Fluorine in PDB 8zyj: Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form

Enzymatic activity of Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form

All present enzymatic activity of Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form:
7.2.2.13;

Other elements in 8zyj:

The structure of Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form also contains other interesting chemical elements:

Sodium (Na) 1 atom
Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form (pdb code 8zyj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form, PDB code: 8zyj:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8zyj

Go back to Fluorine Binding Sites List in 8zyj
Fluorine binding site 1 out of 3 in the Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F384

b:48.0
occ:1.00
 F1 A:BFD384 0.0 48.0 1.0
BE A:BFD384 1.8 24.2 1.0
MG A:MG1101 1.9 36.7 1.0
O A:HOH1277 2.4 36.0 1.0
OD2 A:BFD384 2.5 32.3 1.0
O A:HOH1204 2.7 39.4 1.0
OD1 A:BFD384 2.8 39.1 1.0
O A:THR386 2.8 33.0 1.0
F3 A:BFD384 2.9 48.4 1.0
F2 A:BFD384 3.0 42.0 1.0
CG A:BFD384 3.0 32.1 1.0
CB A:THR386 3.6 26.6 1.0
CA A:GLY228 3.6 26.3 1.0
C A:THR386 3.7 33.2 1.0
N A:THR386 3.7 34.9 1.0
CA A:THR386 3.8 20.9 1.0
O A:SER224 3.8 38.2 1.0
OD1 A:ASP723 4.1 35.0 1.0
ND2 A:ASN726 4.2 33.3 1.0
OD1 A:ASN726 4.3 36.7 1.0
OG1 A:THR386 4.4 30.1 1.0
N A:GLY228 4.4 35.4 1.0
CB A:BFD384 4.5 23.2 1.0
OD2 A:ASP727 4.5 49.7 1.0
CG2 A:THR386 4.5 31.3 1.0
C A:GLY228 4.6 38.8 1.0
C A:LYS385 4.6 27.2 1.0
O A:GLY228 4.6 44.3 1.0
CG A:ASN726 4.7 34.9 1.0
N A:LYS385 4.8 27.4 1.0
NZ A:LYS704 4.9 33.3 1.0
N A:GLY387 4.9 22.8 1.0
C A:SER224 5.0 35.1 1.0

Fluorine binding site 2 out of 3 in 8zyj

Go back to Fluorine Binding Sites List in 8zyj
Fluorine binding site 2 out of 3 in the Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F384

b:42.0
occ:1.00
 F2 A:BFD384 0.0 42.0 1.0
BE A:BFD384 1.8 24.2 1.0
OG1 A:THR623 2.2 43.1 1.0
OD1 A:BFD384 2.7 39.1 1.0
N A:THR386 2.9 34.9 1.0
F3 A:BFD384 2.9 48.4 1.0
F1 A:BFD384 3.0 48.0 1.0
CB A:THR623 3.2 32.9 1.0
N A:LYS385 3.3 27.4 1.0
OG1 A:THR386 3.4 30.1 1.0
CG A:BFD384 3.6 32.1 1.0
CB A:THR386 3.6 26.6 1.0
CB A:LYS385 3.7 21.6 1.0
C A:LYS385 3.7 27.2 1.0
CA A:LYS385 3.7 19.5 1.0
CA A:THR623 3.7 29.8 1.0
CA A:THR386 3.8 20.9 1.0
OD2 A:BFD384 3.8 32.3 1.0
O A:GLY228 3.9 44.3 1.0
N A:GLY624 4.0 26.7 1.0
CA A:GLY228 4.0 26.3 1.0
C A:BFD384 4.4 34.7 1.0
C A:THR623 4.4 29.1 1.0
O A:THR386 4.4 33.0 1.0
MG A:MG1101 4.4 36.7 1.0
C A:GLY228 4.4 38.8 1.0
NZ A:LYS385 4.5 33.3 1.0
CG2 A:THR623 4.5 29.6 1.0
CE A:LYS385 4.6 28.9 1.0
CG A:LYS385 4.6 27.1 1.0
C A:THR386 4.6 33.2 1.0
CB A:BFD384 4.7 23.2 1.0
CA A:BFD384 4.7 30.1 1.0
N A:ASP625 4.8 42.9 1.0
CB A:ASP625 4.8 38.4 1.0
O A:LYS385 4.8 35.6 1.0
O A:VAL622 4.8 45.6 1.0
NZ A:LYS704 4.9 33.3 1.0
N A:THR623 5.0 33.7 1.0

Fluorine binding site 3 out of 3 in 8zyj

Go back to Fluorine Binding Sites List in 8zyj
Fluorine binding site 3 out of 3 in the Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of Human Testis-Specific Na+,K+-Atpase ALPHA4 in Ouabain-Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F384

b:48.4
occ:1.00
 F3 A:BFD384 0.0 48.4 1.0
BE A:BFD384 1.7 24.2 1.0
ND2 A:ASN726 2.5 33.3 1.0
OD1 A:BFD384 2.8 39.1 1.0
F1 A:BFD384 2.9 48.0 1.0
F2 A:BFD384 2.9 42.0 1.0
N A:GLY624 3.1 26.7 1.0
CA A:GLY228 3.2 26.3 1.0
NZ A:LYS704 3.2 33.3 1.0
CG A:ASN726 3.7 34.9 1.0
N A:GLY228 3.8 35.4 1.0
CA A:GLY624 3.8 24.3 1.0
OG1 A:THR623 3.8 43.1 1.0
O A:THR227 3.9 50.0 1.0
CG A:BFD384 4.0 32.1 1.0
C A:THR623 4.0 29.1 1.0
CA A:THR623 4.0 29.8 1.0
C A:THR227 4.1 40.3 1.0
OD1 A:ASN726 4.1 36.7 1.0
CE A:LYS704 4.1 36.7 1.0
O A:HOH1204 4.3 39.4 1.0
OD2 A:BFD384 4.3 32.3 1.0
C A:GLY228 4.4 38.8 1.0
CB A:THR623 4.5 32.9 1.0
MG A:MG1101 4.5 36.7 1.0
O A:GLY228 4.6 44.3 1.0
C A:GLY624 4.6 35.7 1.0
N A:ASP625 4.9 42.9 1.0
CB A:ASN726 4.9 28.6 1.0
O A:HOH1277 5.0 36.0 1.0
OD1 A:ASP727 5.0 47.5 1.0

Reference:

K.Abe, J.Mcdermott, H.V.Madapally, P.Marimuthu, C.C.Gopalasingam, C.Gerle, H.Shigematsu, H.Khandelia, G.Blanco. Molecular Structure of the Na+,K+-Atpase ALPHA4BETA1 Isoform in Its Ouabain-Bound Conformation. Int J Mol Sci V. 25 2024.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS252212397
Page generated: Tue Dec 10 19:58:53 2024

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