Calcium in PDB 6esb: Bk Polyomavirus + 20 Mm GT1B Oligosaccharide

The binding sites of Calcium atom in the Bk Polyomavirus + 20 Mm GT1B Oligosaccharide (pdb code 6esb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Bk Polyomavirus + 20 Mm GT1B Oligosaccharide, PDB code: 6esb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Bk Polyomavirus + 20 Mm GT1B Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bk Polyomavirus + 20 Mm GT1B Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca403 b:88.2 occ:1.00 O 1:SER213 2.5 30.9 1.0 OE2 1:GLU216 2.6 31.8 1.0 OE2 5:GLU48 2.6 23.7 1.0 OE1 5:GLU48 2.9 23.7 1.0 CD 5:GLU48 3.1 23.7 1.0 C 1:SER213 3.2 30.9 1.0 CD 1:GLU216 3.6 31.8 1.0 CA 1:SER213 3.8 30.9 1.0 CG 1:GLU216 3.9 31.8 1.0 N 1:ARG214 4.1 39.6 1.0 CB 1:SER213 4.5 30.9 1.0 OH 5:TYR285 4.5 23.4 1.0 O 1:PRO212 4.6 29.1 1.0 CA 1:ARG214 4.6 39.6 1.0 CG 5:GLU48 4.6 23.7 1.0 OE1 1:GLU216 4.7 31.8 1.0 NZ 5:LYS287 4.8 22.6 1.0 CE 5:LYS287 4.9 22.6 1.0 N 1:SER213 5.0 30.9 1.0

Calcium binding site 2 out of 6 in the Bk Polyomavirus + 20 Mm GT1B Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bk Polyomavirus + 20 Mm GT1B Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ 1:Ca404 b:88.2 occ:1.00 O 2:SER213 2.5 24.4 1.0 OE2 2:GLU216 2.6 25.5 1.0 OE2 1:GLU48 2.6 23.5 1.0 OE1 1:GLU48 2.8 23.5 1.0 CD 1:GLU48 3.1 23.5 1.0 C 2:SER213 3.5 24.4 1.0 CD 2:GLU216 3.6 25.5 1.0 CG 2:GLU216 3.8 25.5 1.0 CA 2:SER213 4.2 24.4 1.0 N 2:ARG214 4.4 26.9 1.0 OH 1:TYR285 4.6 21.9 1.0 CA 2:ARG214 4.6 26.9 1.0 CG 1:GLU48 4.6 23.5 1.0 OE1 2:GLU216 4.7 25.5 1.0 NZ 1:LYS287 4.8 21.6 1.0 CB 2:SER213 4.9 24.4 1.0

Calcium binding site 3 out of 6 in the Bk Polyomavirus + 20 Mm GT1B Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bk Polyomavirus + 20 Mm GT1B Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ 2:Ca403 b:88.2 occ:1.00 OE1 6:GLU330 2.5 23.6 1.0 O 3:SER213 2.5 22.0 1.0 OE2 2:GLU48 2.5 20.7 1.0 OE2 3:GLU216 2.5 23.9 1.0 OE1 2:GLU48 2.6 20.7 1.0 CD 2:GLU48 2.9 20.7 1.0 CD 6:GLU330 3.2 23.6 1.0 OE2 6:GLU330 3.4 23.6 1.0 C 3:SER213 3.5 22.0 1.0 CD 3:GLU216 3.6 23.9 1.0 CG 3:GLU216 3.9 23.9 1.0 CA 3:SER213 4.1 22.0 1.0 CG 6:GLU330 4.4 23.6 1.0 CG 2:GLU48 4.4 20.7 1.0 CB 3:SER213 4.4 22.0 1.0 NH2 6:ARG332 4.4 22.2 1.0 N 3:ARG214 4.5 24.4 1.0 OE1 3:GLU216 4.6 23.9 1.0 CB 6:GLU330 4.7 23.6 1.0 CA 3:ARG214 4.7 24.4 1.0 OH 2:TYR285 4.8 16.8 1.0 CZ 6:ARG332 4.9 22.2 1.0 NE 6:ARG332 4.9 22.2 1.0

