Calcium in PDB 6zlz: Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle

The structure of Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle, PDB code: 6zlz was solved by N.J.Bayer, T.Stehle, B.S.Blaum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.97 / 3.52
Space group	I 2 2 2 7
Cell size a, b, c (Å), α, β, γ (°)	554.830, 560.990, 573.660, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / n/a

The binding sites of Calcium atom in the Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle (pdb code 6zlz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle, PDB code: 6zlz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:0.1 occ:0.47 OE2 C:GLU353 2.5 0.8 1.0 OE1 C:GLU353 2.5 0.8 1.0 O A:SER236 2.6 0.8 1.0 OE1 A:GLU239 2.7 0.2 1.0 CD C:GLU353 2.7 0.8 1.0 OE2 A:GLU239 2.7 0.2 1.0 CD A:GLU239 2.9 0.2 1.0 C A:SER236 3.5 0.8 1.0 CG C:GLU353 3.8 0.8 1.0 CB C:GLU353 4.0 0.8 1.0 CG A:GLU239 4.0 0.2 1.0 NE C:ARG355 4.2 1.0 1.0 CA A:LYS237 4.3 0.3 1.0 CA A:SER236 4.3 0.8 1.0 N A:LYS237 4.3 0.3 1.0 NH2 C:ARG355 4.4 1.0 1.0 CB A:SER236 4.5 0.0 1.0 CZ C:ARG355 4.7 1.0 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:0.1 occ:0.75 OE2 B:GLU56 2.6 0.1 1.0 OE1 B:GLU56 2.6 0.1 1.0 O C:SER236 2.6 0.4 1.0 OE1 A:GLU353 2.6 0.2 1.0 OE2 C:GLU239 2.6 0.7 1.0 OE1 C:GLU239 2.7 0.7 1.0 OE2 A:GLU353 2.7 0.2 1.0 CD C:GLU239 2.8 0.7 1.0 CD A:GLU353 2.8 0.2 1.0 CD B:GLU56 2.9 0.1 1.0 C C:SER236 3.3 0.4 1.0 CG C:GLU239 3.9 0.7 1.0 CA C:SER236 3.9 0.4 1.0 CG A:GLU353 4.0 0.2 1.0 N C:LYS237 4.2 0.7 1.0 CB A:GLU353 4.2 0.2 1.0 CB C:SER236 4.2 0.6 1.0 CG B:GLU56 4.2 0.1 1.0 CA C:LYS237 4.4 0.7 1.0 NH2 A:ARG355 4.6 0.8 1.0 NE A:ARG355 4.7 0.8 1.0 CZ A:ARG355 4.7 0.8 1.0 OH B:TYR308 4.9 0.2 1.0 CB B:GLU56 5.0 0.1 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:0.1 occ:0.81 OE2 F:GLU56 2.6 0.5 1.0 OE1 B:GLU239 2.6 0.2 1.0 OE1 F:GLU56 2.6 0.5 1.0 OE2 B:GLU239 2.6 0.2 1.0 O B:SER236 2.6 0.6 1.0 CD F:GLU56 2.9 0.5 1.0 CD B:GLU239 2.9 0.2 1.0 C B:SER236 3.6 0.6 1.0 CG F:GLU56 4.3 0.5 1.0 CG B:GLU239 4.4 0.2 1.0 CA B:SER236 4.5 0.6 1.0 CA B:LYS237 4.5 0.9 1.0 N B:LYS237 4.5 0.9 1.0 CB B:SER236 4.9 0.0 1.0 OH F:TYR308 5.0 0.1 1.0 C B:LYS237 5.0 0.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:0.1 occ:0.96 O D:SER236 2.6 0.2 1.0 OE1 C:GLU56 2.6 100.0 1.0 OE2 C:GLU56 2.6 100.0 1.0 OE1 D:GLU239 2.6 0.1 1.0 OE2 D:GLU239 2.6 0.1 1.0 CD D:GLU239 2.9 0.1 1.0 CD C:GLU56 2.9 100.0 1.0 C D:SER236 3.4 0.2 1.0 CA D:SER236 3.8 0.2 1.0 CB D:SER236 4.3 99.4 1.0 CG D:GLU239 4.4 0.1 1.0 CG C:GLU56 4.4 100.0 1.0 OH C:TYR308 4.5 98.9 1.0 N D:LYS237 4.5 0.3 1.0 O D:PRO235 4.6 99.8 1.0 CA D:LYS237 4.9 0.3 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca501 b:0.1 occ:1.00 OE2 D:GLU56 2.6 0.1 1.0 O E:SER236 2.6 0.4 1.0 OE1 D:GLU56 2.6 0.1 1.0 OE1 E:GLU239 2.6 0.8 1.0 OE2 E:GLU239 2.6 0.8 1.0 CD D:GLU56 2.8 0.1 1.0 CD E:GLU239 2.9 0.8 1.0 C E:SER236 3.4 0.4 1.0 CA E:SER236 4.0 0.4 1.0 CB E:SER236 4.2 0.8 1.0 CG D:GLU56 4.2 0.1 1.0 N E:LYS237 4.3 0.8 1.0 CG E:GLU239 4.4 0.8 1.0 CA E:LYS237 4.5 0.8 1.0 OH D:TYR308 4.9 99.0 1.0 OG E:SER236 5.0 0.8 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Merkel Cell Polyomavirus Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca501 b:0.1 occ:0.46 OE2 E:GLU56 2.6 0.1 1.0 OE1 E:GLU56 2.6 0.1 1.0 OE2 F:GLU239 2.6 0.1 1.0 OE1 F:GLU239 2.7 0.1 1.0 O F:SER236 2.7 0.1 1.0 CD E:GLU56 2.9 0.1 1.0 CD F:GLU239 2.9 0.1 1.0 C F:SER236 3.9 0.1 1.0 CG E:GLU56 4.3 0.1 1.0 CG F:GLU239 4.4 0.1 1.0 OH E:TYR308 4.6 0.2 1.0 CA F:SER236 4.7 0.1 1.0 ND2 E:ASN310 4.9 0.5 1.0 CB F:GLU239 4.9 0.1 1.0 N F:LYS237 5.0 0.3 1.0

N.J.Bayer, D.Januliene, G.Zocher, T.Stehle, A.Moeller, B.S.Blaum. Structure of Merkel Cell Polyomavirus Capsid and Interaction with Its Glycosaminoglycan Attachment Receptor. J.Virol. V. 94 2020.
ISSN: ESSN 1098-5514
PubMed: 32699083
DOI: 10.1128/JVI.01664-19