Atomistry » Fluorine » PDB 5avz-5btd » 5aw0
Atomistry »
  Fluorine »
    PDB 5avz-5btd »
      5aw0 »

Fluorine in PDB 5aw0: 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: 5aw0 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 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.203, 50.994, 164.505, 90.00, 104.77, 90.00
R / Rfree (%) 28.3 / 27.7

Other elements in 5aw0:

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 5aw0). 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: 5aw0:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5aw0

Go back to Fluorine Binding Sites List in 5aw0
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:0.5
occ:1.00
 F1 A:MF42001 0.0 0.5 1.0
MG A:MF42001 2.0 0.1 1.0
OD2 A:ASP376 2.4 98.0 1.0
NZ A:LYS698 2.7 0.8 1.0
ND2 A:ASN720 2.9 1.0 1.0
N A:GLY618 3.1 97.5 1.0
F2 A:MF42001 3.2 0.8 1.0
F4 A:MF42001 3.2 0.5 1.0
F3 A:MF42001 3.3 0.7 1.0
O A:THR219 3.4 1.0 1.0
CE A:LYS698 3.6 0.3 1.0
CG A:ASP376 3.6 99.2 1.0
CA A:THR617 3.7 97.1 1.0
C A:THR617 3.9 97.2 1.0
OG1 A:THR617 3.9 97.3 1.0
CG A:ASN720 4.0 0.0 1.0
CA A:GLY618 4.0 98.0 1.0
OD1 A:ASN720 4.2 0.1 1.0
OD1 A:ASP721 4.3 0.6 1.0
CB A:THR617 4.3 97.0 1.0
OD1 A:ASP376 4.3 98.5 1.0
O A:VAL616 4.3 98.3 1.0
C A:THR219 4.3 0.4 1.0
CA A:GLY220 4.4 0.7 1.0
CB A:ASP376 4.6 98.9 1.0
MG A:MG2002 4.6 99.2 1.0
N A:GLY220 4.7 0.8 1.0
N A:THR617 4.8 97.5 1.0
CD A:LYS698 4.9 0.4 1.0
N A:ASP619 4.9 99.1 1.0
C A:GLY618 5.0 98.6 1.0
CA A:ASP376 5.0 99.0 1.0

Fluorine binding site 2 out of 4 in 5aw0

Go back to Fluorine Binding Sites List in 5aw0
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:0.8
occ:1.00
 F2 A:MF42001 0.0 0.8 1.0
MG A:MG2002 1.9 99.2 1.0
MG A:MF42001 2.0 0.1 1.0
OD2 A:ASP376 2.6 98.0 1.0
OD1 A:ASP376 2.7 98.5 1.0
O A:THR378 2.9 98.0 1.0
CG A:ASP376 3.1 99.2 1.0
F4 A:MF42001 3.2 0.5 1.0
F1 A:MF42001 3.2 0.5 1.0
CB A:THR378 3.2 98.1 1.0
F3 A:MF42001 3.4 0.7 1.0
N A:THR378 3.5 97.7 1.0
O A:GLY220 3.5 0.7 1.0
CA A:THR378 3.6 98.0 1.0
C A:THR378 3.6 98.3 1.0
CA A:GLY220 3.7 0.7 1.0
OD2 A:ASP717 3.8 0.6 1.0
C A:GLY220 4.0 0.9 1.0
OG1 A:THR378 4.1 98.4 1.0
CG2 A:THR378 4.2 96.1 1.0
C A:LYS377 4.5 97.9 1.0
O A:THR219 4.5 1.0 1.0
CB A:ASP376 4.6 98.9 1.0
N A:LYS377 4.6 98.4 1.0
OE1 A:GLU221 4.7 0.1 1.0
OD1 A:ASN720 4.8 0.1 1.0
CG A:ASP717 4.9 0.7 1.0
N A:GLY220 4.9 0.8 1.0
N A:GLY379 4.9 98.6 1.0
ND2 A:ASN720 4.9 1.0 1.0
OD2 A:ASP721 5.0 0.9 1.0

