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Potassium in PDB 5avs: Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 3.5 Min

Protein crystallography data

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 3.5 Min, PDB code: 5avs 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 (°) 221.904, 50.871, 164.190, 90.00, 104.45, 90.00
R / Rfree (%) 28.5 / 28.4

Other elements in 5avs:

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 3.5 Min also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Magnesium (Mg) 2 atoms
Thallium (Tl) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 3.5 Min (pdb code 5avs). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 3.5 Min, PDB code: 5avs:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 5avs

Go back to Potassium Binding Sites List in 5avs
Potassium 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 3.5 Min


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 3.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2003

b:77.3
occ:0.18
TL A:TL2004 0.0 77.3 0.8
OD2 A:ASP811 2.7 74.6 1.0
OG A:SER782 2.7 74.1 1.0
O A:THR779 2.7 69.8 1.0
O A:HOH2101 2.7 79.5 1.0
OD1 A:ASN783 2.8 72.0 1.0
OD1 A:ASP811 3.2 75.6 1.0
CG A:ASP811 3.2 74.1 1.0
N A:ASN783 3.8 74.0 1.0
OE2 A:GLU786 3.8 79.4 1.0
C A:SER782 3.8 73.6 1.0
CG A:ASN783 3.8 73.2 1.0
CB A:SER782 3.9 73.3 1.0
C A:THR779 3.9 69.7 1.0
TL A:TL2005 4.1 77.2 1.0
OE1 A:GLU786 4.2 80.1 1.0
O A:SER782 4.2 73.8 1.0
CA A:ASN783 4.2 74.1 1.0
CA A:SER782 4.3 73.3 1.0
CG2 A:THR779 4.3 69.0 1.0
CD A:GLU786 4.3 79.8 1.0
OD2 A:ASP815 4.4 74.2 1.0
CB A:ASP811 4.5 73.3 1.0
N A:SER782 4.5 72.7 1.0
CB A:ASN783 4.6 74.0 1.0
CA A:THR779 4.7 69.2 1.0
ND2 A:ASN783 4.7 72.7 1.0
N A:LEU780 4.8 70.3 1.0
CB A:PRO333 4.8 74.1 1.0
O A:LEU780 4.8 71.2 1.0
CA A:PRO333 4.9 73.9 1.0
CA A:LEU780 4.9 70.8 1.0
C A:LEU780 5.0 71.1 1.0

Potassium binding site 2 out of 2 in 5avs

Go back to Potassium Binding Sites List in 5avs
Potassium 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 3.5 Min


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 3.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2006

b:72.8
occ:0.21
TL A:TL2007 0.0 72.8 0.8
O A:ALA728 2.7 59.4 1.0
O A:LYS726 2.8 60.5 1.0
OD1 A:ASP747 3.0 68.0 1.0
O A:LEU725 3.0 58.1 1.0
C A:LYS726 3.6 60.1 1.0
C A:ALA728 3.8 59.5 1.0
CG A:ASP747 3.8 66.5 1.0
OD2 A:ASP747 3.9 67.5 1.0
CA A:LYS726 4.0 59.9 1.0
N A:GLY731 4.0 57.8 1.0
C A:LEU725 4.1 58.5 1.0
N A:ALA728 4.3 59.6 1.0
O A:ASP729 4.4 59.7 1.0
C A:ASP729 4.4 59.3 1.0
CA A:ALA728 4.4 59.6 1.0
N A:LYS726 4.5 59.2 1.0
O A:ALA745 4.5 64.9 1.0
CA A:ILE730 4.5 58.7 1.0
N A:ILE730 4.5 58.9 1.0
N A:LYS727 4.6 59.8 1.0
C A:ILE730 4.6 58.3 1.0
C A:LYS727 4.6 59.8 1.0
CB A:ALA728 4.6 59.4 1.0
CA A:GLY731 4.8 57.6 1.0
N A:ASP729 4.8 59.5 1.0
O A:LYS727 5.0 59.8 1.0
CA A:ASP729 5.0 59.6 1.0

Reference:

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
Page generated: Sun Dec 13 23:54:06 2020

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