Atomistry » Calcium » PDB 4m93-4mpp » 4mby
Atomistry »
  Calcium »
    PDB 4m93-4mpp »
      4mby »

Calcium in PDB 4mby: Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose

Protein crystallography data

The structure of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose, PDB code: 4mby was solved by Z.M.Khan, U.Neu, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.82 / 1.48
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.530, 97.210, 234.660, 90.00, 96.25, 90.00
R / Rfree (%) 16.5 / 18.6

Other elements in 4mby:

The structure of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose (pdb code 4mby). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose, PDB code: 4mby:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 4mby

Go back to Calcium Binding Sites List in 4mby
Calcium binding site 1 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:22.0
occ:0.65
 O A:HOH716 1.9 13.5 1.0
O B:HOH813 2.0 35.5 1.0
O B:HOH744 2.3 43.6 1.0
OE1 A:GLU46 2.3 25.6 0.6
O B:SER214 2.4 12.7 1.0
OE2 A:GLU46 2.7 22.1 0.6
OE1 A:GLU46 2.7 29.2 0.4
CD A:GLU46 2.9 23.1 0.6
OE2 A:GLU46 2.9 29.2 0.4
CD A:GLU46 3.0 28.3 0.4
O B:HOH783 3.2 35.7 1.0
C B:SER214 3.5 11.8 1.0
OE2 B:GLU217 3.6 27.2 1.0
O A:HOH732 4.1 37.1 1.0
CA B:SER214 4.3 12.2 1.0
O B:HOH562 4.3 18.1 1.0
CG A:GLU46 4.3 24.5 0.4
CG A:GLU46 4.4 21.3 0.6
CB B:SER214 4.4 13.5 1.0
O B:HOH764 4.4 36.5 1.0
N B:LYS215 4.6 12.0 1.0
O B:HOH739 4.6 27.2 1.0
CA B:LYS215 4.8 12.1 1.0
CD B:GLU217 4.9 25.1 1.0
OG B:SER214 4.9 14.7 1.0

Calcium binding site 2 out of 10 in 4mby

Go back to Calcium Binding Sites List in 4mby
Calcium binding site 2 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:21.8
occ:0.60
 O C:HOH703 1.9 33.1 1.0
O B:HOH684 2.1 12.3 1.0
O C:HOH696 2.3 44.5 1.0
O C:SER214 2.3 13.9 1.0
OE1 B:GLU46 2.5 23.6 0.5
OE1 B:GLU46 2.6 29.6 0.5
O B:HOH775 2.7 41.7 1.0
OE2 B:GLU46 2.8 18.8 0.5
CD B:GLU46 3.0 20.5 0.5
OE2 B:GLU46 3.1 26.3 0.5
CD B:GLU46 3.1 27.5 0.5
C C:SER214 3.5 12.6 1.0
O B:HOH814 3.6 45.4 1.0
OE2 C:GLU217 3.7 29.1 1.0
O B:HOH758 4.2 38.0 1.0
CA C:SER214 4.2 12.8 1.0
O C:HOH565 4.3 19.0 1.0
CB C:SER214 4.3 13.9 1.0
CG B:GLU46 4.4 25.1 0.5
O B:HOH788 4.4 40.3 1.0
CG B:GLU46 4.4 20.1 0.5
O C:HOH655 4.5 35.1 1.0
O C:HOH682 4.6 27.7 1.0
N C:LYS215 4.6 12.1 1.0
CA C:LYS215 4.8 12.8 1.0
OG C:SER214 4.9 16.0 1.0
CD C:GLU217 4.9 26.2 1.0

Calcium binding site 3 out of 10 in 4mby

Go back to Calcium Binding Sites List in 4mby
Calcium binding site 3 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:23.6
occ:0.60
 O D:HOH759 1.9 36.3 1.0
O D:HOH672 2.0 13.7 1.0
OE1 C:GLU46 2.3 28.7 0.5
O D:SER214 2.3 15.9 1.0
O D:HOH719 2.4 41.8 1.0
OE1 C:GLU46 2.6 28.1 0.5
OE2 C:GLU46 2.7 22.7 0.5
OE2 C:GLU46 2.9 24.3 0.5
CD C:GLU46 3.0 27.0 0.5
CD C:GLU46 3.0 25.6 0.5
O C:HOH603 3.1 38.1 1.0
C D:SER214 3.5 14.9 1.0
OE2 D:GLU217 3.6 30.2 1.0
O C:HOH794 4.2 39.5 1.0
CA D:SER214 4.2 14.8 1.0
O D:HOH543 4.2 20.9 1.0
O D:HOH750 4.2 37.4 1.0
CB D:SER214 4.4 16.8 1.0
CG C:GLU46 4.4 23.8 0.5
CG C:GLU46 4.5 23.0 0.5
O D:HOH652 4.6 31.4 1.0
N D:LYS215 4.6 14.7 1.0
O C:HOH776 4.8 40.3 1.0
CA D:LYS215 4.8 14.5 1.0
CD D:GLU217 4.8 27.4 1.0
OG D:SER214 4.9 19.0 1.0

