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Fluorine in PDB 5avz: Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 55 Min

Protein crystallography data

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 55 Min, PDB code: 5avz 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 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 222.704, 50.914, 164.695, 90.00, 104.52, 90.00
R / Rfree (%) 29.7 / 29.8

Other elements in 5avz:

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 55 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 55 Min (pdb code 5avz). 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 55 Min, PDB code: 5avz:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5avz

Go back to Fluorine Binding Sites List in 5avz
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 55 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 55 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:99.8
occ:1.00
 F1 A:MF42001 0.0 99.8 1.0
MG A:MF42001 2.0 0.4 1.0
OD2 A:ASP376 2.4 93.3 1.0
NZ A:LYS698 2.7 96.1 1.0
ND2 A:ASN720 2.9 96.3 1.0
N A:GLY618 3.1 92.9 1.0
F2 A:MF42001 3.2 99.1 1.0
F4 A:MF42001 3.2 97.8 1.0
F3 A:MF42001 3.3 0.0 1.0
O A:THR219 3.4 96.3 1.0
CE A:LYS698 3.6 96.7 1.0
CG A:ASP376 3.6 94.5 1.0
CA A:THR617 3.7 92.4 1.0
C A:THR617 3.9 92.5 1.0
OG1 A:THR617 3.9 92.6 1.0
CG A:ASN720 4.0 97.3 1.0
CA A:GLY618 4.0 93.3 1.0
OD1 A:ASN720 4.2 97.4 1.0
OD1 A:ASP721 4.3 99.9 1.0
CB A:THR617 4.3 92.3 1.0
OD1 A:ASP376 4.3 93.8 1.0
O A:VAL616 4.3 93.7 1.0
C A:THR219 4.3 96.7 1.0
CA A:GLY220 4.4 96.0 1.0
CB A:ASP376 4.6 94.2 1.0
MG A:MG2002 4.6 94.6 1.0
N A:GLY220 4.7 96.1 1.0
N A:THR617 4.8 92.8 1.0
CD A:LYS698 4.9 96.7 1.0
N A:ASP619 4.9 94.4 1.0
C A:GLY618 5.0 93.9 1.0
CA A:ASP376 5.0 94.3 1.0

Fluorine binding site 2 out of 4 in 5avz

Go back to Fluorine Binding Sites List in 5avz
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 55 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 55 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:99.1
occ:1.00
 F2 A:MF42001 0.0 99.1 1.0
MG A:MG2002 1.9 94.6 1.0
MG A:MF42001 2.0 0.4 1.0
OD2 A:ASP376 2.6 93.3 1.0
OD1 A:ASP376 2.7 93.8 1.0
O A:THR378 2.9 93.3 1.0
CG A:ASP376 3.1 94.5 1.0
F4 A:MF42001 3.2 97.8 1.0
F1 A:MF42001 3.2 99.8 1.0
CB A:THR378 3.2 93.4 1.0
F3 A:MF42001 3.4 0.0 1.0
N A:THR378 3.5 93.0 1.0
O A:GLY220 3.5 96.0 1.0
CA A:THR378 3.6 93.3 1.0
C A:THR378 3.6 93.6 1.0
CA A:GLY220 3.7 96.0 1.0
OD2 A:ASP717 3.8 97.9 1.0
C A:GLY220 4.0 96.2 1.0
OG1 A:THR378 4.1 93.7 1.0
CG2 A:THR378 4.2 91.4 1.0
C A:LYS377 4.5 93.2 1.0
O A:THR219 4.5 96.3 1.0
CB A:ASP376 4.6 94.2 1.0
N A:LYS377 4.6 93.7 1.0
OE1 A:GLU221 4.7 99.4 1.0
OD1 A:ASN720 4.8 97.4 1.0
CG A:ASP717 4.9 97.0 1.0
N A:GLY220 4.9 96.1 1.0
ND2 A:ASN720 4.9 96.3 1.0
N A:GLY379 4.9 93.9 1.0
OD2 A:ASP721 5.0 99.2 1.0

