Thallium in PDB 5avt: Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 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 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
|
Other elements in 5avt:
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:
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 5 Min
(pdb code 5avt). 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 5 Min, PDB code: 5avt:
Jump to Thallium binding site number:
1;
2;
3;
Thallium binding site 1 out
of 3 in 5avt
Go back to
Thallium Binding Sites List in 5avt
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 5 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 5 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl2004
b:74.2
occ:0.85
|
K
|
A:K2003
|
0.0
|
74.2
|
0.1
|
OD2
|
A:ASP811
|
2.7
|
71.5
|
1.0
|
OG
|
A:SER782
|
2.7
|
71.1
|
1.0
|
O
|
A:THR779
|
2.7
|
66.7
|
1.0
|
O
|
A:HOH2101
|
2.7
|
76.5
|
1.0
|
OD1
|
A:ASN783
|
2.8
|
69.0
|
1.0
|
OD1
|
A:ASP811
|
3.2
|
72.5
|
1.0
|
CG
|
A:ASP811
|
3.2
|
71.0
|
1.0
|
N
|
A:ASN783
|
3.8
|
70.9
|
1.0
|
OE2
|
A:GLU786
|
3.8
|
76.3
|
1.0
|
C
|
A:SER782
|
3.8
|
70.5
|
1.0
|
CG
|
A:ASN783
|
3.8
|
70.2
|
1.0
|
CB
|
A:SER782
|
3.9
|
70.3
|
1.0
|
C
|
A:THR779
|
3.9
|
66.7
|
1.0
|
TL
|
A:TL2005
|
4.1
|
74.1
|
1.0
|
OE1
|
A:GLU786
|
4.2
|
77.1
|
1.0
|
O
|
A:SER782
|
4.2
|
70.8
|
1.0
|
CA
|
A:ASN783
|
4.2
|
71.1
|
1.0
|
CA
|
A:SER782
|
4.3
|
70.2
|
1.0
|
CG2
|
A:THR779
|
4.3
|
66.0
|
1.0
|
CD
|
A:GLU786
|
4.3
|
76.7
|
1.0
|
OD2
|
A:ASP815
|
4.4
|
71.2
|
1.0
|
CB
|
A:ASP811
|
4.5
|
70.2
|
1.0
|
N
|
A:SER782
|
4.5
|
69.7
|
1.0
|
CB
|
A:ASN783
|
4.6
|
71.0
|
1.0
|
CA
|
A:THR779
|
4.7
|
66.2
|
1.0
|
ND2
|
A:ASN783
|
4.7
|
69.6
|
1.0
|
N
|
A:LEU780
|
4.8
|
67.2
|
1.0
|
CB
|
A:PRO333
|
4.8
|
71.0
|
1.0
|
O
|
A:LEU780
|
4.8
|
68.1
|
1.0
|
CA
|
A:PRO333
|
4.9
|
70.9
|
1.0
|
CA
|
A:LEU780
|
4.9
|
67.7
|
1.0
|
C
|
A:LEU780
|
5.0
|
68.0
|
1.0
|
|
Thallium binding site 2 out
of 3 in 5avt
Go back to
Thallium Binding Sites List in 5avt
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 5 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 5 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl2005
b:74.1
occ:1.00
|
O
|
A:VAL332
|
2.8
|
71.3
|
1.0
|
OD2
|
A:ASP811
|
2.9
|
71.5
|
1.0
|
OE2
|
A:GLU786
|
2.9
|
76.3
|
1.0
|
O
|
A:VAL329
|
2.9
|
75.1
|
1.0
|
O
|
A:ALA330
|
3.0
|
73.6
|
1.0
|
OD1
|
A:ASN783
|
3.0
|
69.0
|
1.0
|
OE1
|
A:GLU334
|
3.3
|
70.2
|
1.0
|
CG
|
A:ASP811
|
3.5
|
71.0
|
1.0
|
C
|
A:ALA330
|
3.6
|
73.8
|
1.0
|
OD1
|
A:ASP811
|
3.6
|
72.5
|
1.0
|
C
|
A:VAL332
|
3.7
|
71.3
|
1.0
|
CG2
|
A:ILE807
|
3.9
|
71.7
|
1.0
|
CG
|
A:ASN783
|
4.0
|
70.2
|
1.0
|
CA
|
A:ALA330
|
4.0
|
74.1
|
1.0
|
CD
|
A:GLU334
|
4.1
|
70.1
|
1.0
|
CD
|
A:GLU786
|
4.1
|
76.7
|
1.0
|
C
|
A:VAL329
|
4.1
|
75.5
|
1.0
|
K
|
A:K2003
|
4.1
|
74.2
|
0.1
|
TL
|
A:TL2004
|
4.1
|
74.2
|
0.8
|
CA
|
A:PRO333
|
4.1
|
70.9
|
1.0
|
OE2
|
A:GLU334
|
4.1
|
71.1
|
1.0
|
N
|
A:PRO333
|
4.2
|
71.1
|
1.0
|
N
|
A:ALA330
|
4.5
|
74.7
|
1.0
|
N
|
A:VAL332
|
4.5
|
72.0
|
1.0
|
ND2
|
A:ASN783
|
4.6
|
69.6
|
1.0
|
N
|
A:ASN331
|
4.6
|
73.2
|
1.0
|
CB
|
A:ASP811
|
4.6
|
70.2
|
1.0
|
N
|
A:GLU334
|
4.6
|
70.3
|
1.0
|
OE1
|
A:GLU786
|
4.6
|
77.1
|
1.0
|
C
|
A:ASN331
|
4.7
|
72.5
|
1.0
|
CA
|
A:VAL332
|
4.8
|
71.6
|
1.0
|
C
|
A:PRO333
|
4.9
|
70.7
|
1.0
|
CA
|
A:ASN783
|
4.9
|
71.1
|
1.0
|
CB
|
A:ASN783
|
5.0
|
71.0
|
1.0
|
|
Thallium binding site 3 out
of 3 in 5avt
Go back to
Thallium Binding Sites List in 5avt
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 5 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 5 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Tl2007
b:69.7
occ:0.76
|
K
|
A:K2006
|
0.0
|
69.7
|
0.2
|
O
|
A:ALA728
|
2.7
|
56.4
|
1.0
|
O
|
A:LYS726
|
2.8
|
57.4
|
1.0
|
OD1
|
A:ASP747
|
3.0
|
65.0
|
1.0
|
O
|
A:LEU725
|
3.0
|
55.1
|
1.0
|
C
|
A:LYS726
|
3.6
|
57.1
|
1.0
|
C
|
A:ALA728
|
3.8
|
56.4
|
1.0
|
CG
|
A:ASP747
|
3.8
|
63.5
|
1.0
|
OD2
|
A:ASP747
|
3.9
|
64.4
|
1.0
|
CA
|
A:LYS726
|
4.0
|
56.9
|
1.0
|
N
|
A:GLY731
|
4.0
|
54.7
|
1.0
|
C
|
A:LEU725
|
4.1
|
55.5
|
1.0
|
N
|
A:ALA728
|
4.3
|
56.5
|
1.0
|
O
|
A:ASP729
|
4.4
|
56.6
|
1.0
|
C
|
A:ASP729
|
4.4
|
56.3
|
1.0
|
CA
|
A:ALA728
|
4.4
|
56.6
|
1.0
|
N
|
A:LYS726
|
4.5
|
56.2
|
1.0
|
O
|
A:ALA745
|
4.5
|
61.9
|
1.0
|
CA
|
A:ILE730
|
4.5
|
55.7
|
1.0
|
N
|
A:ILE730
|
4.5
|
55.8
|
1.0
|
N
|
A:LYS727
|
4.5
|
56.8
|
1.0
|
C
|
A:LYS727
|
4.6
|
56.7
|
1.0
|
C
|
A:ILE730
|
4.6
|
55.3
|
1.0
|
CB
|
A:ALA728
|
4.6
|
56.3
|
1.0
|
CA
|
A:GLY731
|
4.8
|
54.6
|
1.0
|
N
|
A:ASP729
|
4.8
|
56.5
|
1.0
|
O
|
A:LYS727
|
5.0
|
56.7
|
1.0
|
CA
|
A:ASP729
|
5.0
|
56.5
|
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
|