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Fluorine in PDB 5avw: Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 16.5 Min

Protein crystallography data

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 16.5 Min, PDB code: 5avw 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 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 222.476, 50.881, 163.810, 90.00, 104.67, 90.00
R / Rfree (%) 26.5 / 25.7

Other elements in 5avw:

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 16.5 Min also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 1 atom
Thallium (Tl) 3 atoms

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 16.5 Min (pdb code 5avw). 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 16.5 Min, PDB code: 5avw:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5avw

Go back to Fluorine Binding Sites List in 5avw
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 16.5 Min


Mono view


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 16.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:55.2
occ:1.00
 F1 A:MF42001 0.0 55.2 1.0
MG A:MF42001 2.0 55.8 1.0
OD2 A:ASP376 2.4 48.7 1.0
NZ A:LYS698 2.7 51.5 1.0
ND2 A:ASN720 2.9 51.7 1.0
N A:GLY618 3.1 48.2 1.0
F2 A:MF42001 3.2 54.5 1.0
F4 A:MF42001 3.2 53.2 1.0
F3 A:MF42001 3.3 56.4 1.0
O A:THR219 3.4 51.7 1.0
CE A:LYS698 3.6 52.0 1.0
CG A:ASP376 3.6 49.8 1.0
CA A:THR617 3.7 47.8 1.0
C A:THR617 3.9 47.8 1.0
OG1 A:THR617 3.9 48.0 1.0
CG A:ASN720 4.0 52.7 1.0
CA A:GLY618 4.0 48.7 1.0
OD1 A:ASN720 4.2 52.8 1.0
OD1 A:ASP721 4.3 55.3 1.0
CB A:THR617 4.3 47.7 1.0
OD1 A:ASP376 4.3 49.1 1.0
O A:VAL616 4.3 49.0 1.0
C A:THR219 4.3 52.0 1.0
CA A:GLY220 4.4 51.4 1.0
CB A:ASP376 4.6 49.5 1.0
MG A:MG2002 4.6 49.9 1.0
N A:GLY220 4.8 51.5 1.0
N A:THR617 4.8 48.2 1.0
CD A:LYS698 4.9 52.0 1.0
N A:ASP619 4.9 49.8 1.0
C A:GLY618 5.0 49.3 1.0
CA A:ASP376 5.0 49.7 1.0

Fluorine binding site 2 out of 4 in 5avw

Go back to Fluorine Binding Sites List in 5avw
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 16.5 Min


Mono view


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 16.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:54.5
occ:1.00
 F2 A:MF42001 0.0 54.5 1.0
MG A:MG2002 1.9 49.9 1.0
MG A:MF42001 2.0 55.8 1.0
OD2 A:ASP376 2.6 48.7 1.0
OD1 A:ASP376 2.7 49.1 1.0
O A:THR378 2.9 48.6 1.0
CG A:ASP376 3.1 49.8 1.0
F4 A:MF42001 3.2 53.2 1.0
F1 A:MF42001 3.2 55.2 1.0
CB A:THR378 3.2 48.8 1.0
F3 A:MF42001 3.4 56.4 1.0
N A:THR378 3.5 48.4 1.0
O A:GLY220 3.5 51.4 1.0
CA A:THR378 3.6 48.7 1.0
C A:THR378 3.6 48.9 1.0
CA A:GLY220 3.7 51.4 1.0
OD2 A:ASP717 3.8 53.2 1.0
C A:GLY220 4.0 51.6 1.0
OG1 A:THR378 4.1 49.1 1.0
CG2 A:THR378 4.2 46.8 1.0
C A:LYS377 4.5 48.6 1.0
O A:THR219 4.5 51.7 1.0
CB A:ASP376 4.6 49.5 1.0
N A:LYS377 4.6 49.1 1.0
OE1 A:GLU221 4.7 54.8 1.0
OD1 A:ASN720 4.8 52.8 1.0
CG A:ASP717 4.9 52.4 1.0
N A:GLY220 4.9 51.5 1.0
N A:GLY379 4.9 49.3 1.0
ND2 A:ASN720 4.9 51.7 1.0
OD2 A:ASP721 5.0 54.6 1.0

Fluorine binding site 3 out of 4 in 5avw

Go back to Fluorine Binding Sites List in 5avw
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 16.5 Min


