Rubidium 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:

Fluorine	(F)	4 atoms
Magnesium	(Mg)	2 atoms
Potassium	(K)	3 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 5.5 Min (pdb code 5aw6). 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 5.5 Min, PDB code: 5aw6:
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 5.5 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 5.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb2004 b:81.7 occ:0.76 K A:K2003 0.0 81.7 0.2 OD2 A:ASP811 2.7 79.0 1.0 OG A:SER782 2.7 78.5 1.0 O A:THR779 2.7 74.2 1.0 O A:HOH2101 2.7 83.9 1.0 OD1 A:ASN783 2.8 76.5 1.0 OD1 A:ASP811 3.2 80.0 1.0 CG A:ASP811 3.2 78.5 1.0 N A:ASN783 3.8 78.4 1.0 OE2 A:GLU786 3.8 83.8 1.0 C A:SER782 3.8 78.0 1.0 CG A:ASN783 3.8 77.7 1.0 CB A:SER782 3.9 77.7 1.0 C A:THR779 3.9 74.1 1.0 K A:K2005 4.1 81.6 0.1 RB A:RB2006 4.1 81.6 0.9 OE1 A:GLU786 4.2 84.5 1.0 O A:SER782 4.2 78.3 1.0 CA A:ASN783 4.2 78.5 1.0 CA A:SER782 4.3 77.7 1.0 CG2 A:THR779 4.3 73.4 1.0 CD A:GLU786 4.3 84.2 1.0 OD2 A:ASP815 4.4 78.7 1.0 CB A:ASP811 4.5 77.7 1.0 N A:SER782 4.5 77.2 1.0 CB A:ASN783 4.6 78.4 1.0 CA A:THR779 4.7 73.6 1.0 ND2 A:ASN783 4.7 77.1 1.0 N A:LEU780 4.8 74.7 1.0 CB A:PRO333 4.8 78.5 1.0 O A:LEU780 4.8 75.6 1.0 CA A:PRO333 4.9 78.3 1.0 CA A:LEU780 4.9 75.2 1.0 C A:LEU780 5.0 75.5 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 5.5 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 5.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb2006 b:81.6 occ:0.95 K A:K2005 0.0 81.6 0.1 O A:VAL332 2.8 78.7 1.0 OD2 A:ASP811 2.9 79.0 1.0 OE2 A:GLU786 2.9 83.8 1.0 O A:VAL329 2.9 82.6 1.0 O A:ALA330 3.0 81.0 1.0 OD1 A:ASN783 3.0 76.5 1.0 OE1 A:GLU334 3.2 77.7 1.0 CG A:ASP811 3.5 78.5 1.0 C A:ALA330 3.6 81.3 1.0 OD1 A:ASP811 3.6 80.0 1.0 C A:VAL332 3.7 78.8 1.0 CG2 A:ILE807 3.9 79.1 1.0 CG A:ASN783 4.0 77.7 1.0 CA A:ALA330 4.0 81.6 1.0 CD A:GLU334 4.1 77.5 1.0 CD A:GLU786 4.1 84.2 1.0 C A:VAL329 4.1 83.0 1.0 K A:K2003 4.1 81.7 0.2 RB A:RB2004 4.1 81.7 0.8 CA A:PRO333 4.1 78.3 1.0 OE2 A:GLU334 4.1 78.6 1.0 N A:PRO333 4.2 78.6 1.0 N A:ALA330 4.5 82.1 1.0 N A:VAL332 4.5 79.4 1.0 ND2 A:ASN783 4.6 77.1 1.0 N A:ASN331 4.6 80.7 1.0 CB A:ASP811 4.6 77.7 1.0 N A:GLU334 4.6 77.8 1.0 OE1 A:GLU786 4.6 84.5 1.0 C A:ASN331 4.7 80.0 1.0 CA A:VAL332 4.8 79.1 1.0 C A:PRO333 4.9 78.1 1.0 CA A:ASN783 4.9 78.5 1.0 CB A:ASN783 5.0 78.4 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 5.5 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 5.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb2008 b:77.2 occ:0.73 K A:K2007 0.0 77.2 0.3 O A:ALA728 2.7 63.9 1.0 O A:LYS726 2.8 64.9 1.0 OD2 A:ASP747 3.0 72.5 1.0 O A:LEU725 3.0 62.6 1.0 C A:LYS726 3.6 64.5 1.0 C A:ALA728 3.8 63.9 1.0 CG A:ASP747 3.8 70.9 1.0 OD1 A:ASP747 3.9 71.9 1.0 CA A:LYS726 4.0 64.3 1.0 N A:GLY731 4.0 62.2 1.0 C A:LEU725 4.1 62.9 1.0 N A:ALA728 4.3 64.0 1.0 O A:ASP729 4.4 64.1 1.0 C A:ASP729 4.4 63.8 1.0 CA A:ALA728 4.4 64.1 1.0 N A:LYS726 4.5 63.6 1.0 O A:ALA745 4.5 69.3 1.0 CA A:ILE730 4.5 63.2 1.0 N A:ILE730 4.5 63.3 1.0 N A:LYS727 4.6 64.3 1.0 C A:LYS727 4.6 64.2 1.0 C A:ILE730 4.6 62.7 1.0 CB A:ALA728 4.6 63.8 1.0 CA A:GLY731 4.8 62.0 1.0 N A:ASP729 4.8 63.9 1.0 O A:LYS727 5.0 64.2 1.0 CA A:ASP729 5.0 64.0 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