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Thallium in PDB 5avu: Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 7.0 Min

Protein crystallography data

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 7.0 Min, PDB code: 5avu 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 / 2.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 222.477, 50.895, 163.879, 90.00, 104.72, 90.00
R / Rfree (%) 26.6 / 26.9

Other elements in 5avu:

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 7.0 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 7.0 Min (pdb code 5avu). 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 7.0 Min, PDB code: 5avu:
Jump to Thallium binding site number: 1; 2; 3;

Thallium binding site 1 out of 3 in 5avu

Go back to Thallium Binding Sites List in 5avu
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 7.0 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 7.0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2004

b:68.3
occ:0.88
K A:K2003 0.0 68.3 0.1
OD2 A:ASP811 2.7 65.6 1.0
OG A:SER782 2.7 65.2 1.0
O A:THR779 2.7 60.9 1.0
O A:HOH2101 2.7 70.6 1.0
OD1 A:ASN783 2.8 63.1 1.0
OD1 A:ASP811 3.2 66.6 1.0
CG A:ASP811 3.2 65.2 1.0
N A:ASN783 3.8 65.0 1.0
OE2 A:GLU786 3.8 70.5 1.0
C A:SER782 3.8 64.6 1.0
CG A:ASN783 3.8 64.3 1.0
CB A:SER782 3.9 64.4 1.0
C A:THR779 3.9 60.8 1.0
TL A:TL2005 4.1 68.2 1.0
OE1 A:GLU786 4.2 71.2 1.0
O A:SER782 4.2 64.9 1.0
CA A:ASN783 4.2 65.2 1.0
CA A:SER782 4.3 64.3 1.0
CG2 A:THR779 4.3 60.1 1.0
CD A:GLU786 4.3 70.8 1.0
OD2 A:ASP815 4.4 65.3 1.0
CB A:ASP811 4.5 64.4 1.0
N A:SER782 4.5 63.8 1.0
CB A:ASN783 4.6 65.1 1.0
CA A:THR779 4.7 60.3 1.0
ND2 A:ASN783 4.7 63.7 1.0
N A:LEU780 4.8 61.4 1.0
CB A:PRO333 4.8 65.1 1.0
O A:LEU780 4.8 62.2 1.0
CA A:PRO333 4.9 65.0 1.0
CA A:LEU780 4.9 61.9 1.0
C A:LEU780 5.0 62.1 1.0

Thallium binding site 2 out of 3 in 5avu

Go back to Thallium Binding Sites List in 5avu
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 7.0 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 7.0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2005

b:68.2
occ:1.00
O A:VAL332 2.8 65.4 1.0
OD2 A:ASP811 2.9 65.6 1.0
OE2 A:GLU786 2.9 70.5 1.0
O A:VAL329 2.9 69.2 1.0
O A:ALA330 3.0 67.7 1.0
OD1 A:ASN783 3.0 63.1 1.0
OE1 A:GLU334 3.3 64.3 1.0
CG A:ASP811 3.5 65.2 1.0
C A:ALA330 3.6 68.0 1.0
OD1 A:ASP811 3.6 66.6 1.0
C A:VAL332 3.7 65.5 1.0
CG2 A:ILE807 3.9 65.8 1.0
CG A:ASN783 4.0 64.3 1.0
CA A:ALA330 4.0 68.2 1.0
CD A:GLU334 4.1 64.2 1.0
CD A:GLU786 4.1 70.8 1.0
C A:VAL329 4.1 69.6 1.0
K A:K2003 4.1 68.3 0.1
TL A:TL2004 4.1 68.3 0.9
CA A:PRO333 4.1 65.0 1.0
OE2 A:GLU334 4.1 65.2 1.0
N A:PRO333 4.2 65.2 1.0
N A:ALA330 4.5 68.8 1.0
N A:VAL332 4.5 66.1 1.0
ND2 A:ASN783 4.6 63.7 1.0
N A:ASN331 4.6 67.3 1.0
CB A:ASP811 4.6 64.4 1.0
N A:GLU334 4.6 64.4 1.0
OE1 A:GLU786 4.6 71.2 1.0
C A:ASN331 4.7 66.7 1.0
CA A:VAL332 4.8 65.7 1.0
C A:PRO333 4.9 64.8 1.0
CA A:ASN783 4.9 65.2 1.0
CB A:ASN783 5.0 65.1 1.0

Thallium binding site 3 out of 3 in 5avu

Go back to Thallium Binding Sites List in 5avu
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 7.0 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 7.0 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Tl2007

b:63.9
occ:0.78
K A:K2006 0.0 63.9 0.2
O A:ALA728 2.7 50.5 1.0
O A:LYS726 2.8 51.5 1.0
OD1 A:ASP747 3.0 59.1 1.0
O A:LEU725 3.0 49.2 1.0
C A:LYS726 3.6 51.2 1.0
C A:ALA728 3.8 50.5 1.0
CG A:ASP747 3.8 57.6 1.0
OD2 A:ASP747 3.9 58.6 1.0
CA A:LYS726 4.0 51.0 1.0
N A:GLY731 4.0 48.8 1.0
C A:LEU725 4.1 49.6 1.0
N A:ALA728 4.3 50.6 1.0
O A:ASP729 4.4 50.7 1.0
C A:ASP729 4.4 50.4 1.0
CA A:ALA728 4.4 50.7 1.0
N A:LYS726 4.5 50.3 1.0
O A:ALA745 4.5 56.0 1.0
CA A:ILE730 4.5 49.8 1.0
N A:ILE730 4.5 50.0 1.0
N A:LYS727 4.6 50.9 1.0
C A:ILE730 4.6 49.4 1.0
C A:LYS727 4.6 50.8 1.0
CB A:ALA728 4.6 50.4 1.0
CA A:GLY731 4.8 48.7 1.0
N A:ASP729 4.8 50.6 1.0
O A:LYS727 5.0 50.8 1.0
CA A:ASP729 5.0 50.7 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 02:29:05 2020

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