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Fluorine in PDB 3kdp: 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: 3kdp was solved by J.P.Morth, B.P.Pedersen, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.86 / 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 (%) 24.2 / 28.6

Other elements in 3kdp:

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 3kdp). 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: 3kdp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3kdp

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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:91.1
occ:1.00
 F1 A:MF42001 0.0 91.1 1.0
MG A:MF42001 1.5 93.0 1.0
F2 A:MF42001 2.3 97.2 1.0
F3 A:MF42001 2.4 92.7 1.0
F4 A:MF42001 2.4 88.8 1.0
OD1 A:ASP369 2.8 83.3 1.0
NZ A:LYS691 2.9 57.5 1.0
CG A:ASP369 2.9 84.2 1.0
OD2 A:ASP369 3.2 86.4 1.0
CA A:THR610 3.4 72.5 1.0
N A:GLY611 3.5 60.0 1.0
OG1 A:THR610 3.6 75.0 1.0
ND2 A:ASN713 3.6 60.3 1.0
CE A:LYS691 3.7 57.2 1.0
O A:VAL609 3.8 59.6 1.0
CB A:ASP369 3.8 81.7 1.0
CA A:ASP369 3.9 75.8 1.0
CB A:THR610 4.0 72.8 1.0
C A:THR610 4.0 71.9 1.0
OD1 A:ASN713 4.2 74.4 1.0
N A:LYS370 4.2 0.8 1.0
CG A:ASN713 4.4 69.8 1.0
N A:THR610 4.4 72.0 1.0
MG A:MG2002 4.5 33.1 1.0
C A:VAL609 4.5 56.7 1.0
C A:ASP369 4.6 74.9 1.0
OD1 A:ASP714 4.6 72.5 1.0
CA A:GLY611 4.6 61.3 1.0
O A:THR212 4.7 61.9 1.0
N A:THR371 4.9 67.8 1.0
OD2 A:ASP714 5.0 82.1 1.0

Fluorine binding site 2 out of 8 in 3kdp

Go back to Fluorine Binding Sites List in 3kdp
Fluorine binding site 2 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 2 of Crystal Structure of the Sodium-Potassium Pump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:97.2
occ:1.00
 F2 A:MF42001 0.0 97.2 1.0
MG A:MF42001 1.5 93.0 1.0
OD1 A:ASP369 2.2 83.3 1.0
F1 A:MF42001 2.3 91.1 1.0
MG A:MG2002 2.4 33.1 1.0
F3 A:MF42001 2.4 92.7 1.0
F4 A:MF42001 2.4 88.8 1.0
OD2 A:ASP369 2.5 86.4 1.0
CG A:ASP369 2.7 84.2 1.0
O A:THR371 3.6 79.8 1.0
CB A:THR371 3.6 74.5 1.0
CA A:GLY213 3.8 67.6 1.0
CG2 A:THR371 3.8 80.3 1.0
OD1 A:ASN713 3.8 74.4 1.0
O A:GLY213 4.0 74.6 1.0
N A:THR371 4.1 67.8 1.0
CB A:ASP369 4.1 81.7 1.0
CA A:THR371 4.2 73.3 1.0
C A:GLY213 4.2 71.3 1.0
OD2 A:ASP710 4.3 64.9 1.0
ND2 A:ASN713 4.3 60.3 1.0
C A:THR371 4.3 78.3 1.0
CG A:ASN713 4.4 69.8 1.0
OE1 A:GLU214 4.6 66.7 1.0
O A:THR212 4.6 61.9 1.0
OG1 A:THR610 4.7 75.0 1.0
N A:LYS370 4.7 0.8 1.0
OG1 A:THR371 4.7 72.9 1.0
CA A:ASP369 4.8 75.8 1.0
OD2 A:ASP714 4.8 82.1 1.0
N A:GLY213 5.0 65.7 1.0

