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Fluorine in PDB 5avr: Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min

Protein crystallography data

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min, PDB code: 5avr 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 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 223.127, 50.845, 163.859, 90.00, 104.73, 90.00
R / Rfree (%) 26.5 / 28.1

Other elements in 5avr:

The structure of Kinetics By X-Ray Crystallography: Tl+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Potassium (K) 3 atoms
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 1.5 Min (pdb code 5avr). 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 1.5 Min, PDB code: 5avr:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5avr

Go back to Fluorine Binding Sites List in 5avr
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 1.5 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 1.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:61.9
occ:1.00
 F1 A:MF42001 0.0 61.9 1.0
MG A:MF42001 2.0 62.5 1.0
OD2 A:ASP376 2.4 55.4 1.0
NZ A:LYS698 2.7 58.2 1.0
ND2 A:ASN720 2.9 58.4 1.0
N A:GLY618 3.1 55.0 1.0
F2 A:MF42001 3.2 61.2 1.0
F4 A:MF42001 3.2 59.9 1.0
F3 A:MF42001 3.3 63.1 1.0
O A:THR219 3.4 58.4 1.0
CE A:LYS698 3.6 58.8 1.0
CG A:ASP376 3.6 56.5 1.0
CA A:THR617 3.7 54.5 1.0
C A:THR617 3.9 54.6 1.0
OG1 A:THR617 3.9 54.7 1.0
CG A:ASN720 4.0 59.4 1.0
CA A:GLY618 4.0 55.4 1.0
OD1 A:ASN720 4.2 59.5 1.0
OD1 A:ASP721 4.3 62.0 1.0
CB A:THR617 4.3 54.4 1.0
OD1 A:ASP376 4.3 55.9 1.0
O A:VAL616 4.3 55.8 1.0
C A:THR219 4.3 58.8 1.0
CA A:GLY220 4.4 58.1 1.0
CB A:ASP376 4.6 56.3 1.0
MG A:MG2002 4.6 56.6 1.0
N A:GLY220 4.8 58.2 1.0
N A:THR617 4.8 54.9 1.0
CD A:LYS698 4.9 58.8 1.0
N A:ASP619 4.9 56.5 1.0
C A:GLY618 5.0 56.0 1.0
CA A:ASP376 5.0 56.4 1.0

Fluorine binding site 2 out of 4 in 5avr

Go back to Fluorine Binding Sites List in 5avr
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 1.5 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 1.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:61.2
occ:1.00
 F2 A:MF42001 0.0 61.2 1.0
MG A:MG2002 1.9 56.6 1.0
MG A:MF42001 2.0 62.5 1.0
OD2 A:ASP376 2.6 55.4 1.0
OD1 A:ASP376 2.7 55.9 1.0
O A:THR378 2.9 55.4 1.0
CG A:ASP376 3.1 56.5 1.0
F4 A:MF42001 3.2 59.9 1.0
F1 A:MF42001 3.2 61.9 1.0
CB A:THR378 3.2 55.5 1.0
F3 A:MF42001 3.4 63.1 1.0
N A:THR378 3.5 55.1 1.0
O A:GLY220 3.5 58.1 1.0
CA A:THR378 3.6 55.4 1.0
C A:THR378 3.6 55.7 1.0
CA A:GLY220 3.7 58.1 1.0
OD2 A:ASP717 3.8 60.0 1.0
C A:GLY220 4.0 58.3 1.0
OG1 A:THR378 4.1 55.8 1.0
CG2 A:THR378 4.2 53.5 1.0
C A:LYS377 4.5 55.3 1.0
O A:THR219 4.5 58.4 1.0
CB A:ASP376 4.6 56.3 1.0
N A:LYS377 4.6 55.8 1.0
OE1 A:GLU221 4.7 61.5 1.0
OD1 A:ASN720 4.8 59.5 1.0
CG A:ASP717 4.9 59.1 1.0
N A:GLY220 4.9 58.2 1.0
N A:GLY379 4.9 56.0 1.0
ND2 A:ASN720 4.9 58.4 1.0
OD2 A:ASP721 5.0 61.3 1.0

