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Fluorine in PDB 3b8e: Crystal Structure of the Sodium-Potassium Pump

Enzymatic activity of Crystal Structure of the Sodium-Potassium Pump

All present enzymatic activity of Crystal Structure of the Sodium-Potassium Pump:
3.6.3.9;

Protein crystallography data

The structure of Crystal Structure of the Sodium-Potassium Pump, PDB code: 3b8e was solved by J.P.Morth, P.B.Pedersen, M.S.Toustrup-Jensen, T.L.M.Soerensen, J.Petersen, J.P.Andersen, B.Vilsen, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.930, 261.500, 334.780, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.3

Other elements in 3b8e:

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

Rubidium (Rb) 6 atoms
Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Sodium-Potassium Pump (pdb code 3b8e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of the Sodium-Potassium Pump, PDB code: 3b8e:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3b8e

Go back to Fluorine Binding Sites List in 3b8e
Fluorine binding site 1 out of 8 in the Crystal Structure of the Sodium-Potassium Pump


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:98.1
occ:1.00
 F1 A:MF42001 0.0 98.1 1.0
MG A:MF42001 1.5 98.1 1.0
F2 A:MF42001 2.4 98.1 1.0
F3 A:MF42001 2.4 98.1 1.0
F4 A:MF42001 2.4 98.1 1.0
NZ A:LYS691 2.8 68.6 1.0
CG A:ASP369 3.1 88.3 1.0
OD2 A:ASP369 3.1 88.3 1.0
OD1 A:ASP369 3.3 88.3 1.0
ND2 A:ASN713 3.4 95.6 1.0
O A:VAL609 3.4 68.0 1.0
CA A:THR610 3.4 78.1 1.0
N A:GLY611 3.5 83.6 1.0
OG1 A:THR610 3.7 51.1 1.0
CB A:ASP369 3.8 88.3 1.0
CA A:ASP369 3.9 0.5 1.0
CE A:LYS691 4.0 68.6 1.0
CB A:THR610 4.0 51.1 1.0
C A:THR610 4.0 78.1 1.0
C A:VAL609 4.3 68.0 1.0
CG A:ASN713 4.3 95.6 1.0
N A:THR610 4.3 78.1 1.0
OD1 A:ASP714 4.4 89.9 1.0
OD1 A:ASN713 4.4 95.6 1.0
N A:LYS370 4.4 0.7 1.0
MG A:MG2002 4.6 98.1 1.0
C A:ASP369 4.6 0.5 1.0
CA A:GLY611 4.7 83.6 1.0
O A:THR212 4.9 50.2 1.0
CD A:LYS691 4.9 68.6 1.0

Fluorine binding site 2 out of 8 in 3b8e

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Fluorine binding site 2 out of 8 in the Crystal Structure of the Sodium-Potassium Pump


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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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:98.1
occ:1.00
 F2 A:MF42001 0.0 98.1 1.0
MG A:MF42001 1.5 98.1 1.0
F3 A:MF42001 2.4 98.1 1.0
F1 A:MF42001 2.4 98.1 1.0
F4 A:MF42001 2.4 98.1 1.0
MG A:MG2002 2.5 98.1 1.0
OD2 A:ASP369 2.5 88.3 1.0
OD1 A:ASP369 2.6 88.3 1.0
CG A:ASP369 2.8 88.3 1.0
O A:GLY213 3.6 65.8 1.0
CA A:GLY213 3.6 65.8 1.0
O A:THR371 3.6 67.9 1.0
C A:GLY213 3.8 65.8 1.0
ND2 A:ASN713 3.9 95.6 1.0
OD1 A:ASN713 4.1 95.6 1.0
OE1 A:GLU214 4.1 0.5 1.0
CB A:THR371 4.1 0.0 1.0
OD2 A:ASP710 4.2 85.9 1.0
CB A:ASP369 4.3 88.3 1.0
CG A:ASN713 4.4 95.6 1.0
N A:THR371 4.5 67.9 1.0
O A:THR212 4.5 50.2 1.0
C A:THR371 4.5 67.9 1.0
CA A:THR371 4.6 67.9 1.0
OG1 A:THR610 4.6 51.1 1.0
N A:GLY213 4.8 65.8 1.0
CA A:ASP369 4.9 0.5 1.0
N A:GLU214 4.9 61.2 1.0
OD1 A:ASP710 4.9 85.9 1.0
CG2 A:THR371 4.9 0.0 1.0
OG1 A:THR371 4.9 0.0 1.0
N A:GLY611 5.0 83.6 1.0
CG A:ASP710 5.0 85.9 1.0

