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Fluorine in PDB 7ddf: Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride

Enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride

All present enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride:
7.2.2.13;

Protein crystallography data

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride, PDB code: 7ddf was solved by H.Ogawa, F.Cornelius, R.Kanai, K.Motoyama, B.Vilsen, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.99 / 4.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 114.481, 118.371, 495.388, 90, 90, 90
R / Rfree (%) 19.4 / 24.2

Other elements in 7ddf:

The structure of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride (pdb code 7ddf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride, PDB code: 7ddf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7ddf

Go back to Fluorine Binding Sites List in 7ddf
Fluorine binding site 1 out of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F369

b:91.1
occ:1.00
 F1 A:BFD369 0.0 91.1 1.0
BE A:BFD369 1.5 92.5 1.0
F3 A:BFD369 2.4 97.8 1.0
F2 A:BFD369 2.5 93.9 1.0
OD1 A:BFD369 2.5 89.8 1.0
ND2 A:ASN713 2.8 93.4 1.0
NZ A:LYS691 3.0 89.5 1.0
N A:GLY611 3.2 102.2 1.0
OG1 A:THR610 3.3 94.7 1.0
O A:HOH1203 3.5 87.1 1.0
CA A:GLY213 3.6 116.7 1.0
CA A:THR610 3.6 98.7 1.0
CE A:LYS691 3.8 87.2 1.0
CG A:BFD369 3.9 86.5 1.0
C A:THR610 3.9 101.0 1.0
CB A:THR610 4.0 96.5 1.0
O A:THR212 4.0 125.6 1.0
CG A:ASN713 4.1 93.8 1.0
CA A:GLY611 4.1 103.5 1.0
OD2 A:BFD369 4.3 85.0 1.0
MG A:MG1101 4.3 96.0 1.0
N A:GLY213 4.4 120.8 1.0
O A:GLY213 4.5 111.6 1.0
C A:THR212 4.5 125.4 1.0
C A:GLY213 4.5 112.8 1.0
OD1 A:ASN713 4.5 95.5 1.0
O A:VAL609 4.7 98.7 1.0
OD1 A:ASP714 4.7 102.7 1.0
C A:GLY611 4.8 104.8 1.0
N A:THR610 4.9 98.3 1.0
N A:ASP612 4.9 110.5 1.0

Fluorine binding site 2 out of 6 in 7ddf

Go back to Fluorine Binding Sites List in 7ddf
Fluorine binding site 2 out of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F369

b:93.9
occ:1.00
 F2 A:BFD369 0.0 93.9 1.0
BE A:BFD369 1.5 92.5 1.0
MG A:MG1101 2.0 96.0 1.0
O A:HOH1203 2.3 87.1 1.0
F1 A:BFD369 2.5 91.1 1.0
F3 A:BFD369 2.5 97.8 1.0
OD1 A:BFD369 2.5 89.8 1.0
OD2 A:BFD369 2.6 85.0 1.0
O A:THR371 2.9 91.9 1.0
CG A:BFD369 3.0 86.5 1.0
O A:HOH1205 3.3 87.4 1.0
CA A:GLY213 3.6 116.7 1.0
CB A:THR371 3.8 118.3 1.0
ND2 A:ASN713 3.8 93.4 1.0
C A:THR371 3.9 100.0 1.0
OD1 A:ASP710 3.9 86.7 1.0
N A:THR371 4.0 110.4 1.0
CA A:THR371 4.1 110.1 1.0
OD1 A:ASN713 4.4 95.5 1.0
O A:GLY213 4.4 111.6 1.0
NZ A:LYS691 4.4 89.5 1.0
CB A:BFD369 4.5 87.1 1.0
OD2 A:ASP714 4.5 102.8 1.0
O A:SER209 4.6 128.2 1.0
C A:GLY213 4.6 112.8 1.0
CG A:ASN713 4.6 93.8 1.0
OG1 A:THR371 4.6 119.8 1.0
N A:GLY213 4.6 120.8 1.0
OG1 A:THR610 4.6 94.7 1.0
CG2 A:THR371 4.7 122.1 1.0
N A:LYS370 4.9 99.9 1.0
CG A:ASP710 4.9 88.0 1.0
C A:LYS370 5.0 109.0 1.0
OD1 A:ASP714 5.0 102.7 1.0