Fluorine binding site 3 out of 8 in 3kdp

Go back to Fluorine Binding Sites List in 3kdp
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:92.7
occ:1.00
 F3 A:MF42001 0.0 92.7 1.0
MG A:MF42001 1.5 93.0 1.0
F2 A:MF42001 2.4 97.2 1.0
F1 A:MF42001 2.4 91.1 1.0
F4 A:MF42001 2.5 88.8 1.0
O A:THR212 2.7 61.9 1.0
OE1 A:GLU214 3.0 66.7 1.0
N A:GLY611 3.3 60.0 1.0
CA A:GLY213 3.4 67.6 1.0
OG1 A:THR610 3.6 75.0 1.0
C A:THR212 3.7 67.3 1.0
CA A:GLY611 3.8 61.3 1.0
ND2 A:ASN713 3.9 60.3 1.0
C A:GLY611 4.0 63.2 1.0
C A:GLY213 4.0 71.3 1.0
N A:ASP612 4.0 75.2 1.0
N A:GLY213 4.0 65.7 1.0
OD1 A:ASP369 4.0 83.3 1.0
CD A:GLU214 4.2 71.2 1.0
C A:THR610 4.3 71.9 1.0
CB A:THR371 4.4 74.5 1.0
CA A:THR610 4.4 72.5 1.0
O A:GLY213 4.4 74.6 1.0
O A:GLY611 4.6 65.7 1.0
CG A:ASN713 4.6 69.8 1.0
OD2 A:ASP369 4.6 86.4 1.0
CB A:THR610 4.6 72.8 1.0
CG A:ASP369 4.6 84.2 1.0
N A:GLU214 4.6 88.6 1.0
MG A:MG2002 4.6 33.1 1.0
OD1 A:ASN713 4.6 74.4 1.0
OE2 A:GLU214 4.8 76.1 1.0
NZ A:LYS691 4.9 57.5 1.0
CA A:ASP612 4.9 76.1 1.0
CG2 A:THR371 4.9 80.3 1.0
CB A:ASP612 4.9 79.2 1.0
OG1 A:THR371 4.9 72.9 1.0

Fluorine binding site 4 out of 8 in 3kdp

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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:88.8
occ:1.00
 F4 A:MF42001 0.0 88.8 1.0
MG A:MF42001 1.5 93.0 1.0
F1 A:MF42001 2.4 91.1 1.0
OG1 A:THR610 2.4 75.0 1.0
F2 A:MF42001 2.4 97.2 1.0
F3 A:MF42001 2.5 92.7 1.0
OD1 A:ASP369 2.5 83.3 1.0
N A:THR371 2.9 67.8 1.0
CB A:THR371 3.3 74.5 1.0
N A:LYS370 3.3 0.8 1.0
CB A:THR610 3.5 72.8 1.0
CG A:ASP369 3.6 84.2 1.0
CA A:THR371 3.6 73.3 1.0
CB A:LYS370 3.8 0.3 1.0
C A:LYS370 3.8 0.4 1.0
CA A:LYS370 3.9 0.7 1.0
CA A:THR610 3.9 72.5 1.0
OG1 A:THR371 4.0 72.9 1.0
OE1 A:GLU214 4.1 66.7 1.0
OD2 A:ASP369 4.2 86.4 1.0
N A:GLY611 4.2 60.0 1.0
C A:ASP369 4.2 74.9 1.0
O A:THR371 4.3 79.8 1.0
CG2 A:THR371 4.3 80.3 1.0
MG A:MG2002 4.4 33.1 1.0
CA A:ASP369 4.4 75.8 1.0
C A:THR371 4.5 78.3 1.0
CE A:LYS370 4.5 1.0 1.0
C A:THR610 4.5 71.9 1.0
CB A:ASP369 4.6 81.7 1.0
CG A:LYS370 4.7 0.4 1.0
N A:ASP612 4.8 75.2 1.0
CG2 A:THR610 4.8 71.0 1.0
CB A:ASP612 4.8 79.2 1.0
CD A:GLU214 4.9 71.2 1.0
O A:LYS370 5.0 0.7 1.0
OE2 A:GLU214 5.0 76.1 1.0

