Atomistry » Fluorine » PDB 5avz-5btd » 5aw4
Atomistry »
  Fluorine »
    PDB 5avz-5btd »
      5aw4 »

Fluorine in PDB 5aw4: Kinetics By X-Ray Crystallography: Rb+-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: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min, PDB code: 5aw4 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) 14.96 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 219.821, 50.593, 162.535, 90.00, 104.42, 90.00
R / Rfree (%) 28.6 / 27.5

Other elements in 5aw4:

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

Rubidium (Rb) 3 atoms
Magnesium (Mg) 2 atoms
Potassium (K) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min (pdb code 5aw4). 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: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 1.5 Min, PDB code: 5aw4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5aw4

Go back to Fluorine Binding Sites List in 5aw4
Fluorine binding site 1 out of 4 in the Kinetics By X-Ray Crystallography: Rb+-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: Rb+-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:71.9
occ:1.00
 F1 A:MF42001 0.0 71.9 1.0
MG A:MF42001 2.0 72.5 1.0
OD1 A:ASP376 2.4 65.5 1.0
NZ A:LYS698 2.7 68.2 1.0
ND2 A:ASN720 2.9 68.4 1.0
N A:GLY618 3.1 65.0 1.0
F2 A:MF42001 3.2 71.2 1.0
F4 A:MF42001 3.2 70.0 1.0
F3 A:MF42001 3.3 73.1 1.0
O A:THR219 3.4 68.4 1.0
CE A:LYS698 3.6 68.8 1.0
CG A:ASP376 3.6 66.6 1.0
CA A:THR617 3.7 64.5 1.0
C A:THR617 3.9 64.6 1.0
OG1 A:THR617 3.9 64.7 1.0
CG A:ASN720 4.0 69.4 1.0
CA A:GLY618 4.0 65.5 1.0
OD1 A:ASN720 4.2 69.5 1.0
OD1 A:ASP721 4.3 72.0 1.0
CB A:THR617 4.3 64.5 1.0
OD2 A:ASP376 4.3 65.9 1.0
O A:VAL616 4.3 65.8 1.0
C A:THR219 4.3 68.8 1.0
CA A:GLY220 4.4 68.1 1.0
CB A:ASP376 4.6 66.3 1.0
MG A:MG2002 4.6 66.7 1.0
N A:GLY220 4.8 68.2 1.0
N A:THR617 4.8 65.0 1.0
CD A:LYS698 4.9 68.8 1.0
N A:ASP619 4.9 66.5 1.0
C A:GLY618 5.0 66.1 1.0
CA A:ASP376 5.0 66.5 1.0

Fluorine binding site 2 out of 4 in 5aw4

Go back to Fluorine Binding Sites List in 5aw4
Fluorine binding site 2 out of 4 in the Kinetics By X-Ray Crystallography: Rb+-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: Rb+-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:71.2
occ:1.00
 F2 A:MF42001 0.0 71.2 1.0
MG A:MG2002 1.9 66.7 1.0
MG A:MF42001 2.0 72.5 1.0
OD1 A:ASP376 2.6 65.5 1.0
OD2 A:ASP376 2.7 65.9 1.0
O A:THR378 2.9 65.4 1.0
CG A:ASP376 3.1 66.6 1.0
F4 A:MF42001 3.2 70.0 1.0
F1 A:MF42001 3.2 71.9 1.0
CB A:THR378 3.2 65.5 1.0
F3 A:MF42001 3.4 73.1 1.0
N A:THR378 3.5 65.2 1.0
O A:GLY220 3.5 68.2 1.0
CA A:THR378 3.6 65.4 1.0
C A:THR378 3.6 65.7 1.0
CA A:GLY220 3.7 68.1 1.0
OD1 A:ASP717 3.8 70.0 1.0
C A:GLY220 4.0 68.4 1.0
OG1 A:THR378 4.1 65.8 1.0
CG2 A:THR378 4.2 63.6 1.0
C A:LYS377 4.5 65.3 1.0
O A:THR219 4.5 68.4 1.0
CB A:ASP376 4.6 66.3 1.0
N A:LYS377 4.6 65.8 1.0
OE1 A:GLU221 4.7 71.5 1.0
OD1 A:ASN720 4.8 69.5 1.0
CG A:ASP717 4.9 69.1 1.0
N A:GLY220 4.9 68.2 1.0
N A:GLY379 4.9 66.0 1.0
ND2 A:ASN720 4.9 68.4 1.0
OD2 A:ASP721 5.0 71.3 1.0

