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Fluorine in PDB 7d92: Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry)

Enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (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+ and Anthroylouabain (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+ and Anthroylouabain (P4(3)2(1)2 Symmetry), PDB code: 7d92 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) 14.94 / 3.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.234, 84.234, 646.262, 90, 90, 90
R / Rfree (%) 20.9 / 25.7

Other elements in 7d92:

The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (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+ and Anthroylouabain (P4(3)2(1)2 Symmetry) (pdb code 7d92). 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+ and Anthroylouabain (P4(3)2(1)2 Symmetry), PDB code: 7d92:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7d92

Go back to Fluorine Binding Sites List in 7d92
Fluorine binding site 1 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (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+ and Anthroylouabain (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F369

b:165.0
occ:1.00
F1 A:BFD369 0.0 165.0 1.0
BE A:BFD369 1.5 168.9 1.0
F3 A:BFD369 2.5 162.2 1.0
F2 A:BFD369 2.5 161.5 1.0
OD1 A:BFD369 2.5 171.7 1.0
N A:GLY611 2.8 138.5 1.0
OG1 A:THR610 3.0 114.0 1.0
ND2 A:ASN713 3.1 177.1 1.0
CA A:THR610 3.2 134.1 1.0
NZ A:LYS691 3.3 105.6 1.0
C A:THR610 3.4 140.1 1.0
CA A:GLY213 3.6 171.2 1.0
CB A:THR610 3.6 117.2 1.0
CG A:BFD369 3.8 179.4 1.0
CA A:GLY611 3.8 134.9 1.0
O A:THR212 3.9 155.8 1.0
CE A:LYS691 4.0 105.1 1.0
OD2 A:BFD369 4.1 210.2 1.0
O A:HOH1201 4.2 140.2 1.0
O A:GLY213 4.3 176.4 1.0
CG A:ASN713 4.4 174.5 1.0
C A:GLY213 4.4 173.0 1.0
O A:VAL609 4.4 137.8 1.0
N A:GLY213 4.5 166.2 1.0
N A:THR610 4.5 145.2 1.0
O A:THR610 4.5 143.8 1.0
C A:GLY611 4.6 129.1 1.0
C A:THR212 4.6 159.3 1.0
N A:ASP612 4.6 146.2 1.0
MG A:MG1101 4.8 121.8 1.0
N A:THR371 4.9 158.2 1.0
N A:LYS370 4.9 115.7 1.0
OD1 A:ASN713 4.9 177.6 1.0
C A:VAL609 4.9 135.4 1.0
CB A:THR371 5.0 179.6 1.0
CG2 A:THR610 5.0 106.6 1.0

Fluorine binding site 2 out of 3 in 7d92

Go back to Fluorine Binding Sites List in 7d92
Fluorine binding site 2 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (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+ and Anthroylouabain (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F369

b:161.5
occ:1.00
F2 A:BFD369 0.0 161.5 1.0
BE A:BFD369 1.5 168.9 1.0
MG A:MG1101 2.3 121.8 1.0
OD2 A:BFD369 2.4 210.2 1.0
O A:HOH1201 2.4 140.2 1.0
OD1 A:BFD369 2.5 171.7 1.0
F3 A:BFD369 2.5 162.2 1.0
F1 A:BFD369 2.5 165.0 1.0
CG A:BFD369 2.8 179.4 1.0
O A:THR371 3.0 214.0 1.0
ND2 A:ASN713 3.5 177.1 1.0
O A:HOH1202 3.6 149.1 1.0
CB A:THR371 3.7 179.6 1.0
CA A:GLY213 3.8 171.2 1.0
N A:THR371 3.9 158.2 1.0
C A:THR371 3.9 185.1 1.0
CA A:THR371 4.0 170.0 1.0
OD1 A:ASN713 4.2 177.6 1.0
OD1 A:ASP710 4.3 206.1 1.0
CG A:ASN713 4.3 174.5 1.0
CB A:BFD369 4.3 141.9 1.0
OD2 A:ASP714 4.3 139.9 1.0
NZ A:LYS691 4.3 105.6 1.0
O A:SER209 4.4 122.4 1.0
O A:GLY213 4.5 176.4 1.0
OG1 A:THR610 4.5 114.0 1.0
CG2 A:THR371 4.6 178.9 1.0
OG1 A:THR371 4.6 177.7 1.0
N A:LYS370 4.6 115.7 1.0
C A:GLY213 4.7 173.0 1.0
N A:GLY213 4.8 166.2 1.0
C A:LYS370 4.9 139.9 1.0

Fluorine binding site 3 out of 3 in 7d92

Go back to Fluorine Binding Sites List in 7d92
Fluorine binding site 3 out of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (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+ and Anthroylouabain (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F369

b:162.2
occ:1.00
F3 A:BFD369 0.0 162.2 1.0
BE A:BFD369 1.5 168.9 1.0
OG1 A:THR610 2.4 114.0 1.0
N A:THR371 2.4 158.2 1.0
F1 A:BFD369 2.5 165.0 1.0
F2 A:BFD369 2.5 161.5 1.0
OD1 A:BFD369 2.5 171.7 1.0
N A:LYS370 3.1 115.7 1.0
CB A:THR610 3.2 117.2 1.0
CB A:THR371 3.2 179.6 1.0
CG A:BFD369 3.3 179.4 1.0
CA A:THR371 3.3 170.0 1.0
C A:LYS370 3.4 139.9 1.0
OG1 A:THR371 3.4 177.7 1.0
CA A:LYS370 3.5 127.4 1.0
OD2 A:BFD369 3.5 210.2 1.0
CB A:LYS370 3.5 125.4 1.0
CA A:THR610 3.8 134.1 1.0
O A:THR371 3.8 214.0 1.0
O A:GLY213 4.0 176.4 1.0
C A:THR371 4.0 185.1 1.0
C A:BFD369 4.2 104.1 1.0
N A:GLY611 4.2 138.5 1.0
MG A:MG1101 4.3 121.8 1.0
CG A:LYS370 4.3 126.9 1.0
CA A:GLY213 4.5 171.2 1.0
O A:LYS370 4.5 140.0 1.0
CB A:BFD369 4.5 141.9 1.0
CG2 A:THR610 4.5 106.6 1.0
CA A:BFD369 4.6 110.6 1.0
C A:THR610 4.6 140.1 1.0
CG2 A:THR371 4.6 178.9 1.0
C A:GLY213 4.7 173.0 1.0
O A:HOH1201 4.8 140.2 1.0
O A:VAL609 4.8 137.8 1.0
NZ A:LYS691 4.9 105.6 1.0
CD A:LYS370 5.0 127.5 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 06:22:47 2024

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