Fluorine binding site 3 out of 4 in 5avz

Go back to Fluorine Binding Sites List in 5avz
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 55 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 55 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:0.0
occ:1.00
 F3 A:MF42001 0.0 0.0 1.0
MG A:MF42001 2.0 0.4 1.0
OE1 A:GLU221 2.4 99.4 1.0
O A:THR219 2.6 96.3 1.0
CD A:GLU221 3.3 98.7 1.0
F1 A:MF42001 3.3 99.8 1.0
F4 A:MF42001 3.3 97.8 1.0
N A:ASP619 3.3 94.4 1.0
OG1 A:THR617 3.3 92.6 1.0
CG A:GLU221 3.4 98.1 1.0
F2 A:MF42001 3.4 99.1 1.0
N A:GLY618 3.7 92.9 1.0
C A:GLY220 3.7 96.2 1.0
C A:THR219 3.7 96.7 1.0
OG1 A:THR378 3.8 93.7 1.0
CB A:ASP619 3.8 94.9 1.0
C A:GLY618 3.8 93.9 1.0
CA A:GLY220 3.9 96.0 1.0
CA A:GLY618 3.9 93.3 1.0
CA A:ASP619 4.0 95.1 1.0
O A:GLY220 4.0 96.0 1.0
N A:GLU221 4.0 96.8 1.0
CB A:THR378 4.0 93.4 1.0
N A:GLY220 4.3 96.1 1.0
OE2 A:GLU221 4.4 0.2 1.0
OD2 A:ASP376 4.5 93.3 1.0
CB A:GLU221 4.5 97.7 1.0
CG A:ASP619 4.6 95.6 1.0
CB A:THR617 4.6 92.3 1.0
CA A:GLU221 4.6 97.6 1.0
O A:GLY618 4.6 94.4 1.0
C A:THR617 4.7 92.5 1.0
N A:THR378 4.9 93.0 1.0
CA A:THR219 4.9 97.0 1.0
CA A:THR617 4.9 92.4 1.0
CG2 A:THR378 5.0 91.4 1.0

Fluorine binding site 4 out of 4 in 5avz

Go back to Fluorine Binding Sites List in 5avz
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 55 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 55 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:97.8
occ:1.00
 F4 A:MF42001 0.0 97.8 1.0
MG A:MF42001 2.0 0.4 1.0
OD2 A:ASP376 2.5 93.3 1.0
OG1 A:THR617 2.6 92.6 1.0
N A:LYS377 2.6 93.7 1.0
N A:THR378 2.8 93.0 1.0
CB A:THR617 3.0 92.3 1.0
CB A:LYS377 3.1 93.1 1.0
F2 A:MF42001 3.2 99.1 1.0
CA A:LYS377 3.2 93.3 1.0
F1 A:MF42001 3.2 99.8 1.0
F3 A:MF42001 3.3 0.0 1.0
CG A:ASP376 3.3 94.5 1.0
C A:LYS377 3.5 93.2 1.0
CA A:THR617 3.7 92.4 1.0
C A:ASP376 3.8 94.1 1.0
OG1 A:THR378 3.9 93.7 1.0
OD1 A:ASP376 3.9 93.8 1.0
CA A:THR378 4.0 93.3 1.0
CB A:THR378 4.0 93.4 1.0
CA A:ASP376 4.1 94.3 1.0
CG A:LYS377 4.2 92.7 1.0
N A:GLY618 4.3 92.9 1.0
CB A:ASP376 4.3 94.2 1.0
CG2 A:THR617 4.3 92.1 1.0
O A:VAL616 4.5 93.7 1.0
C A:THR617 4.5 92.5 1.0
OE1 A:GLU221 4.5 99.4 1.0
MG A:MG2002 4.6 94.6 1.0
CE A:LYS377 4.6 94.5 1.0
O A:LYS377 4.7 93.2 1.0
N A:THR617 4.8 92.8 1.0
NZ A:LYS698 4.8 96.1 1.0
O A:THR378 4.8 93.3 1.0
O A:ASP376 4.9 94.2 1.0
CD A:LYS377 4.9 93.1 1.0
C A:THR378 4.9 93.6 1.0
N A:ASP619 4.9 94.4 1.0
C A:VAL616 5.0 93.3 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: Tue Jul 15 02:24:46 2025

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