Holmium in PDB 8d87: Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density

The structure of Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density also contains other interesting chemical elements:

Bromine

(Br)

3 atoms

The binding sites of Holmium atom in the Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density (pdb code 8d87). This binding sites where shown within 5.0 Angstroms radius around Holmium atom.
In total 4 binding sites of Holmium where determined in the Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density, PDB code: 8d87:
Jump to Holmium binding site number: 1; 2; 3; 4;

Holmium binding site 1 out of 4 in the Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 1 of Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density within 5.0Å range: probe atom residue distance (Å) B Occ A:Ho402 b:18.6 occ:1.00 OD2 C:ASP188 1.8 16.4 1.0 OD2 A:ASP188 1.8 36.5 1.0 OD2 B:ASP188 1.9 63.5 1.0 OD1 C:ASP188 2.1 18.4 1.0 OD1 A:ASP188 2.2 39.9 1.0 OD1 B:ASP188 2.2 65.0 1.0 CG C:ASP188 2.3 19.2 1.0 CG A:ASP188 2.3 39.9 1.0 CG B:ASP188 2.3 64.6 1.0 O C:HOH506 3.0 32.4 1.0 O A:HOH503 3.7 26.3 1.0 CB C:ASP188 3.8 19.6 1.0 NZ C:LYS176 3.8 36.7 1.0 NZ A:LYS176 3.9 48.7 1.0 CB A:ASP188 3.9 39.7 1.0 NZ B:LYS176 3.9 63.2 1.0 CB B:ASP188 3.9 64.0 1.0 O C:ASP188 4.7 32.5 1.0 O B:ASP188 4.8 84.4 1.0 O A:ASP188 4.8 64.2 1.0 CA C:ASP188 4.8 32.7 1.0 CA A:ASP188 4.9 64.3 1.0 CA B:ASP188 4.9 83.8 1.0 CE C:LYS176 5.0 36.5 1.0

Holmium binding site 2 out of 4 in the Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 2 of Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density within 5.0Å range: probe atom residue distance (Å) B Occ A:Ho403 b:67.5 occ:1.00 N A:ALA391 2.3 181.3 1.0 CA A:ALA391 2.5 182.8 1.0 OXT A:ALA391 2.5 97.7 1.0 C A:ALA391 2.6 182.9 1.0 CB A:ALA391 2.7 97.8 1.0 C A:TYR390 3.3 106.9 1.0 OE2 C:GLU72 3.3 95.4 1.0 O A:ALA391 3.5 183.2 1.0 OE1 C:GLU72 3.7 97.7 1.0 O A:HOH514 3.7 42.9 1.0 O C:HOH526 3.8 40.7 1.0 CD C:GLU72 3.9 97.1 1.0 CA A:TYR390 3.9 104.5 1.0 O A:TYR390 4.2 107.0 1.0 O A:PRO389 4.3 72.8 1.0 CG A:TYR390 4.7 103.7 1.0 CD2 A:TYR390 4.8 104.3 1.0 CB A:TYR390 4.8 103.3 1.0

Holmium binding site 3 out of 4 in the Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 3 of Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density within 5.0Å range: probe atom residue distance (Å) B Occ B:Ho403 b:77.7 occ:1.00 N B:ALA391 2.4 157.1 1.0 OE1 A:GLU72 2.7 133.6 1.0 CA B:ALA391 2.8 158.5 1.0 CB B:ALA391 2.9 86.4 1.0 OXT B:ALA391 3.0 86.3 1.0 C B:ALA391 3.1 159.2 1.0 C B:TYR390 3.4 104.8 1.0 OE2 A:GLU72 3.4 134.2 1.0 CD A:GLU72 3.4 133.1 1.0 O A:HOH539 3.5 42.8 1.0 CA B:TYR390 3.8 103.3 1.0 O B:PRO389 4.1 73.0 1.0 O B:ALA391 4.1 158.8 1.0 O B:TYR390 4.4 104.0 1.0 CG B:TYR390 4.6 101.4 1.0 CB B:TYR390 4.7 100.7 1.0 CD2 B:TYR390 4.8 101.7 1.0 N B:TYR390 4.8 100.3 1.0 C B:PRO389 4.9 72.2 1.0 CG A:GLU72 4.9 132.2 1.0

Holmium binding site 4 out of 4 in the Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density


Mono view


Stereo pair view

A full contact list of Holmium with other atoms in the Ho binding site number 4 of Fitted Crystal Structure of the Homotrimer of Fusion Glycoprotein E1 From Sfv Into Subtomogram Averaged Chikv E1 Glycoprotein Density within 5.0Å range: probe atom residue distance (Å) B Occ C:Ho402 b:69.9 occ:1.00 N C:ALA391 2.4 188.6 1.0 CA C:ALA391 2.7 189.5 1.0 CB C:ALA391 2.8 45.1 1.0 OXT C:ALA391 2.9 44.6 1.0 C C:ALA391 3.0 190.6 1.0 OE1 B:GLU72 3.4 145.9 1.0 C C:TYR390 3.4 90.7 1.0 CA C:TYR390 3.9 87.7 1.0 O C:ALA391 3.9 189.9 1.0 OE2 B:GLU72 4.1 146.4 1.0 CD B:GLU72 4.1 145.6 1.0 O C:PRO389 4.2 58.6 1.0 O C:TYR390 4.4 89.3 1.0 CG C:TYR390 4.8 88.3 1.0 CB C:TYR390 4.8 87.7 1.0 CD2 C:TYR390 4.9 87.6 1.0 N C:TYR390 5.0 84.9 1.0

V.Mangala Prasad, J.S.Blijleven, J.M.Smit, K.K.Lee. Visualization of Conformational Changes and Membrane Remodeling Leading to Genome Delivery By Viral Class-II Fusion Machinery. Nat Commun V. 13 4772 2022.
ISSN: ESSN 2041-1723
PubMed: 35970990
DOI: 10.1038/S41467-022-32431-9