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

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5 Min, PDB code: 5avt 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 (°)	221.468, 50.933, 164.123, 90.00, 104.52, 90.00
R / Rfree (%)	26.8 / 25.4

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 5 Min also contains other interesting chemical elements:

Fluorine	(F)	4 atoms
Potassium	(K)	2 atoms
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 5 Min (pdb code 5avt). 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 5 Min, PDB code: 5avt:
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 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2001 b:59.3 occ:1.00 MG A:MF42001 0.0 59.3 1.0 F3 A:MF42001 2.0 59.9 1.0 F1 A:MF42001 2.0 58.7 1.0 F4 A:MF42001 2.0 56.7 1.0 F2 A:MF42001 2.0 58.0 1.0 OD2 A:ASP376 2.5 52.2 1.0 OG1 A:THR617 3.3 51.5 1.0 O A:THR219 3.5 55.2 1.0 CG A:ASP376 3.6 53.4 1.0 N A:GLY618 3.8 51.8 1.0 N A:THR378 3.8 52.0 1.0 CB A:THR378 3.8 52.3 1.0 MG A:MG2002 3.9 53.5 1.0 OE1 A:GLU221 3.9 58.3 1.0 OD1 A:ASP376 3.9 52.7 1.0 OG1 A:THR378 4.0 52.6 1.0 CA A:GLY220 4.1 54.9 1.0 CB A:THR617 4.1 51.2 1.0 CA A:THR617 4.3 51.3 1.0 N A:LYS377 4.4 52.6 1.0 O A:GLY220 4.4 55.0 1.0 CA A:THR378 4.4 52.2 1.0 C A:GLY220 4.4 55.2 1.0 ND2 A:ASN720 4.5 55.2 1.0 NZ A:LYS698 4.5 55.0 1.0 C A:THR219 4.5 55.6 1.0 N A:ASP619 4.6 53.3 1.0 C A:THR617 4.6 51.4 1.0 CA A:GLY618 4.6 52.2 1.0 O A:THR378 4.6 52.2 1.0 N A:GLY220 4.8 55.0 1.0 C A:LYS377 4.8 52.1 1.0 CB A:ASP376 4.9 53.1 1.0 CD A:GLU221 4.9 57.6 1.0 CA A:LYS377 5.0 52.2 1.0 C A:GLY618 5.0 52.9 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 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 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2002 b:53.5 occ:1.00 F2 A:MF42001 1.9 58.0 1.0 O A:THR378 1.9 52.2 1.0 OD2 A:ASP717 1.9 56.8 1.0 OD1 A:ASP376 2.0 52.7 1.0 CG A:ASP717 3.0 55.9 1.0 CG A:ASP376 3.0 53.4 1.0 C A:THR378 3.1 52.5 1.0 OD1 A:ASP717 3.3 58.5 1.0 OD2 A:ASP376 3.4 52.2 1.0 CA A:THR378 3.8 52.2 1.0 MG A:MF42001 3.9 59.3 1.0 N A:THR378 4.0 52.0 1.0 CB A:THR378 4.0 52.3 1.0 OG1 A:THR380 4.2 53.9 1.0 N A:GLY379 4.2 52.8 1.0 OD2 A:ASP721 4.2 58.1 1.0 N A:GLY718 4.2 56.5 1.0 O A:GLY220 4.3 55.0 1.0 CB A:ASP717 4.3 55.8 1.0 CB A:ASP376 4.3 53.1 1.0 N A:ASP717 4.4 55.5 1.0 CA A:GLY379 4.5 53.6 1.0 F4 A:MF42001 4.6 56.7 1.0 F1 A:MF42001 4.6 58.7 1.0 CG2 A:THR378 4.6 50.4 1.0 C A:ASP717 4.7 56.3 1.0 CA A:ASP717 4.7 56.0 1.0 CA A:GLY220 4.7 54.9 1.0 N A:THR380 4.7 53.9 1.0 C A:LYS377 4.8 52.1 1.0 CA A:GLY718 4.8 57.1 1.0 C A:GLY379 4.8 54.1 1.0 C A:GLY220 5.0 55.2 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