Chlorine in PDB 6y6a: Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid

The structure of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid, PDB code: 6y6a was solved by L.J.Stroh, N.H.Rustmeier, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.94 / 2.65
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	86.496, 172.063, 245.616, 107.09, 97.93, 93.93
R / Rfree (%)	24.5 / 26.7

The structure of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 53;

Binding sites:

The binding sites of Chlorine atom in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid (pdb code 6y6a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 53 binding sites of Chlorine where determined in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid, PDB code: 6y6a:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 53 in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:45.4 occ:1.00 O B:HOH578 3.0 18.8 1.0 CD2 A:PHE263 4.7 16.5 1.0 CE2 A:PHE263 4.7 16.4 1.0 CG A:TYR272 5.0 23.3 1.0 CD2 A:TYR272 5.0 24.4 1.0 CG A:PHE53 5.0 23.0 1.0

Chlorine binding site 2 out of 53 in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl402 b:52.7 occ:1.00 O B:TYR42 3.1 29.7 1.0 O B:HOH569 3.8 25.1 1.0 C B:TYR42 4.3 33.4 1.0 N B:TYR42 4.5 35.4 1.0 CD2 B:LEU43 4.8 28.9 1.0 CB B:ALA79 4.9 30.9 1.0 CE1 B:TYR42 4.9 47.4 1.0 CD1 B:TYR42 4.9 45.5 1.0 CD1 B:ILE81 4.9 40.3 1.0 CB B:ALA41 5.0 35.2 1.0

Chlorine binding site 3 out of 53 in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl402 b:46.4 occ:1.00 O C:HOH566 2.7 41.8 1.0 O C:HOH603 3.7 15.5 1.0 O C:HOH588 4.7 19.4 1.0 CE2 C:PHE141 4.8 13.4 1.0 O C:HIS139 5.0 14.9 1.0

Chlorine binding site 4 out of 53 in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl403 b:41.2 occ:1.00 CD2 C:PHE263 4.5 17.5 1.0 CD2 C:TYR272 4.6 21.5 1.0 CE2 C:PHE263 4.6 18.1 1.0 CD2 C:PHE53 4.8 16.7 1.0 CE2 C:TYR272 4.8 21.7 1.0 CG C:PHE53 4.8 16.6 1.0 CG C:TYR272 4.8 21.8 1.0

Chlorine binding site 5 out of 53 in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl404 b:47.1 occ:1.00 OE1 C:GLU40 4.3 40.7 1.0 CD2 C:TYR42 4.5 27.7 1.0 CE2 C:TYR42 4.5 28.5 1.0 CB C:GLU40 4.7 27.4 1.0 CB D:SER206 5.0 20.7 1.0

Chlorine binding site 6 out of 53 in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl301 b:36.4 occ:1.00 O D:HOH460 3.0 17.8 1.0 O D:HIS139 4.2 19.9 1.0 C D:HIS139 4.7 20.0 1.0 CB D:HIS139 4.8 18.4 1.0 O D:PHE214 4.8 14.7 1.0 CB D:SER216 4.9 18.2 1.0 N D:SER216 4.9 18.4 1.0 CD2 D:PHE141 5.0 21.6 1.0 CE2 D:PHE141 5.0 21.9 1.0 NH1 D:ARG278 5.0 25.4 1.0

Chlorine binding site 7 out of 53 in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl402 b:47.3 occ:1.00 O F:HOH594 3.6 9.2 1.0 O F:HOH569 3.7 9.7 1.0 CD1 F:LEU246 4.5 22.6 1.0 O F:ILE24 4.6 51.5 1.0 OD1 F:ASN210 4.8 17.8 1.0 CG2 F:VAL26 4.9 35.3 1.0

Chlorine binding site 8 out of 53 in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl403 b:46.0 occ:1.00 O G:HOH547 3.3 15.2 1.0 CG F:PHE53 4.8 23.3 1.0 CD2 F:PHE263 4.8 25.3 1.0 CD2 F:PHE53 4.8 23.1 1.0 CE2 F:PHE263 4.8 25.7 1.0

Chlorine binding site 9 out of 53 in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl402 b:58.3 occ:1.00 O G:HIS139 4.3 23.0 1.0 O G:PHE214 4.6 23.3 1.0 CE2 G:PHE141 4.7 29.6 1.0 CD2 G:PHE141 4.8 28.1 1.0 C G:PHE214 4.8 23.6 1.0 CB G:PHE214 4.8 24.0 1.0 C G:HIS139 4.9 23.0 1.0 N G:GLY215 4.9 24.2 1.0 CA G:GLY215 5.0 24.6 1.0 N G:SER216 5.0 26.1 1.0

Chlorine binding site 10 out of 53 in the Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of Finch Polyomavirus VP1 in Complex with 2-O-Methyl-5-N- Acetyl-Alpha-D-Neuraminic Acid within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl403 b:43.9 occ:1.00 CG G:PHE53 4.5 24.6 1.0 CD2 G:PHE53 4.6 24.3 1.0 CD1 G:PHE53 4.7 24.1 1.0 CE2 G:PHE53 4.9 25.1 1.0 CE1 G:PHE53 4.9 24.7 1.0 CD2 G:PHE263 4.9 34.2 1.0 CE2 G:PHE263 5.0 35.0 1.0 CB G:PHE53 5.0 26.2 1.0

L.J.Stroh, N.H.Rustmeier, B.S.Blaum, J.Botsch, P.Rossler, F.Wedekink, W.I.Lipkin, N.Mishra, T.Stehle. Structural Basis and Evolution of Glycan Receptor Specificities Within the Polyomavirus Family. Mbio V. 11 2020.
ISSN: ESSN 2150-7511
PubMed: 32723915
DOI: 10.1128/MBIO.00745-20