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Fluorine in PDB 5aw5: Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 2.2 Min

Protein crystallography data

The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 2.2 Min, PDB code: 5aw5 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 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 219.497, 50.543, 162.600, 90.00, 104.10, 90.00
R / Rfree (%) 30.3 / 31.6

Other elements in 5aw5:

The structure of Kinetics By X-Ray Crystallography: Rb+-Substitution of Bound K+ in the E2.MGF42-.2K+ Crystal After 2.2 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 2.2 Min (pdb code 5aw5). 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 2.2 Min, PDB code: 5aw5:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5aw5

Go back to Fluorine Binding Sites List in 5aw5
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 2.2 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 2.2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:72.9
occ:1.00
 F1 A:MF42001 0.0 72.9 1.0
MG A:MF42001 2.0 73.5 1.0
OD1 A:ASP376 2.4 66.4 1.0
NZ A:LYS698 2.7 69.2 1.0
ND2 A:ASN720 2.9 69.4 1.0
N A:GLY618 3.1 66.0 1.0
F2 A:MF42001 3.2 72.2 1.0
F4 A:MF42001 3.2 70.9 1.0
F3 A:MF42001 3.3 74.1 1.0
O A:THR219 3.4 69.4 1.0
CE A:LYS698 3.6 69.8 1.0
CG A:ASP376 3.6 67.6 1.0
CA A:THR617 3.7 65.5 1.0
C A:THR617 3.9 65.6 1.0
OG1 A:THR617 3.9 65.7 1.0
CG A:ASN720 4.0 70.4 1.0
CA A:GLY618 4.0 66.4 1.0
OD1 A:ASN720 4.2 70.5 1.0
OD1 A:ASP721 4.3 73.0 1.0
CB A:THR617 4.3 65.4 1.0
OD2 A:ASP376 4.3 66.9 1.0
O A:VAL616 4.3 66.8 1.0
C A:THR219 4.3 69.8 1.0
CA A:GLY220 4.4 69.1 1.0
CB A:ASP376 4.6 67.3 1.0
MG A:MG2002 4.6 67.7 1.0
N A:GLY220 4.7 69.2 1.0
N A:THR617 4.8 65.9 1.0
CD A:LYS698 4.9 69.8 1.0
N A:ASP619 4.9 67.5 1.0
C A:GLY618 5.0 67.0 1.0
CA A:ASP376 5.0 67.5 1.0

Fluorine binding site 2 out of 4 in 5aw5

Go back to Fluorine Binding Sites List in 5aw5
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 2.2 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 2.2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:72.2
occ:1.00
 F2 A:MF42001 0.0 72.2 1.0
MG A:MG2002 1.9 67.7 1.0
MG A:MF42001 2.0 73.5 1.0
OD1 A:ASP376 2.6 66.4 1.0
OD2 A:ASP376 2.7 66.9 1.0
O A:THR378 2.9 66.4 1.0
CG A:ASP376 3.0 67.6 1.0
F4 A:MF42001 3.2 70.9 1.0
F1 A:MF42001 3.2 72.9 1.0
CB A:THR378 3.2 66.5 1.0
F3 A:MF42001 3.4 74.1 1.0
N A:THR378 3.5 66.1 1.0
O A:GLY220 3.5 69.1 1.0
CA A:THR378 3.6 66.4 1.0
C A:THR378 3.6 66.7 1.0
CA A:GLY220 3.7 69.1 1.0
OD1 A:ASP717 3.8 71.0 1.0
C A:GLY220 4.0 69.3 1.0
OG1 A:THR378 4.1 66.8 1.0
CG2 A:THR378 4.2 64.5 1.0
C A:LYS377 4.5 66.3 1.0
O A:THR219 4.5 69.4 1.0
CB A:ASP376 4.6 67.3 1.0
N A:LYS377 4.6 66.8 1.0
OE1 A:GLU221 4.7 72.5 1.0
OD1 A:ASN720 4.8 70.5 1.0
CG A:ASP717 4.9 70.1 1.0
N A:GLY220 4.9 69.2 1.0
N A:GLY379 4.9 67.0 1.0
ND2 A:ASN720 4.9 69.4 1.0
OD2 A:ASP721 5.0 72.3 1.0

