Potassium in PDB 5avr: Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min, PDB code: 5avr 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)	15.00 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	223.127, 50.845, 163.859, 90.00, 104.73, 90.00
R / Rfree (%)	26.5 / 28.1

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Magnesium	(Mg)	2 atoms
Thallium	(Tl)	3 atoms

The binding sites of Potassium atom in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min (pdb code 5avr). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min, PDB code: 5avr:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:K2003 b:77.4 occ:0.30 TL A:TL2004 0.0 77.4 0.7 OD2 A:ASP811 2.7 74.7 1.0 OG A:SER782 2.7 74.2 1.0 O A:THR779 2.7 69.9 1.0 O A:HOH2101 2.7 79.7 1.0 OD1 A:ASN783 2.8 72.2 1.0 OD1 A:ASP811 3.2 75.7 1.0 CG A:ASP811 3.2 74.2 1.0 N A:ASN783 3.8 74.1 1.0 OE2 A:GLU786 3.8 79.5 1.0 C A:SER782 3.8 73.7 1.0 CG A:ASN783 3.8 73.4 1.0 CB A:SER782 3.9 73.4 1.0 C A:THR779 3.9 69.8 1.0 K A:K2005 4.1 77.3 0.0 TL A:TL2006 4.1 77.3 1.0 OE1 A:GLU786 4.2 80.2 1.0 O A:SER782 4.2 74.0 1.0 CA A:ASN783 4.2 74.3 1.0 CA A:SER782 4.3 73.4 1.0 CG2 A:THR779 4.3 69.2 1.0 CD A:GLU786 4.3 79.9 1.0 OD2 A:ASP815 4.4 74.4 1.0 CB A:ASP811 4.5 73.4 1.0 N A:SER782 4.5 72.9 1.0 CB A:ASN783 4.6 74.2 1.0 CA A:THR779 4.7 69.3 1.0 ND2 A:ASN783 4.7 72.8 1.0 N A:LEU780 4.8 70.4 1.0 CB A:PRO333 4.8 74.2 1.0 O A:LEU780 4.8 71.3 1.0 CA A:PRO333 4.9 74.1 1.0 CA A:LEU780 4.9 70.9 1.0 C A:LEU780 5.0 71.2 1.0

Potassium binding site 2 out of 3 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:K2005 b:77.3 occ:0.03 TL A:TL2006 0.0 77.3 1.0 O A:VAL332 2.8 74.4 1.0 OD2 A:ASP811 2.9 74.7 1.0 OE2 A:GLU786 2.9 79.5 1.0 O A:VAL329 2.9 78.3 1.0 O A:ALA330 3.0 76.7 1.0 OD1 A:ASN783 3.0 72.2 1.0 OE1 A:GLU334 3.3 73.4 1.0 CG A:ASP811 3.5 74.2 1.0 C A:ALA330 3.6 77.0 1.0 OD1 A:ASP811 3.6 75.7 1.0 C A:VAL332 3.7 74.5 1.0 CG2 A:ILE807 3.9 74.8 1.0 CG A:ASN783 4.0 73.4 1.0 CA A:ALA330 4.0 77.3 1.0 CD A:GLU334 4.1 73.2 1.0 CD A:GLU786 4.1 79.9 1.0 C A:VAL329 4.1 78.7 1.0 K A:K2003 4.1 77.4 0.3 TL A:TL2004 4.1 77.4 0.7 CA A:PRO333 4.1 74.1 1.0 OE2 A:GLU334 4.1 74.3 1.0 N A:PRO333 4.2 74.3 1.0 N A:ALA330 4.5 77.8 1.0 N A:VAL332 4.5 75.1 1.0 ND2 A:ASN783 4.6 72.8 1.0 N A:ASN331 4.6 76.4 1.0 CB A:ASP811 4.6 73.4 1.0 N A:GLU334 4.6 73.5 1.0 OE1 A:GLU786 4.6 80.2 1.0 C A:ASN331 4.7 75.7 1.0 CA A:VAL332 4.8 74.8 1.0 C A:PRO333 4.9 73.8 1.0 CA A:ASN783 4.9 74.3 1.0 CB A:ASN783 5.0 74.2 1.0

Potassium binding site 3 out of 3 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:K2007 b:72.9 occ:0.16 TL A:TL2008 0.0 72.9 0.8 O A:ALA728 2.7 59.6 1.0 O A:LYS726 2.8 60.6 1.0 OD1 A:ASP747 3.0 68.2 1.0 O A:LEU725 3.0 58.3 1.0 C A:LYS726 3.6 60.2 1.0 C A:ALA728 3.8 59.6 1.0 CG A:ASP747 3.8 66.7 1.0 OD2 A:ASP747 3.9 67.6 1.0 CA A:LYS726 4.0 60.0 1.0 N A:GLY731 4.0 57.9 1.0 C A:LEU725 4.1 58.6 1.0 N A:ALA728 4.3 59.7 1.0 O A:ASP729 4.4 59.8 1.0 C A:ASP729 4.4 59.5 1.0 CA A:ALA728 4.4 59.8 1.0 N A:LYS726 4.5 59.3 1.0 O A:ALA745 4.5 65.0 1.0 CA A:ILE730 4.5 58.9 1.0 N A:ILE730 4.5 59.0 1.0 N A:LYS727 4.5 60.0 1.0 C A:LYS727 4.6 59.9 1.0 C A:ILE730 4.6 58.5 1.0 CB A:ALA728 4.6 59.5 1.0 CA A:GLY731 4.8 57.8 1.0 N A:ASP729 4.8 59.6 1.0 O A:LYS727 5.0 59.9 1.0 CA A:ASP729 5.0 59.7 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