Fluorine binding site 3 out of 6 in 7ddf

Go back to Fluorine Binding Sites List in 7ddf
Fluorine binding site 3 out of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F369

b:97.8
occ:1.00
 F3 A:BFD369 0.0 97.8 1.0
BE A:BFD369 1.5 92.5 1.0
OG1 A:THR610 2.4 94.7 1.0
F1 A:BFD369 2.4 91.1 1.0
F2 A:BFD369 2.5 93.9 1.0
OD1 A:BFD369 2.5 89.8 1.0
N A:THR371 3.0 110.4 1.0
CB A:THR610 3.2 96.5 1.0
CG A:BFD369 3.3 86.5 1.0
N A:LYS370 3.4 99.9 1.0
OD2 A:BFD369 3.4 85.0 1.0
CB A:THR371 3.6 118.3 1.0
OG1 A:THR371 3.7 119.8 1.0
CB A:LYS370 3.7 111.4 1.0
CA A:THR371 3.8 110.1 1.0
CA A:THR610 3.8 98.7 1.0
CA A:LYS370 3.8 107.0 1.0
C A:LYS370 3.8 109.0 1.0
O A:THR371 4.0 91.9 1.0
MG A:MG1101 4.1 96.0 1.0
N A:GLY611 4.1 102.2 1.0
O A:GLY213 4.2 111.6 1.0
C A:THR371 4.4 100.0 1.0
C A:BFD369 4.4 92.5 1.0
O A:HOH1203 4.4 87.1 1.0
CA A:GLY213 4.5 116.7 1.0
CG2 A:THR610 4.5 96.2 1.0
CB A:BFD369 4.5 87.1 1.0
C A:THR610 4.5 101.0 1.0
NZ A:LYS691 4.6 89.5 1.0
CA A:BFD369 4.7 89.1 1.0
NZ A:LYS370 4.7 112.2 1.0
O A:VAL609 4.8 98.7 1.0
CE A:LYS370 4.8 113.8 1.0
C A:GLY213 4.8 112.8 1.0
CG A:LYS370 4.9 114.2 1.0
O A:LYS370 5.0 108.7 1.0
N A:THR610 5.0 98.3 1.0

Fluorine binding site 4 out of 6 in 7ddf

Go back to Fluorine Binding Sites List in 7ddf
Fluorine binding site 4 out of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F369

b:114.1
occ:1.00
 F1 C:BFD369 0.0 114.1 1.0
BE C:BFD369 1.5 113.2 1.0
F3 C:BFD369 2.5 115.2 1.0
F2 C:BFD369 2.5 113.3 1.0
OD1 C:BFD369 2.5 111.5 1.0
ND2 C:ASN713 2.6 125.1 1.0
NZ C:LYS691 3.1 138.6 1.0
OG1 C:THR610 3.2 116.4 1.0
N C:GLY611 3.2 114.8 1.0
CA C:GLY213 3.3 157.2 1.0
O C:HOH1201 3.7 111.3 1.0
CA C:THR610 3.7 112.6 1.0
CE C:LYS691 3.7 137.9 1.0
CG C:ASN713 3.8 124.5 1.0
CG C:BFD369 3.9 108.4 1.0
CB C:THR610 3.9 115.6 1.0
C C:THR610 3.9 114.0 1.0
O C:THR212 4.1 154.4 1.0
CA C:GLY611 4.1 115.7 1.0
N C:GLY213 4.1 155.8 1.0
OD2 C:BFD369 4.3 107.8 1.0
OD1 C:ASN713 4.3 125.2 1.0
C C:GLY213 4.4 158.5 1.0
O C:GLY213 4.4 157.9 1.0
C C:THR212 4.4 154.4 1.0
MG C:MG1101 4.4 113.2 1.0
C C:GLY611 4.8 117.0 1.0
O C:VAL609 4.8 105.0 1.0
OD1 C:ASP714 4.9 119.7 1.0
N C:ASP612 4.9 123.9 1.0
CB C:ASN713 5.0 123.0 1.0
N C:THR610 5.0 108.4 1.0

