Fluorine in PDB 5avx: Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min
Protein crystallography data
The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min, PDB code: 5avx
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)
|
15.00 /
3.30
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
221.053,
50.768,
163.397,
90.00,
103.67,
90.00
|
R / Rfree (%)
|
31.5 /
31.2
|
Other elements in 5avx:
The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min
(pdb code 5avx). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min, PDB code: 5avx:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 5avx
Go back to
Fluorine Binding Sites List in 5avx
Fluorine binding site 1 out
of 4 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min
![](/pictures/F/pdb/av/5avx-F-sphere_01.jpg) Mono view
![](/pictures/F/pdb/av/5avx-F-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2001
b:0.4
occ:1.00
|
F1
|
A:MF42001
|
0.0
|
0.4
|
1.0
|
MG
|
A:MF42001
|
2.0
|
0.0
|
1.0
|
OD2
|
A:ASP376
|
2.4
|
0.9
|
1.0
|
NZ
|
A:LYS698
|
2.7
|
0.7
|
1.0
|
ND2
|
A:ASN720
|
2.9
|
0.9
|
1.0
|
N
|
A:GLY618
|
3.1
|
0.4
|
1.0
|
F2
|
A:MF42001
|
3.2
|
0.7
|
1.0
|
F4
|
A:MF42001
|
3.2
|
0.4
|
1.0
|
F3
|
A:MF42001
|
3.3
|
0.6
|
1.0
|
O
|
A:THR219
|
3.4
|
0.9
|
1.0
|
CE
|
A:LYS698
|
3.6
|
0.2
|
1.0
|
CG
|
A:ASP376
|
3.6
|
0.0
|
1.0
|
CA
|
A:THR617
|
3.7
|
1.0
|
1.0
|
C
|
A:THR617
|
3.9
|
0.0
|
1.0
|
OG1
|
A:THR617
|
3.9
|
0.2
|
1.0
|
CG
|
A:ASN720
|
4.0
|
0.9
|
1.0
|
CA
|
A:GLY618
|
4.0
|
0.9
|
1.0
|
OD1
|
A:ASN720
|
4.2
|
0.9
|
1.0
|
OD1
|
A:ASP721
|
4.3
|
0.5
|
1.0
|
CB
|
A:THR617
|
4.3
|
0.9
|
1.0
|
OD1
|
A:ASP376
|
4.3
|
0.3
|
1.0
|
O
|
A:VAL616
|
4.3
|
0.2
|
1.0
|
C
|
A:THR219
|
4.3
|
0.2
|
1.0
|
CA
|
A:GLY220
|
4.4
|
0.6
|
1.0
|
CB
|
A:ASP376
|
4.6
|
0.7
|
1.0
|
MG
|
A:MG2002
|
4.6
|
0.1
|
1.0
|
N
|
A:GLY220
|
4.8
|
0.7
|
1.0
|
N
|
A:THR617
|
4.8
|
0.4
|
1.0
|
CD
|
A:LYS698
|
4.9
|
0.2
|
1.0
|
N
|
A:ASP619
|
4.9
|
1.0
|
1.0
|
C
|
A:GLY618
|
5.0
|
0.5
|
1.0
|
CA
|
A:ASP376
|
5.0
|
0.9
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 5avx
Go back to
Fluorine Binding Sites List in 5avx
Fluorine binding site 2 out
of 4 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min
![](/pictures/F/pdb/av/5avx-F-sphere_02.jpg) Mono view
![](/pictures/F/pdb/av/5avx-F-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2001
b:0.7
occ:1.00
|
F2
|
A:MF42001
|
0.0
|
0.7
|
1.0
|
MG
|
A:MG2002
|
1.9
|
0.1
|
1.0
|
MG
|
A:MF42001
|
2.0
|
0.0
|
1.0
|
OD2
|
A:ASP376
|
2.6
|
0.9
|
1.0
|
OD1
|
A:ASP376
|
2.7
|
0.3
|
1.0
|
O
|
A:THR378
|
2.9
|
0.8
|
1.0
|
CG
|
A:ASP376
|
3.1
|
0.0
|
1.0
|
F4
|
A:MF42001
|
3.2
|
0.4
|
1.0
|
F1
|
A:MF42001
|
3.2
|
0.4
|
1.0
|
CB
|
A:THR378
|
3.2
|
0.9
|
1.0
|
F3
|
A:MF42001
|
3.4
|
0.6
|
1.0
|
N
|
A:THR378
|
3.5
|
0.6
|
1.0
|
O
|
A:GLY220
|
3.5
|
0.6
|
1.0
|
CA
|
A:THR378
|
3.6
|
0.9
|
1.0
|
C
|
A:THR378
|
3.6
|
0.1
|
1.0
|
CA
|
A:GLY220
|
3.7
|
0.6
|
1.0
|
OD2
|
A:ASP717
|
3.8
|
0.4
|
1.0
|
C
|
A:GLY220
|
4.0
|
0.8
|
1.0
|
OG1
|
A:THR378
|
4.1
|
0.3
|
1.0
|
CG2
|
A:THR378
|
4.2
|
0.0
|
1.0
|
C
|
A:LYS377
|
4.5
|
0.8
|
1.0
|
O
|
A:THR219
|
4.5
|
0.9
|
1.0
|
CB
|
A:ASP376
|
4.6
|
0.7
|
1.0
|
N
|
A:LYS377
|
4.6
|
0.3
|
1.0
|
OE1
|
A:GLU221
|
4.7
|
1.0
|
1.0
|
OD1
|
A:ASN720
|
4.8
|
0.9
|
1.0
|
CG
|
A:ASP717
|
4.9
|
0.6
|
1.0
|
N
|
A:GLY220
|
4.9
|
0.7
|
1.0
|
ND2
|
A:ASN720
|
4.9
|
0.9
|
1.0
|
N
|
A:GLY379
|
4.9
|
0.5
|
1.0
|
OD2
|
A:ASP721
|
5.0
|
0.8
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 5avx
Go back to
Fluorine Binding Sites List in 5avx
Fluorine binding site 3 out
of 4 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min
![](/pictures/F/pdb/av/5avx-F-sphere_03.jpg) Mono view
![](/pictures/F/pdb/av/5avx-F-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2001
b:0.6
occ:1.00
|
F3
|
A:MF42001
|
0.0
|
0.6
|
1.0
|
MG
|
A:MF42001
|
2.0
|
0.0
|
1.0
|
OE1
|
A:GLU221
|
2.4
|
1.0
|
1.0
|
O
|
A:THR219
|
2.6
|
0.9
|
1.0
|
CD
|
A:GLU221
|
3.3
|
0.3
|
1.0
|
F1
|
A:MF42001
|
3.3
|
0.4
|
1.0
|
F4
|
A:MF42001
|
3.3
|
0.4
|
1.0
|
N
|
A:ASP619
|
3.3
|
1.0
|
1.0
|
OG1
|
A:THR617
|
3.3
|
0.2
|
1.0
|
CG
|
A:GLU221
|
3.4
|
0.7
|
1.0
|
F2
|
A:MF42001
|
3.4
|
0.7
|
1.0
|
N
|
A:GLY618
|
3.7
|
0.4
|
1.0
|
C
|
A:GLY220
|
3.7
|
0.8
|
1.0
|
C
|
A:THR219
|
3.7
|
0.2
|
1.0
|
OG1
|
A:THR378
|
3.8
|
0.3
|
1.0
|
CB
|
A:ASP619
|
3.8
|
0.5
|
1.0
|
C
|
A:GLY618
|
3.8
|
0.5
|
1.0
|
CA
|
A:GLY220
|
3.9
|
0.6
|
1.0
|
CA
|
A:GLY618
|
3.9
|
0.9
|
1.0
|
CA
|
A:ASP619
|
4.0
|
0.7
|
1.0
|
O
|
A:GLY220
|
4.0
|
0.6
|
1.0
|
N
|
A:GLU221
|
4.0
|
0.3
|
1.0
|
CB
|
A:THR378
|
4.0
|
0.9
