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Fluorine in PDB 3a3y: Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain

Protein crystallography data

The structure of Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain, PDB code: 3a3y was solved by H.Ogawa, T.Shinoda, F.Cornelius, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 222.884, 50.720, 163.342, 90.00, 104.63, 90.00
R / Rfree (%) 24.7 / 29.3

Other elements in 3a3y:

The structure of Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain (pdb code 3a3y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain, PDB code: 3a3y:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3a3y

Go back to Fluorine Binding Sites List in 3a3y
Fluorine binding site 1 out of 4 in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:24.4
occ:1.00
F1 A:MF42001 0.0 24.4 1.0
MG A:MF42001 2.0 23.3 1.0
OD2 A:ASP376 2.6 26.1 1.0
NZ A:LYS698 2.7 27.9 1.0
ND2 A:ASN720 2.9 29.8 1.0
F2 A:MF42001 3.1 23.5 1.0
F4 A:MF42001 3.2 23.9 1.0
F3 A:MF42001 3.4 27.1 1.0
CE A:LYS698 3.4 28.0 1.0
N A:GLY618 3.4 25.6 1.0
CG A:ASP376 3.5 27.0 1.0
O A:HOH5024 3.8 26.1 1.0
O A:THR219 3.8 30.0 1.0
OD1 A:ASP721 3.9 30.6 1.0
CG A:ASN720 3.9 30.2 1.0
CA A:THR617 4.0 24.9 1.0
O A:VAL616 4.1 25.9 1.0
OD1 A:ASN720 4.1 30.6 1.0
C A:THR617 4.2 25.2 1.0
CB A:ASP376 4.2 26.6 1.0
OG1 A:THR617 4.3 23.1 1.0
OD1 A:ASP376 4.3 28.4 1.0
CA A:GLY618 4.3 26.2 1.0
MG A:MG2002 4.4 25.5 1.0
CA A:GLY220 4.6 28.9 1.0
CD A:LYS698 4.7 28.1 1.0
CB A:THR617 4.7 24.4 1.0
C A:THR219 4.7 30.1 1.0
CG A:ASP721 4.8 30.2 1.0
CA A:ASP376 4.8 26.9 1.0
N A:LYS377 4.9 26.6 1.0
OD2 A:ASP721 4.9 30.1 1.0
C A:VAL616 5.0 25.9 1.0
N A:THR617 5.0 25.3 1.0

Fluorine binding site 2 out of 4 in 3a3y

Go back to Fluorine Binding Sites List in 3a3y
Fluorine binding site 2 out of 4 in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:23.5
occ:1.00
F2 A:MF42001 0.0 23.5 1.0
MG A:MG2002 1.9 25.5 1.0
MG A:MF42001 2.0 23.3 1.0
O A:HOH5026 2.5 24.7 1.0
OD2 A:ASP376 2.6 26.1 1.0
O A:HOH5024 2.9 26.1 1.0
F4 A:MF42001 3.1 23.9 1.0
O A:THR378 3.1 26.1 1.0
F1 A:MF42001 3.1 24.4 1.0
OD1 A:ASP376 3.2 28.4 1.0
CG A:ASP376 3.3 27.0 1.0
F3 A:MF42001 3.3 27.1 1.0
O A:GLY220 3.4 28.3 1.0
CB A:THR378 3.5 26.4 1.0
N A:THR378 3.6 26.3 1.0
CA A:GLY220 3.7 28.9 1.0
CA A:THR378 3.8 26.3 1.0
C A:THR378 3.8 26.4 1.0
C A:GLY220 3.9 28.8 1.0
OD2 A:ASP717 4.0 31.2 1.0
OG1 A:THR378 4.2 26.3 1.0
CG2 A:THR378 4.6 26.2 1.0
O A:THR219 4.6 30.0 1.0
OE1 A:GLU221 4.7 30.5 1.0
C A:LYS377 4.7 26.4 1.0
CB A:ASP376 4.7 26.6 1.0
OD1 A:ASN720 4.7 30.6 1.0
ND2 A:ASN720 4.8 29.8 1.0
N A:LYS377 4.8 26.6 1.0
N A:GLY220 4.9 29.6 1.0

