 60.8 1.0 C A:VAL616 5.0 59.6 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