Fluorine binding site 3 out of 8 in 3b8e

Go back to Fluorine Binding Sites List in 3b8e
Fluorine binding site 3 out of 8 in the Crystal Structure of the Sodium-Potassium Pump


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:98.1
occ:1.00
 F3 A:MF42001 0.0 98.1 1.0
MG A:MF42001 1.5 98.1 1.0
F2 A:MF42001 2.4 98.1 1.0
F1 A:MF42001 2.4 98.1 1.0
F4 A:MF42001 2.4 98.1 1.0
N A:GLY611 2.8 83.6 1.0
OG1 A:THR610 3.0 51.1 1.0
O A:THR212 3.2 50.2 1.0
N A:ASP612 3.4 55.8 1.0
OE1 A:GLU214 3.4 0.5 1.0
CA A:GLY611 3.5 83.6 1.0
C A:GLY611 3.8 83.6 1.0
C A:THR610 3.8 78.1 1.0
CA A:THR610 3.9 78.1 1.0
CA A:GLY213 3.9 65.8 1.0
ND2 A:ASN713 4.0 95.6 1.0
CB A:THR610 4.0 51.1 1.0
C A:GLY213 4.2 65.8 1.0
OD2 A:ASP369 4.2 88.3 1.0
C A:THR212 4.2 50.2 1.0
CA A:ASP612 4.4 55.8 1.0
O A:GLY213 4.5 65.8 1.0
CB A:ASP612 4.5 78.3 1.0
CD A:GLU214 4.5 0.5 1.0
N A:GLY213 4.6 65.8 1.0
N A:GLU214 4.6 61.2 1.0
CG A:ASP369 4.7 88.3 1.0
OD1 A:ASP369 4.7 88.3 1.0
O A:GLY611 4.8 83.6 1.0
MG A:MG2002 4.8 98.1 1.0
NZ A:LYS691 4.8 68.6 1.0
CB A:THR371 4.9 0.0 1.0
O A:THR610 4.9 78.1 1.0
CG A:GLU214 5.0 0.5 1.0
OG1 A:THR371 5.0 0.0 1.0

Fluorine binding site 4 out of 8 in 3b8e

Go back to Fluorine Binding Sites List in 3b8e
Fluorine binding site 4 out of 8 in the Crystal Structure of the Sodium-Potassium Pump


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:98.1
occ:1.00
 F4 A:MF42001 0.0 98.1 1.0
MG A:MF42001 1.5 98.1 1.0
F2 A:MF42001 2.4 98.1 1.0
F1 A:MF42001 2.4 98.1 1.0
OD2 A:ASP369 2.4 88.3 1.0
F3 A:MF42001 2.4 98.1 1.0
OG1 A:THR610 2.6 51.1 1.0
N A:THR371 3.1 67.9 1.0
N A:LYS370 3.2 0.7 1.0
CG A:ASP369 3.3 88.3 1.0
CB A:THR610 3.4 51.1 1.0
CB A:THR371 3.7 0.0 1.0
CB A:LYS370 3.8 83.2 1.0
CA A:LYS370 3.8 0.7 1.0
C A:ASP369 3.8 0.5 1.0
CA A:THR610 3.9 78.1 1.0
C A:LYS370 3.9 0.7 1.0
CA A:THR371 3.9 67.9 1.0
OD1 A:ASP369 3.9 88.3 1.0
OG1 A:THR371 4.0 0.0 1.0
CA A:ASP369 4.0 0.5 1.0
O A:THR371 4.1 67.9 1.0
OE1 A:GLU214 4.1 0.5 1.0
N A:GLY611 4.2 83.6 1.0
CB A:ASP369 4.3 88.3 1.0
MG A:MG2002 4.3 98.1 1.0
C A:THR371 4.5 67.9 1.0
O A:VAL609 4.5 68.0 1.0
C A:THR610 4.6 78.1 1.0
O A:ASP369 4.7 0.5 1.0
N A:ASP612 4.8 55.8 1.0
CG2 A:THR610 4.8 51.1 1.0
CE A:LYS370 4.9 83.2 1.0
CB A:ASP612 4.9 78.3 1.0
CG A:LYS370 5.0 83.2 1.0
O A:LYS370 5.0 0.7 1.0
N A:THR610 5.0 78.1 1.0

Fluorine binding site 5 out of 8 in 3b8e

Go back to Fluorine Binding Sites List in 3b8e
Fluorine binding site 5 out of 8 in the Crystal Structure of the Sodium-Potassium Pump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Sodium-Potassium Pump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2001

b:98.1
occ:1.00
 F1 C:MF42001 0.0 98.1 1.0
MG C:MF42001 1.5 98.1 1.0
F4 C:MF42001 2.4 98.1 1.0
F2 C:MF42001 2.4 98.1 1.0
F3 C:MF42001 2.4 98.1 1.0
NZ C:LYS691 2.8 72.9 1.0
CG C:ASP369 3.1 72.4 1.0
OD2 C:ASP369 3.1 72.4 1.0
OD1 C:ASP369 3.3 72.4 1.0
ND2 C:ASN713 3.4 74.0 1.0
O C:VAL609 3.4 66.4 1.0
CA C:THR610 3.5 48.5 1.0
N C:GLY611 3.6 71.3 1.0
OG1 C:THR610 3.7 60.8 1.0
CB C:ASP369 3.8 72.4 1.0
CA C:ASP369 3.9 97.3 1.0
CB C:THR610 4.0 60.8 1.0
CE C:LYS691 4.0 72.9 1.0
C C:THR610 4.1 48.5 1.0
C C:VAL609 4.3 66.4 1.0
OD1 C:ASP714 4.3 85.5 1.0
CG C:ASN713 4.3 74.0 1.0
N C:THR610 4.3 48.5 1.0
OD1 C:ASN713 4.4 74.0 1.0
N C:LYS370 4.4 0.1 1.0
MG C:MG2002 4.6 98.1 1.0
C C:ASP369 4.6 97.3 1.0
CA C:GLY611 4.7 71.3 1.0
O C:THR212 4.9 71.4 1.0
CD C:LYS691 5.0 72.9 1.0

Fluorine binding site 6 out of 8 in 3b8e

Go back to Fluorine Binding Sites List in 3b8e
Fluorine binding site 6 out of 8 in the Crystal Structure of the Sodium-Potassium Pump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Sodium-Potassium Pump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2001

b:98.1
occ:1.00
 F2 C:MF42001 0.0 98.1 1.0
MG C:MF42001 1.5 98.1 1.0
F3 C:MF42001 2.4 98.1 1.0
F4 C:MF42001 2.4 98.1 1.0
F1 C:MF42001 2.4 98.1 1.0
MG C:MG2002 2.5 98.1 1.0
OD2 C:ASP369 2.5 72.4 1.0
OD1 C:ASP369 2.6 72.4 1.0
CG C:ASP369 2.8 72.4 1.0
O C:GLY213 3.6 73.8 1.0
CA C:GLY213 3.6 73.8 1.0
O C:THR371 3.6 75.8 1.0
C C:GLY213 3.8 73.8 1.0
ND2 C:ASN713 3.9 74.0 1.0
CB C:THR371 4.1 0.5 1.0
OE1 C:GLU214 4.1 0.1 1.0
OD1 C:ASN713 4.1 74.0 1.0
OD2 C:ASP710 4.2 85.4 1.0
CB C:ASP369 4.3 72.4 1.0
CG C:ASN713 4.4 74.0 1.0
N C:THR371 4.5 75.8 1.0
C C:THR371 4.5 75.8 1.0
O C:THR212 4.5 71.4 1.0
CA C:THR371 4.6 75.8 1.0
OG1 C:THR610 4.6 60.8 1.0
N C:GLY213 4.8 73.8 1.0
CA C:ASP369 4.9 97.3 1.0
N C:GLU214 4.9 59.0 1.0
OD1 C:ASP710 4.9 85.4 1.0
CG2 C:THR371 4.9 0.5 1.0
OG1 C:THR371 4.9 0.5 1.0
CG C:ASP710 5.0 85.4 1.0
N C:GLY611 5.0 71.3 1.0