Fluorine binding site 3 out of 4 in 5avr

Go back to Fluorine Binding Sites List in 5avr
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 1.5 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 1.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:63.1
occ:1.00
 F3 A:MF42001 0.0 63.1 1.0
MG A:MF42001 2.0 62.5 1.0
OE1 A:GLU221 2.4 61.5 1.0
O A:THR219 2.6 58.4 1.0
CD A:GLU221 3.3 60.8 1.0
F1 A:MF42001 3.3 61.9 1.0
F4 A:MF42001 3.3 59.9 1.0
N A:ASP619 3.3 56.5 1.0
OG1 A:THR617 3.3 54.7 1.0
CG A:GLU221 3.4 60.2 1.0
F2 A:MF42001 3.4 61.2 1.0
N A:GLY618 3.7 55.0 1.0
C A:GLY220 3.7 58.3 1.0
C A:THR219 3.7 58.8 1.0
OG1 A:THR378 3.8 55.8 1.0
CB A:ASP619 3.8 57.0 1.0
C A:GLY618 3.8 56.0 1.0
CA A:GLY220 3.9 58.1 1.0
CA A:GLY618 3.9 55.4 1.0
CA A:ASP619 4.0 57.2 1.0
O A:GLY220 4.0 58.1 1.0
N A:GLU221 4.0 58.9 1.0
CB A:THR378 4.0 55.5 1.0
N A:GLY220 4.3 58.2 1.0
OE2 A:GLU221 4.4 62.3 1.0
OD2 A:ASP376 4.5 55.4 1.0
CB A:GLU221 4.5 59.8 1.0
CG A:ASP619 4.6 57.7 1.0
CB A:THR617 4.6 54.4 1.0
CA A:GLU221 4.6 59.6 1.0
O A:GLY618 4.6 56.5 1.0
C A:THR617 4.7 54.6 1.0
N A:THR378 4.9 55.1 1.0
CA A:THR219 4.9 59.0 1.0
CA A:THR617 4.9 54.5 1.0
CG2 A:THR378 5.0 53.5 1.0

Fluorine binding site 4 out of 4 in 5avr

Go back to Fluorine Binding Sites List in 5avr
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 1.5 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 1.5 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:59.9
occ:1.00
 F4 A:MF42001 0.0 59.9 1.0
MG A:MF42001 2.0 62.5 1.0
OD2 A:ASP376 2.5 55.4 1.0
OG1 A:THR617 2.6 54.7 1.0
N A:LYS377 2.6 55.8 1.0
N A:THR378 2.8 55.1 1.0
CB A:THR617 3.0 54.4 1.0
CB A:LYS377 3.1 55.2 1.0
F2 A:MF42001 3.2 61.2 1.0
CA A:LYS377 3.2 55.4 1.0
F1 A:MF42001 3.2 61.9 1.0
F3 A:MF42001 3.3 63.1 1.0
CG A:ASP376 3.3 56.5 1.0
C A:LYS377 3.5 55.3 1.0
CA A:THR617 3.7 54.5 1.0
C A:ASP376 3.8 56.2 1.0
OD1 A:ASP376 3.9 55.9 1.0
OG1 A:THR378 3.9 55.8 1.0
CA A:THR378 4.0 55.4 1.0
CB A:THR378 4.0 55.5 1.0
CA A:ASP376 4.1 56.4 1.0
CG A:LYS377 4.2 54.8 1.0
N A:GLY618 4.3 55.0 1.0
CB A:ASP376 4.3 56.3 1.0
CG2 A:THR617 4.3 54.2 1.0
O A:VAL616 4.5 55.8 1.0
C A:THR617 4.5 54.6 1.0
OE1 A:GLU221 4.5 61.5 1.0
MG A:MG2002 4.6 56.6 1.0
CE A:LYS377 4.6 56.5 1.0
O A:LYS377 4.7 55.3 1.0
N A:THR617 4.8 54.9 1.0
NZ A:LYS698 4.8 58.2 1.0
O A:THR378 4.8 55.4 1.0
O A:ASP376 4.9 56.3 1.0
CD A:LYS377 4.9 55.2 1.0
C A:THR378 4.9 55.7 1.0
N A:ASP619 4.9 56.5 1.0
C A:VAL616 5.0 55.4 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 07:52:15 2024

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