Fluorine binding site 3 out of 4 in 5aw4

Go back to Fluorine Binding Sites List in 5aw4
Fluorine binding site 3 out of 4 in the Kinetics By X-Ray Crystallography: Rb+-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: Rb+-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:73.1
occ:1.00
 F3 A:MF42001 0.0 73.1 1.0
MG A:MF42001 2.0 72.5 1.0
OE1 A:GLU221 2.4 71.5 1.0
O A:THR219 2.6 68.4 1.0
CD A:GLU221 3.3 70.8 1.0
F1 A:MF42001 3.3 71.9 1.0
F4 A:MF42001 3.3 70.0 1.0
N A:ASP619 3.3 66.5 1.0
OG1 A:THR617 3.3 64.7 1.0
CG A:GLU221 3.4 70.3 1.0
F2 A:MF42001 3.4 71.2 1.0
N A:GLY618 3.7 65.0 1.0
C A:GLY220 3.7 68.4 1.0
C A:THR219 3.7 68.8 1.0
OG1 A:THR378 3.8 65.8 1.0
CB A:ASP619 3.8 67.0 1.0
C A:GLY618 3.8 66.1 1.0
CA A:GLY220 3.9 68.1 1.0
CA A:GLY618 3.9 65.5 1.0
CA A:ASP619 4.0 67.2 1.0
O A:GLY220 4.0 68.2 1.0
N A:GLU221 4.0 68.9 1.0
CB A:THR378 4.0 65.5 1.0
N A:GLY220 4.3 68.2 1.0
OE2 A:GLU221 4.4 72.4 1.0
OD1 A:ASP376 4.5 65.5 1.0
CB A:GLU221 4.5 69.8 1.0
CG A:ASP619 4.6 67.7 1.0
CB A:THR617 4.6 64.5 1.0
CA A:GLU221 4.6 69.7 1.0
O A:GLY618 4.6 66.6 1.0
C A:THR617 4.7 64.6 1.0
N A:THR378 4.9 65.2 1.0
CA A:THR219 4.9 69.1 1.0
CA A:THR617 4.9 64.5 1.0
CG2 A:THR378 5.0 63.6 1.0

Fluorine binding site 4 out of 4 in 5aw4

Go back to Fluorine Binding Sites List in 5aw4
Fluorine binding site 4 out of 4 in the Kinetics By X-Ray Crystallography: Rb+-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: Rb+-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:70.0
occ:1.00
 F4 A:MF42001 0.0 70.0 1.0
MG A:MF42001 2.0 72.5 1.0
OD1 A:ASP376 2.5 65.5 1.0
OG1 A:THR617 2.6 64.7 1.0
N A:LYS377 2.6 65.8 1.0
N A:THR378 2.8 65.2 1.0
CB A:THR617 3.0 64.5 1.0
CB A:LYS377 3.1 65.2 1.0
F2 A:MF42001 3.2 71.2 1.0
CA A:LYS377 3.2 65.4 1.0
F1 A:MF42001 3.2 71.9 1.0
F3 A:MF42001 3.3 73.1 1.0
CG A:ASP376 3.3 66.6 1.0
C A:LYS377 3.5 65.3 1.0
CA A:THR617 3.7 64.5 1.0
C A:ASP376 3.8 66.3 1.0
OD2 A:ASP376 3.9 65.9 1.0
OG1 A:THR378 3.9 65.8 1.0
CA A:THR378 4.0 65.4 1.0
CB A:THR378 4.0 65.5 1.0
CA A:ASP376 4.1 66.5 1.0
CG A:LYS377 4.2 64.8 1.0
N A:GLY618 4.3 65.0 1.0
CB A:ASP376 4.3 66.3 1.0
CG2 A:THR617 4.3 64.2 1.0
O A:VAL616 4.5 65.8 1.0
C A:THR617 4.5 64.6 1.0
OE1 A:GLU221 4.5 71.5 1.0
MG A:MG2002 4.6 66.7 1.0
CE A:LYS377 4.6 66.6 1.0
O A:LYS377 4.7 65.3 1.0
N A:THR617 4.8 65.0 1.0
NZ A:LYS698 4.8 68.2 1.0
O A:THR378 4.8 65.4 1.0
O A:ASP376 4.9 66.3 1.0
CD A:LYS377 4.9 65.2 1.0
C A:THR378 4.9 65.7 1.0
N A:ASP619 4.9 66.5 1.0
C A:VAL616 5.0 65.4 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: Tue Jul 15 02:25:58 2025

Last articles

Mg in 7N8M
Mg in 7N8L
Mg in 7N8E
Mg in 7N32
Mg in 7N8K
Mg in 7N6I
Mg in 7N78
Mg in 7N77
Mg in 7N73
Mg in 7N74
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy