Rubidium in PDB 5aw7: Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min

The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min, PDB code: 5aw7 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)	14.96 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	219.234, 50.521, 162.571, 90.00, 104.27, 90.00
R / Rfree (%)	29 / 29.3

The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Magnesium	(Mg)	2 atoms
Potassium	(K)	2 atoms

The binding sites of Rubidium atom in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min (pdb code 5aw7). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 3 binding sites of Rubidium where determined in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min, PDB code: 5aw7:
Jump to Rubidium binding site number: 1; 2; 3;

Rubidium binding site 1 out of 3 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb2004 b:87.4 occ:0.77 K A:K2003 0.0 87.4 0.2 OD2 A:ASP811 2.7 84.7 1.0 OG A:SER782 2.7 84.2 1.0 O A:THR779 2.7 79.9 1.0 O A:HOH2101 2.7 89.6 1.0 OD1 A:ASN783 2.8 82.1 1.0 OD1 A:ASP811 3.2 85.7 1.0 CG A:ASP811 3.2 84.2 1.0 N A:ASN783 3.8 84.1 1.0 OE2 A:GLU786 3.8 89.5 1.0 C A:SER782 3.8 83.7 1.0 CG A:ASN783 3.8 83.3 1.0 CB A:SER782 3.9 83.4 1.0 C A:THR779 3.9 79.8 1.0 RB A:RB2005 4.1 87.3 1.0 OE1 A:GLU786 4.2 90.2 1.0 O A:SER782 4.2 84.0 1.0 CA A:ASN783 4.2 84.2 1.0 CA A:SER782 4.3 83.4 1.0 CG2 A:THR779 4.3 79.1 1.0 CD A:GLU786 4.3 89.9 1.0 OD2 A:ASP815 4.4 84.4 1.0 CB A:ASP811 4.5 83.4 1.0 N A:SER782 4.5 82.8 1.0 CB A:ASN783 4.6 84.1 1.0 CA A:THR779 4.7 79.3 1.0 ND2 A:ASN783 4.7 82.8 1.0 N A:LEU780 4.8 80.4 1.0 CB A:PRO333 4.8 84.2 1.0 O A:LEU780 4.8 81.3 1.0 CA A:PRO333 4.9 84.0 1.0 CA A:LEU780 4.9 80.9 1.0 C A:LEU780 5.0 81.2 1.0

Rubidium binding site 2 out of 3 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb2005 b:87.3 occ:1.00 O A:VAL332 2.8 84.4 1.0 OD2 A:ASP811 2.9 84.7 1.0 OE2 A:GLU786 2.9 89.5 1.0 O A:VAL329 2.9 88.3 1.0 O A:ALA330 3.0 86.7 1.0 OD1 A:ASN783 3.0 82.1 1.0 OE1 A:GLU334 3.2 83.4 1.0 CG A:ASP811 3.5 84.2 1.0 C A:ALA330 3.6 87.0 1.0 OD1 A:ASP811 3.6 85.7 1.0 C A:VAL332 3.7 84.5 1.0 CG2 A:ILE807 3.9 84.8 1.0 CG A:ASN783 4.0 83.3 1.0 CA A:ALA330 4.0 87.3 1.0 CD A:GLU334 4.1 83.2 1.0 CD A:GLU786 4.1 89.9 1.0 C A:VAL329 4.1 88.7 1.0 K A:K2003 4.1 87.4 0.2 RB A:RB2004 4.1 87.4 0.8 CA A:PRO333 4.1 84.0 1.0 OE2 A:GLU334 4.1 84.3 1.0 N A:PRO333 4.2 84.2 1.0 N A:ALA330 4.5 87.8 1.0 N A:VAL332 4.5 85.1 1.0 ND2 A:ASN783 4.6 82.8 1.0 N A:ASN331 4.6 86.3 1.0 CB A:ASP811 4.6 83.4 1.0 N A:GLU334 4.6 83.5 1.0 OE1 A:GLU786 4.6 90.2 1.0 C A:ASN331 4.7 85.7 1.0 CA A:VAL332 4.8 84.8 1.0 C A:PRO333 4.9 83.8 1.0 CA A:ASN783 4.9 84.2 1.0 CB A:ASN783 5.0 84.1 1.0

Rubidium binding site 3 out of 3 in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 11.3 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb2007 b:82.9 occ:0.91 K A:K2006 0.0 82.9 0.1 O A:ALA728 2.7 69.5 1.0 O A:LYS726 2.8 70.6 1.0 OD2 A:ASP747 3.0 78.2 1.0 O A:LEU725 3.0 68.2 1.0 C A:LYS726 3.6 70.2 1.0 C A:ALA728 3.8 69.6 1.0 CG A:ASP747 3.8 76.6 1.0 OD1 A:ASP747 3.9 77.6 1.0 CA A:LYS726 4.0 70.0 1.0 N A:GLY731 4.0 67.9 1.0 C A:LEU725 4.1 68.6 1.0 N A:ALA728 4.3 69.7 1.0 O A:ASP729 4.4 69.8 1.0 C A:ASP729 4.4 69.5 1.0 CA A:ALA728 4.4 69.8 1.0 N A:LYS726 4.5 69.3 1.0 O A:ALA745 4.5 75.0 1.0 CA A:ILE730 4.5 68.8 1.0 N A:ILE730 4.5 69.0 1.0 N A:LYS727 4.6 70.0 1.0 C A:ILE730 4.6 68.4 1.0 C A:LYS727 4.6 69.9 1.0 CB A:ALA728 4.6 69.5 1.0 CA A:GLY731 4.8 67.7 1.0 N A:ASP729 4.8 69.6 1.0 O A:LYS727 5.0 69.9 1.0 CA A:ASP729 5.0 69.7 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