Fluorine binding site 3 out of 4 in 3a3y

Go back to Fluorine Binding Sites List in 3a3y
Fluorine binding site 3 out of 4 in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:27.1
occ:1.00
F3 A:MF42001 0.0 27.1 1.0
MG A:MF42001 2.0 23.3 1.0
O A:THR219 2.5 30.0 1.0
OE1 A:GLU221 2.7 30.5 1.0
F2 A:MF42001 3.3 23.5 1.0
F4 A:MF42001 3.4 23.9 1.0
F1 A:MF42001 3.4 24.4 1.0
CD A:GLU221 3.4 30.3 1.0
N A:ASP619 3.4 27.0 1.0
C A:GLY220 3.5 28.8 1.0
OG1 A:THR617 3.5 23.1 1.0
C A:THR219 3.6 30.1 1.0
N A:GLY618 3.6 25.6 1.0
CG A:GLU221 3.6 29.1 1.0
CA A:GLY220 3.6 28.9 1.0
O A:GLY220 3.8 28.3 1.0
C A:GLY618 3.8 26.9 1.0
CA A:GLY618 3.8 26.2 1.0
N A:GLU221 3.9 28.9 1.0
OG1 A:THR378 3.9 26.3 1.0
CB A:ASP619 4.0 27.6 1.0
N A:GLY220 4.1 29.6 1.0
CA A:ASP619 4.1 27.6 1.0
CB A:THR378 4.3 26.4 1.0
OE2 A:GLU221 4.5 31.3 1.0
OD2 A:ASP376 4.5 26.1 1.0
CA A:GLU221 4.6 28.8 1.0
CB A:GLU221 4.6 28.8 1.0
C A:THR617 4.6 25.2 1.0
O A:GLY618 4.7 27.4 1.0
CB A:THR617 4.8 24.4 1.0
CA A:THR219 4.8 30.5 1.0
ND2 A:ASN720 4.8 29.8 1.0
CG A:ASP619 4.9 28.8 1.0
CA A:THR617 4.9 24.9 1.0
N A:THR378 5.0 26.3 1.0

Fluorine binding site 4 out of 4 in 3a3y

Go back to Fluorine Binding Sites List in 3a3y
Fluorine binding site 4 out of 4 in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:23.9
occ:1.00
F4 A:MF42001 0.0 23.9 1.0
MG A:MF42001 2.0 23.3 1.0
OD2 A:ASP376 2.2 26.1 1.0
N A:THR378 2.6 26.3 1.0
N A:LYS377 2.6 26.6 1.0
OG1 A:THR617 2.7 23.1 1.0
CB A:LYS377 3.0 26.0 1.0
CA A:LYS377 3.0 26.2 1.0
F2 A:MF42001 3.1 23.5 1.0
F1 A:MF42001 3.2 24.4 1.0
C A:LYS377 3.3 26.4 1.0
CG A:ASP376 3.3 27.0 1.0
F3 A:MF42001 3.4 27.1 1.0
CB A:THR617 3.4 24.4 1.0
OG1 A:THR378 3.7 26.3 1.0
CA A:THR378 3.7 26.3 1.0
C A:ASP376 3.7 26.9 1.0
CB A:THR378 3.9 26.4 1.0
CA A:THR617 3.9 24.9 1.0
OD1 A:ASP376 4.1 28.4 1.0
CG A:LYS377 4.1 26.7 1.0
CA A:ASP376 4.2 26.9 1.0
CB A:ASP376 4.3 26.6 1.0
MG A:MG2002 4.4 25.5 1.0
N A:GLY618 4.4 25.6 1.0
O A:LYS377 4.5 26.6 1.0
OE1 A:GLU221 4.5 30.5 1.0
O A:VAL616 4.6 25.9 1.0
O A:THR378 4.6 26.1 1.0
CE A:LYS377 4.6 28.4 1.0
C A:THR378 4.6 26.4 1.0
C A:THR617 4.7 25.2 1.0
O A:ASP376 4.8 27.0 1.0
CG2 A:THR617 4.8 23.9 1.0
CD A:LYS377 4.8 28.3 1.0
NZ A:LYS698 4.9 27.9 1.0
N A:THR617 5.0 25.3 1.0

Reference:

H.Ogawa, T.Shinoda, F.Cornelius, C.Toyoshima. Crystal Structure of the Sodium-Potassium Pump (Na+,K+-Atpase) with Bound Potassium and Ouabain. Proc.Natl.Acad.Sci.Usa V. 106 13742 2009.
ISSN: ISSN 0027-8424
PubMed: 19666591
DOI: 10.1073/PNAS.0907054106
Page generated: Sun Dec 13 11:42:50 2020

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