Fluorine binding site 3 out of 4 in 5aw0

Go back to Fluorine Binding Sites List in 5aw0
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:0.7
occ:1.00
 F3 A:MF42001 0.0 0.7 1.0
MG A:MF42001 2.0 0.1 1.0
OE1 A:GLU221 2.4 0.1 1.0
O A:THR219 2.6 1.0 1.0
CD A:GLU221 3.3 0.4 1.0
F1 A:MF42001 3.3 0.5 1.0
F4 A:MF42001 3.3 0.5 1.0
N A:ASP619 3.3 99.1 1.0
OG1 A:THR617 3.3 97.3 1.0
CG A:GLU221 3.4 0.8 1.0
F2 A:MF42001 3.4 0.8 1.0
N A:GLY618 3.7 97.5 1.0
C A:GLY220 3.7 0.9 1.0
C A:THR219 3.7 0.4 1.0
OG1 A:THR378 3.8 98.4 1.0
CB A:ASP619 3.8 99.6 1.0
C A:GLY618 3.8 98.6 1.0
CA A:GLY220 3.9 0.7 1.0
CA A:GLY618 3.9 98.0 1.0
CA A:ASP619 4.0 99.8 1.0
O A:GLY220 4.0 0.7 1.0
N A:GLU221 4.0 0.5 1.0
CB A:THR378 4.0 98.1 1.0
N A:GLY220 4.3 0.8 1.0
OE2 A:GLU221 4.4 0.9 1.0
OD2 A:ASP376 4.5 98.0 1.0
CB A:GLU221 4.5 0.4 1.0
CG A:ASP619 4.6 0.3 1.0
CB A:THR617 4.6 97.0 1.0
CA A:GLU221 4.6 0.2 1.0
O A:GLY618 4.6 99.1 1.0
C A:THR617 4.7 97.2 1.0
N A:THR378 4.9 97.7 1.0
CA A:THR219 4.9 0.7 1.0
CA A:THR617 4.9 97.1 1.0
CG2 A:THR378 5.0 96.1 1.0

Fluorine binding site 4 out of 4 in 5aw0

Go back to Fluorine Binding Sites List in 5aw0
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:0.5
occ:1.00
 F4 A:MF42001 0.0 0.5 1.0
MG A:MF42001 2.0 0.1 1.0
OD2 A:ASP376 2.5 98.0 1.0
OG1 A:THR617 2.6 97.3 1.0
N A:LYS377 2.6 98.4 1.0
N A:THR378 2.8 97.7 1.0
CB A:THR617 3.0 97.0 1.0
CB A:LYS377 3.1 97.8 1.0
F2 A:MF42001 3.2 0.8 1.0
CA A:LYS377 3.2 98.0 1.0
F1 A:MF42001 3.2 0.5 1.0
F3 A:MF42001 3.3 0.7 1.0
CG A:ASP376 3.3 99.2 1.0
C A:LYS377 3.5 97.9 1.0
CA A:THR617 3.7 97.1 1.0
C A:ASP376 3.8 98.8 1.0
OD1 A:ASP376 3.9 98.5 1.0
OG1 A:THR378 3.9 98.4 1.0
CA A:THR378 4.0 98.0 1.0
CB A:THR378 4.0 98.1 1.0
CA A:ASP376 4.1 99.0 1.0
CG A:LYS377 4.2 97.4 1.0
N A:GLY618 4.3 97.5 1.0
CB A:ASP376 4.3 98.9 1.0
CG2 A:THR617 4.4 96.8 1.0
O A:VAL616 4.5 98.3 1.0
C A:THR617 4.5 97.2 1.0
OE1 A:GLU221 4.5 0.1 1.0
MG A:MG2002 4.6 99.2 1.0
CE A:LYS377 4.6 99.1 1.0
O A:LYS377 4.7 97.9 1.0
N A:THR617 4.8 97.5 1.0
NZ A:LYS698 4.8 0.8 1.0
O A:THR378 4.8 98.0 1.0
O A:ASP376 4.9 98.9 1.0
CD A:LYS377 4.9 97.8 1.0
C A:THR378 4.9 98.3 1.0
N A:ASP619 4.9 99.1 1.0
C A:VAL616 5.0 98.0 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 07:57:34 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy