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Thallium in PDB 5aw1: Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 85 Min

Protein crystallography data

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 85 Min, PDB code: 5aw1 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 / 3.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 222.035, 50.855, 163.971, 90.00, 104.02, 90.00
R / Rfree (%) 29.7 / 30.5

Other elements in 5aw1:

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 85 Min also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Magnesium (Mg) 2 atoms
Potassium (K) 2 atoms

Thallium Binding Sites:

The binding sites of Thallium atom in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 85 Min (pdb code 5aw1). This binding sites where shown within 5.0 Angstroms radius around Thallium atom.
In total 3 binding sites of Thallium where determined in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 85 Min, PDB code: 5aw1:
Jump to Thallium binding site number: 1; 2; 3;

Thallium binding site 1 out of 3 in 5aw1

Go back to Thallium Binding Sites List in 5aw1
Thallium binding site 1 out of 3 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 85 Min


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 1 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 85 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2004

b:0.1
occ:0.98
K A:K2003 0.0 0.1 0.0
OD2 A:ASP811 2.7 0.4 1.0
OG A:SER782 2.7 0.9 1.0
O A:THR779 2.7 0.6 1.0
O A:HOH2101 2.7 0.3 1.0
OD1 A:ASN783 2.8 0.8 1.0
OD1 A:ASP811 3.2 0.4 1.0
CG A:ASP811 3.2 0.9 1.0
N A:ASN783 3.8 0.8 1.0
OE2 A:GLU786 3.8 0.2 1.0
C A:SER782 3.8 0.4 1.0
CG A:ASN783 3.8 0.1 1.0
CB A:SER782 3.9 0.1 1.0
C A:THR779 3.9 0.5 1.0
TL A:TL2005 4.1 0.0 1.0
OE1 A:GLU786 4.2 0.9 1.0
O A:SER782 4.2 0.7 1.0
CA A:ASN783 4.2 0.9 1.0
CA A:SER782 4.3 0.1 1.0
CG2 A:THR779 4.3 0.8 1.0
CD A:GLU786 4.3 0.6 1.0
OD2 A:ASP815 4.4 0.1 1.0
CB A:ASP811 4.5 0.1 1.0
N A:SER782 4.5 0.6 1.0
CB A:ASN783 4.6 0.8 1.0
CA A:THR779 4.7 0.0 1.0
ND2 A:ASN783 4.7 0.5 1.0
N A:LEU780 4.8 0.1 1.0
CB A:PRO333 4.8 0.9 1.0
O A:LEU780 4.8 1.0 1.0
CA A:PRO333 4.9 0.8 1.0
CA A:LEU780 4.9 0.6 1.0
C A:LEU780 5.0 0.9 1.0

Thallium binding site 2 out of 3 in 5aw1

Go back to Thallium Binding Sites List in 5aw1
Thallium binding site 2 out of 3 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 85 Min


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 2 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 85 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2005

b:0.0
occ:1.00
O A:VAL332 2.8 0.1 1.0
OD2 A:ASP811 2.9 0.4 1.0
OE2 A:GLU786 2.9 0.2 1.0
O A:VAL329 2.9 1.0 1.0
O A:ALA330 3.0 0.4 1.0
OD1 A:ASN783 3.0 0.8 1.0
OE1 A:GLU334 3.3 0.1 1.0
CG A:ASP811 3.5 0.9 1.0
C A:ALA330 3.6 0.7 1.0
OD1 A:ASP811 3.6 0.4 1.0
C A:VAL332 3.7 0.2 1.0
CG2 A:ILE807 3.9 0.5 1.0
CG A:ASN783 4.0 0.1 1.0
CA A:ALA330 4.0 1.0 1.0
CD A:GLU334 4.1 0.9 1.0
CD A:GLU786 4.1 0.6 1.0
C A:VAL329 4.1 0.4 1.0
K A:K2003 4.1 0.1 0.0
TL A:TL2004 4.1 0.1 1.0
CA A:PRO333 4.1 0.8 1.0
OE2 A:GLU334 4.1 1.0 1.0
N A:PRO333 4.2 1.0 1.0
N A:ALA330 4.5 0.5 1.0
N A:VAL332 4.5 0.8 1.0
ND2 A:ASN783 4.6 0.5 1.0
N A:ASN331 4.6 0.1 1.0
CB A:ASP811 4.6 0.1 1.0
N A:GLU334 4.6 0.2 1.0
OE1 A:GLU786 4.6 0.9 1.0
C A:ASN331 4.7 0.4 1.0
CA A:VAL332 4.8 0.5 1.0
C A:PRO333 4.9 0.5 1.0
CA A:ASN783 4.9 0.9 1.0
CB A:ASN783 5.0 0.8 1.0

Thallium binding site 3 out of 3 in 5aw1

Go back to Thallium Binding Sites List in 5aw1
Thallium binding site 3 out of 3 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 85 Min


Mono view


Stereo pair view

A full contact list of Thallium with other atoms in the Tl binding site number 3 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 85 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2007

b:0.6
occ:0.66
K A:K2006 0.0 0.6 0.3
O A:ALA728 2.7 0.3 1.0
O A:LYS726 2.8 0.3 1.0
OD1 A:ASP747 3.0 0.9 1.0
O A:LEU725 3.0 1.0 1.0
C A:LYS726 3.6 0.9 1.0
C A:ALA728 3.8 0.3 1.0
CG A:ASP747 3.8 0.3 1.0
OD2 A:ASP747 3.9 0.3 1.0
CA A:LYS726 4.0 0.7 1.0
N A:GLY731 4.0 0.6 1.0
C A:LEU725 4.1 0.3 1.0
N A:ALA728 4.3 0.4 1.0
O A:ASP729 4.4 0.5 1.0
C A:ASP729 4.4 0.2 1.0
CA A:ALA728 4.4 0.5 1.0
N A:LYS726 4.5 0.0 1.0
O A:ALA745 4.5 0.7 1.0
CA A:ILE730 4.5 0.6 1.0
N A:ILE730 4.5 0.7 1.0
N A:LYS727 4.6 0.7 1.0
C A:LYS727 4.6 0.6 1.0
C A:ILE730 4.6 0.1 1.0
CB A:ALA728 4.6 0.2 1.0
CA A:GLY731 4.8 0.4 1.0
N A:ASP729 4.8 0.3 1.0
O A:LYS727 5.0 0.6 1.0
CA A:ASP729 5.0 0.4 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: Wed Dec 16 02:29:11 2020

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