Calcium binding site 4 out of 10 in 4mby

Go back to Calcium Binding Sites List in 4mby
Calcium binding site 4 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:24.8
occ:0.60
 O E:HOH756 1.9 33.5 1.0
O D:HOH671 2.0 15.4 1.0
OE2 D:GLU46 2.3 36.7 0.6
OE1 D:GLU46 2.4 24.5 0.4
O E:SER214 2.4 16.4 1.0
OE2 D:GLU46 2.6 21.7 0.4
CD D:GLU46 2.8 23.4 0.4
OE1 D:GLU46 2.9 31.2 0.6
CD D:GLU46 2.9 33.1 0.6
O D:HOH755 2.9 35.6 1.0
C E:SER214 3.6 14.8 1.0
OE2 E:GLU217 3.6 33.2 1.0
O E:HOH562 4.3 20.9 1.0
CA E:SER214 4.3 15.6 1.0
CG D:GLU46 4.3 21.8 0.4
O E:HOH762 4.3 36.5 1.0
CG D:GLU46 4.3 28.3 0.6
CB E:SER214 4.4 17.3 1.0
N E:LYS215 4.6 13.9 1.0
O E:HOH595 4.7 35.0 1.0
CA E:LYS215 4.9 14.4 1.0
CD E:GLU217 4.9 29.8 1.0
OG E:SER214 5.0 18.6 1.0

Calcium binding site 5 out of 10 in 4mby

Go back to Calcium Binding Sites List in 4mby
Calcium binding site 5 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:21.1
occ:0.60
 O A:HOH501 1.9 14.6 1.0
O A:HOH764 2.0 36.7 1.0
OE1 E:GLU46 2.3 33.1 0.5
O A:SER214 2.3 13.7 1.0
O A:HOH504 2.4 44.9 1.0
OE1 E:GLU46 2.5 26.3 0.5
OE2 E:GLU46 2.7 21.3 0.5
O E:HOH691 2.9 40.0 1.0
CD E:GLU46 3.0 23.5 0.5
CD E:GLU46 3.0 27.4 0.5
OE2 E:GLU46 3.0 24.1 0.5
C A:SER214 3.5 13.7 1.0
OE2 A:GLU217 3.6 34.0 1.0
O A:HOH557 4.2 19.8 1.0
CA A:SER214 4.3 13.3 1.0
CB A:SER214 4.5 14.7 1.0
CG E:GLU46 4.5 23.8 0.5
CG E:GLU46 4.5 21.3 0.5
O A:HOH679 4.5 41.3 1.0
N A:LYS215 4.6 13.2 1.0
O A:HOH662 4.6 28.4 1.0
CA A:LYS215 4.8 13.4 1.0
CD A:GLU217 4.8 30.5 1.0
OG A:SER214 4.9 16.0 1.0

Calcium binding site 6 out of 10 in 4mby

Go back to Calcium Binding Sites List in 4mby
Calcium binding site 6 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca401

b:25.2
occ:0.60
 O G:HOH679 2.0 41.3 1.0
O G:HOH633 2.1 22.5 1.0
O G:HOH501 2.3 40.3 1.0
O G:SER214 2.3 20.3 1.0
O F:HOH679 2.3 40.4 1.0
OE1 F:GLU46 2.4 40.2 1.0
OE2 F:GLU46 2.6 31.4 1.0
CD F:GLU46 2.9 34.2 1.0
C G:SER214 3.5 19.8 1.0
OE2 G:GLU217 3.7 36.1 1.0
CA G:SER214 4.2 19.2 1.0
O G:HOH523 4.3 25.4 1.0
CG F:GLU46 4.4 29.1 1.0
CB G:SER214 4.4 21.6 1.0
O G:HOH669 4.5 37.3 1.0
N G:LYS215 4.6 18.2 1.0
CA G:LYS215 4.8 18.5 1.0
CD G:GLU217 4.9 31.1 1.0
OG G:SER214 4.9 22.5 1.0
OH F:TYR286 5.0 22.8 1.0

Calcium binding site 7 out of 10 in 4mby

Go back to Calcium Binding Sites List in 4mby
Calcium binding site 7 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca401

b:23.9
occ:0.60
 O H:HOH642 2.0 16.9 1.0
O H:HOH690 2.2 38.9 1.0
O H:HOH502 2.2 41.4 1.0
OE1 G:GLU46 2.3 29.5 0.5
O H:SER214 2.4 19.3 1.0
OE1 G:GLU46 2.5 31.3 0.5
OE2 G:GLU46 2.7 25.7 0.5
O G:HOH640 2.9 40.3 1.0
CD G:GLU46 3.0 28.5 0.5
OE2 G:GLU46 3.0 27.6 0.5
CD G:GLU46 3.0 29.2 0.5
C H:SER214 3.5 18.2 1.0
OE2 H:GLU217 3.6 35.3 1.0
CA H:SER214 4.3 18.9 1.0
O H:HOH554 4.3 20.9 1.0
CG G:GLU46 4.4 26.8 0.5
CG G:GLU46 4.4 26.2 0.5
CB H:SER214 4.5 20.6 1.0
N H:LYS215 4.6 18.0 1.0
O H:HOH664 4.7 35.6 1.0
CD H:GLU217 4.8 32.6 1.0
CA H:LYS215 4.8 18.0 1.0
OG H:SER214 5.0 22.0 1.0