Fluorine binding site 7 out of 8 in 3b8e

Go back to Fluorine Binding Sites List in 3b8e
Fluorine binding site 7 out of 8 in the Crystal Structure of the Sodium-Potassium Pump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the Sodium-Potassium Pump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2001

b:98.1
occ:1.00
 F3 C:MF42001 0.0 98.1 1.0
MG C:MF42001 1.5 98.1 1.0
F2 C:MF42001 2.4 98.1 1.0
F4 C:MF42001 2.4 98.1 1.0
F1 C:MF42001 2.4 98.1 1.0
N C:GLY611 2.8 71.3 1.0
OG1 C:THR610 3.1 60.8 1.0
O C:THR212 3.2 71.4 1.0
OE1 C:GLU214 3.4 0.1 1.0
N C:ASP612 3.4 40.1 1.0
CA C:GLY611 3.5 71.3 1.0
C C:GLY611 3.8 71.3 1.0
C C:THR610 3.8 48.5 1.0
CA C:GLY213 3.9 73.8 1.0
CA C:THR610 3.9 48.5 1.0
ND2 C:ASN713 4.1 74.0 1.0
CB C:THR610 4.1 60.8 1.0
C C:GLY213 4.1 73.8 1.0
OD2 C:ASP369 4.2 72.4 1.0
C C:THR212 4.2 71.4 1.0
CA C:ASP612 4.4 40.1 1.0
CD C:GLU214 4.4 0.1 1.0
CB C:ASP612 4.4 77.5 1.0
O C:GLY213 4.4 73.8 1.0
N C:GLY213 4.6 73.8 1.0
N C:GLU214 4.6 59.0 1.0
CG C:ASP369 4.7 72.4 1.0
OD1 C:ASP369 4.7 72.4 1.0
O C:GLY611 4.8 71.3 1.0
MG C:MG2002 4.8 98.1 1.0
CB C:THR371 4.8 0.5 1.0
NZ C:LYS691 4.9 72.9 1.0
CG C:GLU214 4.9 0.1 1.0
O C:THR610 4.9 48.5 1.0
OG1 C:THR371 5.0 0.5 1.0

Fluorine binding site 8 out of 8 in 3b8e

Go back to Fluorine Binding Sites List in 3b8e
Fluorine binding site 8 out of 8 in the Crystal Structure of the Sodium-Potassium Pump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the Sodium-Potassium Pump within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2001

b:98.1
occ:1.00
 F4 C:MF42001 0.0 98.1 1.0
MG C:MF42001 1.5 98.1 1.0
F2 C:MF42001 2.4 98.1 1.0
F3 C:MF42001 2.4 98.1 1.0
F1 C:MF42001 2.4 98.1 1.0
OD2 C:ASP369 2.4 72.4 1.0
OG1 C:THR610 2.6 60.8 1.0
N C:THR371 3.1 75.8 1.0
N C:LYS370 3.2 0.1 1.0
CG C:ASP369 3.3 72.4 1.0
CB C:THR610 3.4 60.8 1.0
CB C:THR371 3.7 0.5 1.0
CB C:LYS370 3.8 59.4 1.0
CA C:LYS370 3.8 0.1 1.0
CA C:THR371 3.9 75.8 1.0
C C:ASP369 3.9 97.3 1.0
C C:LYS370 3.9 0.1 1.0
CA C:THR610 3.9 48.5 1.0
OD1 C:ASP369 3.9 72.4 1.0
OG1 C:THR371 4.0 0.5 1.0
O C:THR371 4.0 75.8 1.0
CA C:ASP369 4.1 97.3 1.0
OE1 C:GLU214 4.1 0.1 1.0
MG C:MG2002 4.3 98.1 1.0
N C:GLY611 4.3 71.3 1.0
CB C:ASP369 4.3 72.4 1.0
C C:THR371 4.4 75.8 1.0
O C:VAL609 4.5 66.4 1.0
C C:THR610 4.6 48.5 1.0
N C:ASP612 4.7 40.1 1.0
O C:ASP369 4.8 97.3 1.0
CG2 C:THR610 4.8 60.8 1.0
CE C:LYS370 4.9 59.4 1.0
CB C:ASP612 4.9 77.5 1.0
CG C:LYS370 5.0 59.4 1.0
O C:LYS370 5.0 0.1 1.0
N C:THR610 5.0 48.5 1.0

Reference:

J.P.Morth, B.P.Pedersen, M.S.Toustrup-Jensen, T.L.Sorensen, J.Petersen, J.P.Andersen, B.Vilsen, P.Nissen. Crystal Structure of the Sodium-Potassium Pump. Nature V. 450 1043 2007.
ISSN: ISSN 0028-0836
PubMed: 18075585
DOI: 10.1038/NATURE06419
Page generated: Mon Jul 14 15:17:06 2025

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