Fluorine binding site 3 out of 4 in 5aw5

Go back to Fluorine Binding Sites List in 5aw5
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 2.2 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 2.2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:74.1
occ:1.00
 F3 A:MF42001 0.0 74.1 1.0
MG A:MF42001 2.0 73.5 1.0
OE1 A:GLU221 2.4 72.5 1.0
O A:THR219 2.6 69.4 1.0
CD A:GLU221 3.3 71.8 1.0
F1 A:MF42001 3.3 72.9 1.0
F4 A:MF42001 3.3 70.9 1.0
N A:ASP619 3.3 67.5 1.0
OG1 A:THR617 3.3 65.7 1.0
CG A:GLU221 3.4 71.2 1.0
F2 A:MF42001 3.4 72.2 1.0
N A:GLY618 3.7 66.0 1.0
C A:GLY220 3.7 69.3 1.0
C A:THR219 3.7 69.8 1.0
OG1 A:THR378 3.8 66.8 1.0
CB A:ASP619 3.8 68.0 1.0
C A:GLY618 3.8 67.0 1.0
CA A:GLY220 3.9 69.1 1.0
CA A:GLY618 3.9 66.4 1.0
CA A:ASP619 4.0 68.2 1.0
O A:GLY220 4.0 69.1 1.0
N A:GLU221 4.0 69.9 1.0
CB A:THR378 4.0 66.5 1.0
N A:GLY220 4.3 69.2 1.0
OE2 A:GLU221 4.4 73.3 1.0
OD1 A:ASP376 4.5 66.4 1.0
CB A:GLU221 4.5 70.8 1.0
CG A:ASP619 4.6 68.7 1.0
CB A:THR617 4.6 65.4 1.0
CA A:GLU221 4.6 70.7 1.0
O A:GLY618 4.6 67.5 1.0
C A:THR617 4.7 65.6 1.0
N A:THR378 4.9 66.1 1.0
CA A:THR219 4.9 70.1 1.0
CA A:THR617 4.9 65.5 1.0
CG2 A:THR378 5.0 64.5 1.0

Fluorine binding site 4 out of 4 in 5aw5

Go back to Fluorine Binding Sites List in 5aw5
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 2.2 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 2.2 Min within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:70.9
occ:1.00
 F4 A:MF42001 0.0 70.9 1.0
MG A:MF42001 2.0 73.5 1.0
OD1 A:ASP376 2.5 66.4 1.0
OG1 A:THR617 2.6 65.7 1.0
N A:LYS377 2.6 66.8 1.0
N A:THR378 2.8 66.1 1.0
CB A:THR617 3.0 65.4 1.0
CB A:LYS377 3.1 66.2 1.0
F2 A:MF42001 3.2 72.2 1.0
CA A:LYS377 3.2 66.4 1.0
F1 A:MF42001 3.2 72.9 1.0
F3 A:MF42001 3.3 74.1 1.0
CG A:ASP376 3.3 67.6 1.0
C A:LYS377 3.5 66.3 1.0
CA A:THR617 3.7 65.5 1.0
C A:ASP376 3.8 67.2 1.0
OD2 A:ASP376 3.9 66.9 1.0
OG1 A:THR378 3.9 66.8 1.0
CA A:THR378 4.0 66.4 1.0
CB A:THR378 4.0 66.5 1.0
CA A:ASP376 4.1 67.5 1.0
CG A:LYS377 4.2 65.8 1.0
N A:GLY618 4.3 66.0 1.0
CB A:ASP376 4.3 67.3 1.0
CG2 A:THR617 4.4 65.2 1.0
O A:VAL616 4.5 66.8 1.0
C A:THR617 4.5 65.6 1.0
OE1 A:GLU221 4.5 72.5 1.0
MG A:MG2002 4.6 67.7 1.0
CE A:LYS377 4.6 67.5 1.0
O A:LYS377 4.7 66.3 1.0
N A:THR617 4.8 65.9 1.0
NZ A:LYS698 4.8 69.2 1.0
O A:THR378 4.8 66.4 1.0
O A:ASP376 4.9 67.3 1.0
CD A:LYS377 4.9 66.2 1.0
C A:THR378 4.9 66.7 1.0
N A:ASP619 4.9 67.5 1.0
C A:VAL616 5.0 66.4 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 07:57:34 2024

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