|
1.0
|
N
|
A:GLY220
|
4.3
|
0.7
|
1.0
|
OE2
|
A:GLU221
|
4.4
|
0.8
|
1.0
|
OD2
|
A:ASP376
|
4.5
|
0.9
|
1.0
|
CB
|
A:GLU221
|
4.5
|
0.3
|
1.0
|
CG
|
A:ASP619
|
4.6
|
0.1
|
1.0
|
CB
|
A:THR617
|
4.6
|
0.9
|
1.0
|
CA
|
A:GLU221
|
4.6
|
0.1
|
1.0
|
O
|
A:GLY618
|
4.6
|
0.0
|
1.0
|
C
|
A:THR617
|
4.7
|
0.0
|
1.0
|
N
|
A:THR378
|
4.9
|
0.6
|
1.0
|
CA
|
A:THR219
|
4.9
|
0.5
|
1.0
|
CA
|
A:THR617
|
4.9
|
1.0
|
1.0
|
CG2
|
A:THR378
|
5.0
|
0.0
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 5avx
Go back to
Fluorine Binding Sites List in 5avx
Fluorine binding site 4 out
of 4 in the Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min
![](/pictures/F/pdb/av/5avx-F-sphere_04.jpg) Mono view
![](/pictures/F/pdb/av/5avx-F-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 20 Min within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2001
b:0.4
occ:1.00
|
F4
|
A:MF42001
|
0.0
|
0.4
|
1.0
|
MG
|
A:MF42001
|
2.0
|
0.0
|
1.0
|
OD2
|
A:ASP376
|
2.5
|
0.9
|
1.0
|
OG1
|
A:THR617
|
2.6
|
0.2
|
1.0
|
N
|
A:LYS377
|
2.6
|
0.3
|
1.0
|
N
|
A:THR378
|
2.8
|
0.6
|
1.0
|
CB
|
A:THR617
|
3.0
|
0.9
|
1.0
|
CB
|
A:LYS377
|
3.1
|
0.7
|
1.0
|
F2
|
A:MF42001
|
3.2
|
0.7
|
1.0
|
CA
|
A:LYS377
|
3.2
|
0.8
|
1.0
|
F1
|
A:MF42001
|
3.2
|
0.4
|
1.0
|
F3
|
A:MF42001
|
3.3
|
0.6
|
1.0
|
CG
|
A:ASP376
|
3.3
|
0.0
|
1.0
|
C
|
A:LYS377
|
3.5
|
0.8
|
1.0
|
CA
|
A:THR617
|
3.7
|
1.0
|
1.0
|
C
|
A:ASP376
|
3.8
|
0.7
|
1.0
|
OD1
|
A:ASP376
|
3.9
|
0.3
|
1.0
|
OG1
|
A:THR378
|
3.9
|
0.3
|
1.0
|
CA
|
A:THR378
|
4.0
|
0.9
|
1.0
|
CB
|
A:THR378
|
4.0
|
0.9
|
1.0
|
CA
|
A:ASP376
|
4.1
|
0.9
|
1.0
|
CG
|
A:LYS377
|
4.2
|
0.3
|
1.0
|
N
|
A:GLY618
|
4.3
|
0.4
|
1.0
|
CB
|
A:ASP376
|
4.3
|
0.7
|
1.0
|
CG2
|
A:THR617
|
4.4
|
0.7
|
1.0
|
O
|
A:VAL616
|
4.5
|
0.2
|
1.0
|
C
|
A:THR617
|
4.5
|
0.0
|
1.0
|
OE1
|
A:GLU221
|
4.5
|
1.0
|
1.0
|
MG
|
A:MG2002
|
4.6
|
0.1
|
1.0
|
CE
|
A:LYS377
|
4.6
|
0.0
|
1.0
|
O
|
A:LYS377
|
4.7
|
0.8
|
1.0
|
N
|
A:THR617
|
4.8
|
0.4
|
1.0
|
NZ
|
A:LYS698
|
4.8
|
0.7
|
1.0
|
O
|
A:THR378
|
4.8
|
0.8
|
1.0
|
O
|
A:ASP376
|
4.9
|
0.8
|
1.0
|
CD
|
A:LYS377
|
4.9
|
0.7
|
1.0
|
C
|
A:THR378
|
4.9
|
0.1
|
1.0
|
N
|
A:ASP619
|
4.9
|
1.0
|
1.0
|
C
|
A:VAL616
|
5.0
|
0.8
|
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: Thu Aug 1 07:56:04 2024
|