Mono view


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 16.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:56.4
occ:1.00
 F3 A:MF42001 0.0 56.4 1.0
MG A:MF42001 2.0 55.8 1.0
OE1 A:GLU221 2.4 54.8 1.0
O A:THR219 2.6 51.7 1.0
CD A:GLU221 3.3 54.1 1.0
F1 A:MF42001 3.3 55.2 1.0
F4 A:MF42001 3.3 53.2 1.0
N A:ASP619 3.3 49.8 1.0
OG1 A:THR617 3.3 48.0 1.0
CG A:GLU221 3.4 53.5 1.0
F2 A:MF42001 3.4 54.5 1.0
N A:GLY618 3.7 48.2 1.0
C A:GLY220 3.7 51.6 1.0
C A:THR219 3.7 52.0 1.0
OG1 A:THR378 3.8 49.1 1.0
CB A:ASP619 3.8 50.3 1.0
C A:GLY618 3.8 49.3 1.0
CA A:GLY220 3.9 51.4 1.0
CA A:GLY618 3.9 48.7 1.0
CA A:ASP619 4.0 50.5 1.0
O A:GLY220 4.0 51.4 1.0
N A:GLU221 4.0 52.1 1.0
CB A:THR378 4.0 48.8 1.0
N A:GLY220 4.3 51.5 1.0
OE2 A:GLU221 4.4 55.6 1.0
OD2 A:ASP376 4.5 48.7 1.0
CB A:GLU221 4.5 53.1 1.0
CG A:ASP619 4.6 51.0 1.0
CB A:THR617 4.6 47.7 1.0
CA A:GLU221 4.6 52.9 1.0
O A:GLY618 4.6 49.8 1.0
C A:THR617 4.7 47.8 1.0
N A:THR378 4.9 48.4 1.0
CA A:THR219 4.9 52.3 1.0
CA A:THR617 4.9 47.8 1.0
CG2 A:THR378 5.0 46.8 1.0

Fluorine binding site 4 out of 4 in 5avw

Go back to Fluorine Binding Sites List in 5avw
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 16.5 Min


Mono view


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 16.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:53.2
occ:1.00
 F4 A:MF42001 0.0 53.2 1.0
MG A:MF42001 2.0 55.8 1.0
OD2 A:ASP376 2.5 48.7 1.0
OG1 A:THR617 2.6 48.0 1.0
N A:LYS377 2.6 49.1 1.0
N A:THR378 2.8 48.4 1.0
CB A:THR617 3.0 47.7 1.0
CB A:LYS377 3.1 48.5 1.0
F2 A:MF42001 3.2 54.5 1.0
CA A:LYS377 3.2 48.6 1.0
F1 A:MF42001 3.2 55.2 1.0
F3 A:MF42001 3.3 56.4 1.0
CG A:ASP376 3.3 49.8 1.0
C A:LYS377 3.5 48.6 1.0
CA A:THR617 3.7 47.8 1.0
C A:ASP376 3.8 49.5 1.0
OD1 A:ASP376 3.9 49.1 1.0
OG1 A:THR378 3.9 49.1 1.0
CA A:THR378 4.0 48.7 1.0
CB A:THR378 4.0 48.8 1.0
CA A:ASP376 4.1 49.7 1.0
CG A:LYS377 4.2 48.1 1.0
N A:GLY618 4.3 48.2 1.0
CB A:ASP376 4.3 49.5 1.0
CG2 A:THR617 4.3 47.5 1.0
O A:VAL616 4.5 49.0 1.0
C A:THR617 4.5 47.8 1.0
OE1 A:GLU221 4.5 54.8 1.0
MG A:MG2002 4.6 49.9 1.0
CE A:LYS377 4.6 49.8 1.0
O A:LYS377 4.7 48.6 1.0
N A:THR617 4.8 48.2 1.0
NZ A:LYS698 4.8 51.5 1.0
O A:THR378 4.8 48.6 1.0
O A:ASP376 4.9 49.5 1.0
CD A:LYS377 4.9 48.5 1.0
C A:THR378 4.9 48.9 1.0
N A:ASP619 4.9 49.8 1.0
C A:VAL616 5.0 48.6 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: Thu Aug 1 07:54:25 2024

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