Fluorine binding site 5 out of 6 in 7ddf

Go back to Fluorine Binding Sites List in 7ddf
Fluorine binding site 5 out of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F369

b:113.3
occ:1.00
 F2 C:BFD369 0.0 113.3 1.0
BE C:BFD369 1.5 113.2 1.0
MG C:MG1101 2.1 113.2 1.0
O C:HOH1201 2.4 111.3 1.0
F3 C:BFD369 2.5 115.2 1.0
F1 C:BFD369 2.5 114.1 1.0
OD1 C:BFD369 2.5 111.5 1.0
OD2 C:BFD369 2.6 107.8 1.0
CG C:BFD369 3.0 108.4 1.0
O C:THR371 3.1 109.5 1.0
O C:HOH1204 3.3 105.9 1.0
CA C:GLY213 3.6 157.2 1.0
ND2 C:ASN713 3.7 125.1 1.0
CB C:THR371 3.8 127.3 1.0
C C:THR371 4.0 113.7 1.0
N C:THR371 4.1 124.0 1.0
OD1 C:ASP710 4.1 106.9 1.0
OD1 C:ASN713 4.2 125.2 1.0
O C:SER209 4.2 134.6 1.0
CA C:THR371 4.2 122.0 1.0
CG C:ASN713 4.3 124.5 1.0
O C:GLY213 4.4 157.9 1.0
NZ C:LYS691 4.4 138.6 1.0
C C:GLY213 4.5 158.5 1.0
CB C:BFD369 4.5 107.2 1.0
OG1 C:THR610 4.5 116.4 1.0
N C:GLY213 4.5 155.8 1.0
OD2 C:ASP714 4.6 120.4 1.0
OG1 C:THR371 4.6 129.5 1.0
CG2 C:THR371 4.8 129.2 1.0
N C:LYS370 4.8 118.8 1.0

Fluorine binding site 6 out of 6 in 7ddf

Go back to Fluorine Binding Sites List in 7ddf
Fluorine binding site 6 out of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F369

b:115.2
occ:1.00
 F3 C:BFD369 0.0 115.2 1.0
BE C:BFD369 1.5 113.2 1.0
OG1 C:THR610 2.3 116.4 1.0
F1 C:BFD369 2.5 114.1 1.0
F2 C:BFD369 2.5 113.3 1.0
OD1 C:BFD369 2.5 111.5 1.0
N C:THR371 3.1 124.0 1.0
CB C:THR610 3.2 115.6 1.0
CG C:BFD369 3.3 108.4 1.0
N C:LYS370 3.4 118.8 1.0
OD2 C:BFD369 3.4 107.8 1.0
CB C:THR371 3.8 127.3 1.0
CB C:LYS370 3.8 123.4 1.0
OG1 C:THR371 3.9 129.5 1.0
CA C:LYS370 3.9 123.0 1.0
CA C:THR610 3.9 112.6 1.0
O C:GLY213 3.9 157.9 1.0
C C:LYS370 4.0 124.8 1.0
CA C:THR371 4.0 122.0 1.0
MG C:MG1101 4.1 113.2 1.0
N C:GLY611 4.2 114.8 1.0
CA C:GLY213 4.2 157.2 1.0
O C:THR371 4.2 109.5 1.0
C C:BFD369 4.4 112.4 1.0
O C:HOH1201 4.4 111.3 1.0
CG2 C:THR610 4.4 116.4 1.0
CB C:BFD369 4.5 107.2 1.0
C C:GLY213 4.5 158.5 1.0
NZ C:LYS691 4.5 138.6 1.0
C C:THR371 4.6 113.7 1.0
C C:THR610 4.6 114.0 1.0
CA C:BFD369 4.6 106.7 1.0
ND2 C:ASN713 4.8 125.1 1.0
O C:VAL609 4.9 105.0 1.0
N C:ASP612 4.9 123.9 1.0
CB C:ASP612 5.0 134.1 1.0

Reference:

R.Kanai, F.Cornelius, H.Ogawa, K.Motoyama, B.Vilsen, C.Toyoshima. Binding of Cardiotonic Steroids to Na + ,K + -Atpase in the E2P State. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33318128
DOI: 10.1073/PNAS.2020438118
Page generated: Fri Aug 2 06:27:01 2024

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