Fluorine in PDB 7d91: Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry)

Enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry)

All present enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry):
7.2.2.13;

Protein crystallography data

The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry), PDB code: 7d91 was solved by R.Kanai, F.Cornelius, H.Ogawa, 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) 14.95 / 3.35
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.325, 84.325, 646.36, 90, 90, 90
R / Rfree (%) 21.5 / 26

Other elements in 7d91:

The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry) (pdb code 7d91). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry), PDB code: 7d91:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7d91

Go back to Fluorine Binding Sites List in 7d91
Fluorine binding site 1 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry)


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 Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F369

b:67.1
occ:1.00
F1 A:BFD369 0.0 67.1 1.0
BE A:BFD369 1.5 76.3 1.0
F3 A:BFD369 2.5 71.2 1.0
F2 A:BFD369 2.5 87.9 1.0
OD1 A:BFD369 2.5 48.3 1.0
N A:GLY611 2.8 75.7 1.0
OG1 A:THR610 3.1 73.6 1.0
NZ A:LYS691 3.2 55.3 1.0
CA A:THR610 3.2 77.5 1.0
ND2 A:ASN713 3.2 81.1 1.0
C A:THR610 3.4 69.9 1.0
CB A:THR610 3.7 71.5 1.0
CA A:GLY611 3.8 73.9 1.0
CA A:GLY213 3.8 96.1 1.0
CG A:BFD369 3.8 46.9 1.0
CE A:LYS691 3.9 51.9 1.0
O A:THR212 4.2 107.4 1.0
OD2 A:BFD369 4.2 56.9 1.0
O A:HOH1201 4.4 68.5 1.0
O A:VAL609 4.4 56.0 1.0
O A:GLY213 4.4 103.6 1.0
N A:THR610 4.5 80.1 1.0
CG A:ASN713 4.5 64.3 1.0
O A:THR610 4.5 57.0 1.0
N A:ASP612 4.6 66.8 1.0
C A:GLY213 4.6 102.0 1.0
C A:GLY611 4.6 62.9 1.0
MG A:MG1101 4.6 55.0 1.0
N A:GLY213 4.7 102.4 1.0
N A:LYS370 4.8 55.4 1.0
N A:THR371 4.8 57.9 1.0
C A:THR212 4.9 106.2 1.0
C A:VAL609 4.9 63.0 1.0
OD1 A:ASN713 5.0 57.1 1.0

Fluorine binding site 2 out of 3 in 7d91

Go back to Fluorine Binding Sites List in 7d91
Fluorine binding site 2 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry)


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 Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F369

b:87.9
occ:1.00
F2 A:BFD369 0.0 87.9 1.0
BE A:BFD369 1.5 76.3 1.0
MG A:MG1101 2.2 55.0 1.0
O A:HOH1201 2.4 68.5 1.0
OD1 A:BFD369 2.5 48.3 1.0
F1 A:BFD369 2.5 67.1 1.0
F3 A:BFD369 2.5 71.2 1.0
OD2 A:BFD369 2.5 56.9 1.0
CG A:BFD369 2.9 46.9 1.0
O A:THR371 3.1 87.1 1.0
ND2 A:ASN713 3.4 81.1 1.0
O A:HOH1204 3.5 111.1 1.0
CA A:GLY213 3.9 96.1 1.0
OD1 A:ASN713 4.0 57.1 1.0
CB A:THR371 4.0 63.4 1.0
C A:THR371 4.1 65.8 1.0
N A:THR371 4.1 57.9 1.0
NZ A:LYS691 4.1 55.3 1.0
OD1 A:ASP710 4.1 70.8 1.0
OD2 A:ASP714 4.2 71.9 1.0
CG A:ASN713 4.2 64.3 1.0
CA A:THR371 4.3 56.8 1.0
CB A:BFD369 4.3 46.8 1.0
O A:SER209 4.6 67.5 1.0
O A:GLY213 4.7 103.6 1.0
N A:LYS370 4.8 55.4 1.0
OD1 A:ASP714 4.8 57.1 1.0
CG2 A:THR371 4.8 53.6 1.0
C A:GLY213 4.9 102.0 1.0
OG1 A:THR610 4.9 73.6 1.0
N A:GLY213 4.9 102.4 1.0
OG1 A:THR371 4.9 82.9 1.0
CG A:ASP714 4.9 55.7 1.0

Fluorine binding site 3 out of 3 in 7d91

Go back to Fluorine Binding Sites List in 7d91
Fluorine binding site 3 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry)


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 Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F369

b:71.2
occ:1.00
F3 A:BFD369 0.0 71.2 1.0
BE A:BFD369 1.5 76.3 1.0
N A:THR371 2.4 57.9 1.0
F1 A:BFD369 2.5 67.1 1.0
OD1 A:BFD369 2.5 48.3 1.0
F2 A:BFD369 2.5 87.9 1.0
OG1 A:THR610 2.9 73.6 1.0
N A:LYS370 3.1 55.4 1.0
CB A:THR371 3.2 63.4 1.0
CA A:THR371 3.2 56.8 1.0
CG A:BFD369 3.2 46.9 1.0
C A:LYS370 3.3 56.0 1.0
OD2 A:BFD369 3.4 56.9 1.0
CA A:LYS370 3.4 52.0 1.0
OG1 A:THR371 3.5 82.9 1.0
O A:THR371 3.6 87.1 1.0
CB A:LYS370 3.6 49.4 1.0
CB A:THR610 3.6 71.5 1.0
C A:THR371 3.8 65.8 1.0
MG A:MG1101 4.0 55.0 1.0
CA A:THR610 4.0 77.5 1.0
C A:BFD369 4.1 53.2 1.0
O A:GLY213 4.1 103.6 1.0
N A:GLY611 4.3 75.7 1.0
CG A:LYS370 4.4 52.5 1.0
O A:LYS370 4.4 58.0 1.0
CB A:BFD369 4.5 46.8 1.0
CA A:BFD369 4.5 46.9 1.0
CA A:GLY213 4.6 96.1 1.0
CG2 A:THR371 4.6 53.6 1.0
O A:HOH1201 4.7 68.5 1.0
C A:THR610 4.8 69.9 1.0
NZ A:LYS691 4.8 55.3 1.0
C A:GLY213 4.9 102.0 1.0
O A:VAL609 4.9 56.0 1.0
CD A:LYS370 5.0 50.9 1.0
CG2 A:THR610 5.0 59.4 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: Wed Mar 3 13:33:41 2021

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