Fluorine binding site 5 out of 8 in 3kdp

Go back to Fluorine Binding Sites List in 3kdp
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:95.5
occ:1.00
 F1 C:MF42001 0.0 95.5 1.0
MG C:MF42001 1.5 97.6 1.0
F3 C:MF42001 2.4 99.2 1.0
F2 C:MF42001 2.4 0.8 1.0
F4 C:MF42001 2.4 91.9 1.0
OD1 C:ASP369 2.8 80.8 1.0
NZ C:LYS691 2.9 70.0 1.0
CG C:ASP369 2.9 82.4 1.0
OD2 C:ASP369 3.3 86.8 1.0
CA C:THR610 3.4 71.4 1.0
OG1 C:THR610 3.5 73.9 1.0
N C:GLY611 3.5 75.9 1.0
ND2 C:ASN713 3.7 49.7 1.0
O C:VAL609 3.7 62.8 1.0
CB C:ASP369 3.8 78.2 1.0
CE C:LYS691 3.8 71.6 1.0
CA C:ASP369 3.9 71.4 1.0
CB C:THR610 3.9 71.2 1.0
C C:THR610 4.0 72.9 1.0
N C:LYS370 4.2 74.0 1.0
OD1 C:ASN713 4.2 64.9 1.0
CG C:ASN713 4.4 61.2 1.0
N C:THR610 4.4 70.1 1.0
MG C:MG2002 4.5 32.5 1.0
C C:VAL609 4.5 60.1 1.0
OD1 C:ASP714 4.5 64.4 1.0
C C:ASP369 4.5 69.8 1.0
O C:THR212 4.7 62.6 1.0
CA C:GLY611 4.7 79.7 1.0
N C:THR371 4.9 62.9 1.0
OD2 C:ASP714 4.9 75.2 1.0

Fluorine binding site 6 out of 8 in 3kdp

Go back to Fluorine Binding Sites List in 3kdp
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:0.8
occ:1.00
 F2 C:MF42001 0.0 0.8 1.0
MG C:MF42001 1.5 97.6 1.0
OD1 C:ASP369 2.2 80.8 1.0
MG C:MG2002 2.3 32.5 1.0
F3 C:MF42001 2.4 99.2 1.0
F1 C:MF42001 2.4 95.5 1.0
F4 C:MF42001 2.4 91.9 1.0
OD2 C:ASP369 2.5 86.8 1.0
CG C:ASP369 2.7 82.4 1.0
O C:THR371 3.5 77.0 1.0
CB C:THR371 3.5 72.1 1.0
CG2 C:THR371 3.7 79.9 1.0
CA C:GLY213 3.8 63.7 1.0
OD1 C:ASN713 3.9 64.9 1.0
O C:GLY213 4.0 69.5 1.0
N C:THR371 4.0 62.9 1.0
CA C:THR371 4.1 69.1 1.0
CB C:ASP369 4.2 78.2 1.0
C C:THR371 4.2 74.6 1.0
OD2 C:ASP710 4.2 68.1 1.0
C C:GLY213 4.2 67.4 1.0
ND2 C:ASN713 4.4 49.7 1.0
CG C:ASN713 4.5 61.2 1.0
O C:THR212 4.6 62.6 1.0
OG1 C:THR371 4.7 70.5 1.0
OE1 C:GLU214 4.7 42.0 1.0
OG1 C:THR610 4.7 73.9 1.0
N C:LYS370 4.7 74.0 1.0
CA C:ASP369 4.8 71.4 1.0
OD2 C:ASP714 4.8 75.2 1.0
C C:LYS370 5.0 77.2 1.0

Fluorine binding site 7 out of 8 in 3kdp

Go back to Fluorine Binding Sites List in 3kdp
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:99.2
occ:1.00
 F3 C:MF42001 0.0 99.2 1.0
MG C:MF42001 1.5 97.6 1.0
F2 C:MF42001 2.4 0.8 1.0
F1 C:MF42001 2.4 95.5 1.0
F4 C:MF42001 2.5 91.9 1.0
O C:THR212 2.7 62.6 1.0
OE1 C:GLU214 3.1 42.0 1.0
CA C:GLY213 3.3 63.7 1.0
N C:GLY611 3.3 75.9 1.0
OG1 C:THR610 3.6 73.9 1.0
C C:THR212 3.7 70.8 1.0
ND2 C:ASN713 3.9 49.7 1.0
CA C:GLY611 3.9 79.7 1.0
C C:GLY213 4.0 67.4 1.0
N C:GLY213 4.0 64.1 1.0
C C:GLY611 4.0 82.7 1.0
OD1 C:ASP369 4.0 80.8 1.0
N C:ASP612 4.1 61.3 1.0
CD C:GLU214 4.2 47.1 1.0
C C:THR610 4.3 72.9 1.0
CB C:THR371 4.3 72.1 1.0
O C:GLY213 4.4 69.5 1.0
CA C:THR610 4.4 71.4 1.0
CG C:ASN713 4.6 61.2 1.0
O C:GLY611 4.6 87.2 1.0
MG C:MG2002 4.6 32.5 1.0
CG C:ASP369 4.6 82.4 1.0
OD2 C:ASP369 4.6 86.8 1.0
N C:GLU214 4.6 70.2 1.0
OD1 C:ASN713 4.6 64.9 1.0
CB C:THR610 4.6 71.2 1.0
OE2 C:GLU214 4.8 50.6 1.0
CG2 C:THR371 4.8 79.9 1.0
OG1 C:THR371 4.9 70.5 1.0
CA C:ASP612 4.9 63.4 1.0
CB C:ASP612 4.9 64.5 1.0
NZ C:LYS691 4.9 70.0 1.0

Fluorine binding site 8 out of 8 in 3kdp

Go back to Fluorine Binding Sites List in 3kdp
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:91.9
occ:1.00
 F4 C:MF42001 0.0 91.9 1.0
MG C:MF42001 1.5 97.6 1.0
F2 C:MF42001 2.4 0.8 1.0
F1 C:MF42001 2.4 95.5 1.0
OG1 C:THR610 2.4 73.9 1.0
F3 C:MF42001 2.5 99.2 1.0
OD1 C:ASP369 2.6 80.8 1.0
N C:THR371 2.9 62.9 1.0
CB C:THR371 3.2 72.1 1.0
N C:LYS370 3.4 74.0 1.0
CB C:THR610 3.5 71.2 1.0
CA C:THR371 3.6 69.1 1.0
CG C:ASP369 3.6 82.4 1.0
CB C:LYS370 3.8 73.1 1.0
C C:LYS370 3.8 77.2 1.0
CA C:LYS370 3.9 73.5 1.0
OG1 C:THR371 3.9 70.5 1.0
CA C:THR610 4.0 71.4 1.0
OE1 C:GLU214 4.1 42.0 1.0
OD2 C:ASP369 4.2 86.8 1.0
O C:THR371 4.2 77.0 1.0
C C:ASP369 4.2 69.8 1.0
N C:GLY611 4.3 75.9 1.0
CG2 C:THR371 4.3 79.9 1.0
MG C:MG2002 4.4 32.5 1.0
C C:THR371 4.4 74.6 1.0
CA C:ASP369 4.5 71.4 1.0
CE C:LYS370 4.5 79.4 1.0
C C:THR610 4.6 72.9 1.0
CB C:ASP369 4.6 78.2 1.0
CG C:LYS370 4.7 74.3 1.0
CG2 C:THR610 4.8 70.9 1.0
N C:ASP612 4.8 61.3 1.0
CB C:ASP612 4.8 64.5 1.0
OE2 C:GLU214 4.9 50.6 1.0
CD C:GLU214 4.9 47.1 1.0
O C:LYS370 4.9 77.8 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: Wed Jul 31 19:51:21 2024

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