Rubidium in PDB 5aw5: Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 2.2 Min

The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 2.2 Min, PDB code: 5aw5 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 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	219.497, 50.543, 162.600, 90.00, 104.10, 90.00
R / Rfree (%)	30.3 / 31.6

The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 2.2 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 2.2 Min (pdb code 5aw5). 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 2.2 Min, PDB code: 5aw5:
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 2.2 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 2.2 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb2004 b:88.4 occ:0.69 K A:K2003 0.0 88.4 0.3 OD2 A:ASP811 2.7 85.7 1.0 OG A:SER782 2.7 85.3 1.0 O A:THR779 2.7 80.9 1.0 O A:HOH2101 2.7 90.7 1.0 OD1 A:ASN783 2.8 83.2 1.0 OD1 A:ASP811 3.2 86.7 1.0 CG A:ASP811 3.2 85.2 1.0 N A:ASN783 3.8 85.1 1.0 OE2 A:GLU786 3.8 90.5 1.0 C A:SER782 3.8 84.7 1.0 CG A:ASN783 3.8 84.4 1.0 CB A:SER782 3.9 84.5 1.0 C A:THR779 3.9 80.9 1.0 K A:K2005 4.1 88.3 0.1 RB A:RB2006 4.1 88.3 0.9 OE1 A:GLU786 4.2 91.2 1.0 O A:SER782 4.2 85.0 1.0 CA A:ASN783 4.2 85.3 1.0 CA A:SER782 4.3 84.4 1.0 CG2 A:THR779 4.3 80.2 1.0 CD A:GLU786 4.3 90.9 1.0 OD2 A:ASP815 4.4 85.4 1.0 CB A:ASP811 4.5 84.4 1.0 N A:SER782 4.5 83.9 1.0 CB A:ASN783 4.6 85.2 1.0 CA A:THR779 4.7 80.3 1.0 ND2 A:ASN783 4.7 83.8 1.0 N A:LEU780 4.8 81.4 1.0 CB A:PRO333 4.8 85.2 1.0 O A:LEU780 4.8 82.3 1.0 CA A:PRO333 4.9 85.1 1.0 CA A:LEU780 4.9 81.9 1.0 C A:LEU780 5.0 82.2 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 2.2 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 2.2 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb2006 b:88.3 occ:0.86 K A:K2005 0.0 88.3 0.1 O A:VAL332 2.8 85.5 1.0 OD2 A:ASP811 2.9 85.7 1.0 OE2 A:GLU786 2.9 90.5 1.0 O A:VAL329 2.9 89.3 1.0 O A:ALA330 3.0 87.8 1.0 OD1 A:ASN783 3.0 83.2 1.0 OE1 A:GLU334 3.3 84.4 1.0 CG A:ASP811 3.5 85.2 1.0 C A:ALA330 3.6 88.0 1.0 OD1 A:ASP811 3.6 86.7 1.0 C A:VAL332 3.7 85.5 1.0 CG2 A:ILE807 3.9 85.8 1.0 CG A:ASN783 4.0 84.4 1.0 CA A:ALA330 4.0 88.3 1.0 CD A:GLU334 4.1 84.3 1.0 CD A:GLU786 4.1 90.9 1.0 C A:VAL329 4.1 89.7 1.0 K A:K2003 4.1 88.4 0.3 RB A:RB2004 4.1 88.4 0.7 CA A:PRO333 4.1 85.1 1.0 OE2 A:GLU334 4.1 85.3 1.0 N A:PRO333 4.2 85.3 1.0 N A:ALA330 4.5 88.8 1.0 N A:VAL332 4.5 86.2 1.0 ND2 A:ASN783 4.6 83.8 1.0 N A:ASN331 4.6 87.4 1.0 CB A:ASP811 4.6 84.4 1.0 N A:GLU334 4.6 84.5 1.0 OE1 A:GLU786 4.6 91.2 1.0 C A:ASN331 4.7 86.7 1.0 CA A:VAL332 4.8 85.8 1.0 C A:PRO333 4.9 84.8 1.0 CA A:ASN783 4.9 85.3 1.0 CB A:ASN783 5.0 85.2 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 2.2 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 2.2 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb2008 b:83.9 occ:0.74 K A:K2007 0.0 83.9 0.3 O A:ALA728 2.7 70.6 1.0 O A:LYS726 2.8 71.6 1.0 OD2 A:ASP747 3.0 79.2 1.0 O A:LEU725 3.0 69.3 1.0 C A:LYS726 3.6 71.2 1.0 C A:ALA728 3.8 70.6 1.0 CG A:ASP747 3.8 77.7 1.0 OD1 A:ASP747 3.9 78.6 1.0 CA A:LYS726 4.0 71.1 1.0 N A:GLY731 4.0 68.9 1.0 C A:LEU725 4.1 69.7 1.0 N A:ALA728 4.3 70.7 1.0 O A:ASP729 4.4 70.8 1.0 C A:ASP729 4.4 70.5 1.0 CA A:ALA728 4.4 70.8 1.0 N A:LYS726 4.5 70.3 1.0 O A:ALA745 4.5 76.0 1.0 CA A:ILE730 4.5 69.9 1.0 N A:ILE730 4.5 70.0 1.0 N A:LYS727 4.6 71.0 1.0 C A:ILE730 4.6 69.5 1.0 C A:LYS727 4.6 70.9 1.0 CB A:ALA728 4.6 70.5 1.0 CA A:GLY731 4.8 68.8 1.0 N A:ASP729 4.8 70.7 1.0 O A:LYS727 5.0 70.9 1.0 CA A:ASP729 5.0 70.7 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