Calcium binding site 4 out of 6 in the Bk Polyomavirus + 20 Mm GT1B Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bk Polyomavirus + 20 Mm GT1B Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ 3:Ca403 b:88.2 occ:1.00 O 4:SER213 2.5 26.2 1.0 OE2 3:GLU48 2.5 21.1 1.0 OE2 4:GLU216 2.7 30.0 1.0 OE1 3:GLU48 3.1 21.1 1.0 CD 3:GLU48 3.2 21.1 1.0 C 4:SER213 3.4 26.2 1.0 CD 4:GLU216 3.8 30.0 1.0 CA 4:SER213 4.1 26.2 1.0 CG 4:GLU216 4.1 30.0 1.0 N 4:ARG214 4.2 29.7 1.0 OH 3:TYR285 4.5 19.7 1.0 CA 4:ARG214 4.5 29.7 1.0 CG 3:GLU48 4.7 21.1 1.0 O 4:PRO212 4.7 24.9 1.0 NZ 3:LYS287 4.8 18.3 1.0 OE1 4:GLU216 4.8 30.0 1.0 CB 4:SER213 5.0 26.2 1.0

Calcium binding site 5 out of 6 in the Bk Polyomavirus + 20 Mm GT1B Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Bk Polyomavirus + 20 Mm GT1B Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ 3:Ca404 b:88.2 occ:1.00 O 6:SER213 2.5 18.9 1.0 OE2 6:GLU216 2.6 22.2 1.0 OE1 3:GLU330 3.1 26.0 1.0 CD 3:GLU330 3.5 26.0 1.0 C 6:SER213 3.5 18.9 1.0 CD 6:GLU216 3.6 22.2 1.0 OE2 3:GLU330 3.6 26.0 1.0 CG 6:GLU216 3.9 22.2 1.0 CA 6:SER213 4.2 18.9 1.0 NH2 3:ARG332 4.2 23.1 1.0 N 6:ARG214 4.5 19.7 1.0 CG 3:GLU330 4.6 26.0 1.0 CZ 3:ARG332 4.7 23.1 1.0 OE1 6:GLU216 4.7 22.2 1.0 CB 6:SER213 4.8 18.9 1.0 NE 3:ARG332 4.8 23.1 1.0 CA 6:ARG214 4.9 19.7 1.0

Calcium binding site 6 out of 6 in the Bk Polyomavirus + 20 Mm GT1B Oligosaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Bk Polyomavirus + 20 Mm GT1B Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ 4:Ca403 b:88.2 occ:1.00 O 5:SER213 2.5 27.2 1.0 OE2 4:GLU48 2.5 22.0 1.0 OE1 4:GLU48 3.0 22.0 1.0 OE2 5:GLU216 3.1 29.8 1.0 CD 4:GLU48 3.1 22.0 1.0 C 5:SER213 3.4 27.2 1.0 CD 5:GLU216 4.0 29.8 1.0 CA 5:SER213 4.0 27.2 1.0 CG 5:GLU216 4.2 29.8 1.0 N 5:ARG214 4.4 30.9 1.0 OH 4:TYR285 4.5 22.3 1.0 CG 4:GLU48 4.6 22.0 1.0 NZ 4:LYS287 4.7 19.7 1.0 CB 5:SER213 4.7 27.2 1.0 CA 5:ARG214 4.8 30.9 1.0 O 5:PRO212 4.8 27.2 1.0 CE 4:LYS287 5.0 19.7 1.0

D.L.Hurdiss, M.Frank, J.S.Snowden, A.Macdonald, N.A.Ranson. The Structure of An Infectious Human Polyomavirus and Its Interactions with Cellular Receptors. Structure V. 26 839 2018.
ISSN: ISSN 1878-4186
PubMed: 29706532
DOI: 10.1016/J.STR.2018.03.019