Calcium binding site 8 out of 10 in 4mby

Go back to Calcium Binding Sites List in 4mby
Calcium binding site 8 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca401

b:28.1
occ:0.70
 O H:HOH635 2.0 18.5 1.0
O I:HOH501 2.1 42.4 1.0
O I:HOH674 2.3 42.7 1.0
O I:SER214 2.4 20.9 1.0
OE1 H:GLU46 2.5 30.2 0.5
OE2 H:GLU46 2.7 28.0 0.5
OE1 H:GLU46 2.8 32.4 0.5
OE2 H:GLU46 2.9 31.0 0.5
CD H:GLU46 3.0 29.5 0.5
CD H:GLU46 3.1 31.3 0.5
C I:SER214 3.5 20.1 1.0
OE2 I:GLU217 3.6 38.5 1.0
CA I:SER214 4.2 20.0 1.0
O I:HOH547 4.2 23.5 1.0
CG H:GLU46 4.4 28.3 0.5
CB I:SER214 4.4 20.5 1.0
CG H:GLU46 4.5 27.1 0.5
N I:LYS215 4.6 19.0 1.0
O I:HOH708 4.7 36.0 1.0
CA I:LYS215 4.8 19.3 1.0
CD I:GLU217 4.8 31.5 1.0
OG I:SER214 5.0 21.5 1.0

Calcium binding site 9 out of 10 in 4mby

Go back to Calcium Binding Sites List in 4mby
Calcium binding site 9 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca401

b:25.1
occ:0.60
 O J:HOH503 1.9 35.5 1.0
O J:HOH513 2.0 15.3 1.0
O J:HOH716 2.3 46.8 1.0
O J:SER214 2.3 17.7 1.0
OE2 I:GLU46 2.4 31.7 0.6
OE2 I:GLU46 2.5 29.2 0.4
OE1 I:GLU46 2.6 33.0 0.4
CD I:GLU46 2.9 30.3 0.4
OE1 I:GLU46 2.9 27.4 0.6
CD I:GLU46 3.0 28.9 0.6
O I:HOH743 3.1 43.0 1.0
C J:SER214 3.5 17.2 1.0
OE2 J:GLU217 3.7 36.7 1.0
CA J:SER214 4.2 17.4 1.0
O I:HOH749 4.3 40.7 1.0
O J:HOH521 4.3 21.6 1.0
CG I:GLU46 4.4 27.6 0.4
CB J:SER214 4.4 18.5 1.0
O J:HOH755 4.4 42.8 1.0
CG I:GLU46 4.4 25.8 0.6
O J:HOH666 4.5 31.2 1.0
N J:LYS215 4.6 16.5 1.0
CA J:LYS215 4.8 16.5 1.0
OG J:SER214 4.9 21.5 1.0
CD J:GLU217 4.9 30.1 1.0
CB I:GLU46 5.0 25.0 0.4

Calcium binding site 10 out of 10 in 4mby

Go back to Calcium Binding Sites List in 4mby
Calcium binding site 10 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactose within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca401

b:26.6
occ:0.60
 O F:HOH503 2.0 16.0 1.0
O F:HOH502 2.1 38.7 1.0
O F:SER214 2.3 20.6 1.0
OE1 J:GLU46 2.4 41.3 0.6
O J:HOH658 2.6 43.0 1.0
OE1 J:GLU46 2.7 41.5 0.4
OE2 J:GLU46 2.7 38.5 0.4
O J:HOH751 2.9 41.5 1.0
OE2 J:GLU46 2.9 38.2 0.6
CD J:GLU46 3.0 36.9 0.6
CD J:GLU46 3.1 37.1 0.4
C F:SER214 3.5 18.8 1.0
OE2 F:GLU217 3.6 33.3 1.0
CA F:SER214 4.2 18.3 1.0
O J:HOH504 4.3 41.7 1.0
O F:HOH657 4.3 36.2 1.0
O F:HOH539 4.3 22.4 1.0
CB F:SER214 4.4 19.0 1.0
CG J:GLU46 4.5 29.7 0.6
CG J:GLU46 4.5 30.0 0.4
N F:LYS215 4.6 18.2 1.0
CA F:LYS215 4.8 18.3 1.0
CD F:GLU217 4.9 30.0 1.0
OG F:SER214 4.9 20.4 1.0

Reference:

U.Neu, Z.M.Khan, B.Schuch, A.S.Palma, Y.Liu, M.Pawlita, T.Feizi, T.Stehle. Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands. Plos Pathog. V. 9 03714 2013.
ISSN: ISSN 1553-7366
PubMed: 24204265
DOI: 10.1371/JOURNAL.PPAT.1003714
Page generated: Wed Jul 9 00:20:30 2025

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy