Magnesium in PDB 5avv: Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 8.5 Min

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 8.5 Min, PDB code: 5avv 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)	14.99 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	220.991, 50.841, 163.358, 90.00, 104.02, 90.00
R / Rfree (%)	27.9 / 29.3

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 8.5 Min also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Potassium	(K)	1 atom
Thallium	(Tl)	3 atoms

The binding sites of Magnesium atom in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 8.5 Min (pdb code 5avv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 8.5 Min, PDB code: 5avv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 8.5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 8.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:71.9 occ:1.00 MG A:MF42001 0.0 71.9 1.0 F3 A:MF42001 2.0 72.5 1.0 F1 A:MF42001 2.0 71.2 1.0 F4 A:MF42001 2.0 69.3 1.0 F2 A:MF42001 2.0 70.5 1.0 OD2 A:ASP376 2.5 64.8 1.0 OG1 A:THR617 3.3 64.0 1.0 O A:THR219 3.5 67.7 1.0 CG A:ASP376 3.6 65.9 1.0 N A:GLY618 3.8 64.3 1.0 N A:THR378 3.8 64.5 1.0 CB A:THR378 3.8 64.8 1.0 MG A:MG2002 3.9 66.0 1.0 OE1 A:GLU221 3.9 70.9 1.0 OD1 A:ASP376 3.9 65.2 1.0 OG1 A:THR378 4.0 65.1 1.0 CA A:GLY220 4.1 67.4 1.0 CB A:THR617 4.1 63.8 1.0 CA A:THR617 4.3 63.9 1.0 N A:LYS377 4.4 65.2 1.0 O A:GLY220 4.4 67.5 1.0 CA A:THR378 4.4 64.8 1.0 C A:GLY220 4.4 67.7 1.0 ND2 A:ASN720 4.5 67.7 1.0 NZ A:LYS698 4.5 67.5 1.0 C A:THR219 4.5 68.1 1.0 N A:ASP619 4.6 65.9 1.0 C A:THR617 4.6 63.9 1.0 CA A:GLY618 4.6 64.8 1.0 O A:THR378 4.6 64.7 1.0 N A:GLY220 4.8 67.5 1.0 C A:LYS377 4.8 64.7 1.0 CB A:ASP376 4.9 65.6 1.0 CD A:GLU221 4.9 70.2 1.0 CA A:LYS377 5.0 64.7 1.0 C A:GLY618 5.0 65.4 1.0

Magnesium binding site 2 out of 2 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 8.5 Min


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 8.5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:66.0 occ:1.00 F2 A:MF42001 1.9 70.5 1.0 O A:THR378 1.9 64.7 1.0 OD2 A:ASP717 2.0 69.3 1.0 OD1 A:ASP376 2.0 65.2 1.0 CG A:ASP717 3.0 68.4 1.0 CG A:ASP376 3.0 65.9 1.0 C A:THR378 3.1 65.0 1.0 OD1 A:ASP717 3.3 71.1 1.0 OD2 A:ASP376 3.4 64.8 1.0 CA A:THR378 3.8 64.8 1.0 MG A:MF42001 3.9 71.9 1.0 N A:THR378 4.0 64.5 1.0 CB A:THR378 4.0 64.8 1.0 OG1 A:THR380 4.2 66.5 1.0 N A:GLY379 4.2 65.4 1.0 OD2 A:ASP721 4.2 70.6 1.0 N A:GLY718 4.2 69.0 1.0 O A:GLY220 4.3 67.5 1.0 CB A:ASP717 4.3 68.3 1.0 CB A:ASP376 4.3 65.6 1.0 N A:ASP717 4.4 68.0 1.0 CA A:GLY379 4.5 66.1 1.0 F4 A:MF42001 4.6 69.3 1.0 F1 A:MF42001 4.6 71.2 1.0 CG2 A:THR378 4.6 62.9 1.0 C A:ASP717 4.7 68.8 1.0 CA A:ASP717 4.7 68.5 1.0 CA A:GLY220 4.7 67.4 1.0 N A:THR380 4.7 66.5 1.0 C A:LYS377 4.8 64.7 1.0 CA A:GLY718 4.8 69.7 1.0 C A:GLY379 4.8 66.7 1.0 C A:GLY220 5.0 67.7 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