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

Calcium in PDB 4mbx: Structure of Unliganded B-Lymphotropic Polyomavirus VP1

Protein crystallography data

The structure of Structure of Unliganded B-Lymphotropic Polyomavirus VP1, PDB code: 4mbx was solved by Z.M.Khan, U.Neu, B.Schuch, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.38 / 1.92
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.010, 95.920, 231.680, 90.00, 95.82, 90.00
R / Rfree (%) 16.5 / 19.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Unliganded B-Lymphotropic Polyomavirus VP1 (pdb code 4mbx). 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 Unliganded B-Lymphotropic Polyomavirus VP1, PDB code: 4mbx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 4mbx

Go back to Calcium Binding Sites List in 4mbx
Calcium binding site 1 out of 10 in the Structure of Unliganded B-Lymphotropic Polyomavirus VP1


Mono view


Stereo pair view

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

b:24.1
occ:0.50
 O A:HOH731 2.0 36.2 1.0
O A:HOH700 2.2 49.1 1.0
O B:SER214 2.3 19.4 1.0
OE1 A:GLU46 2.6 55.5 1.0
OE2 A:GLU46 2.6 50.3 1.0
CD A:GLU46 2.8 49.2 1.0
C B:SER214 3.5 20.6 1.0
OE2 B:GLU217 3.8 53.1 1.0
CA B:SER214 4.2 19.7 1.0
CG A:GLU46 4.2 40.7 1.0
CB B:SER214 4.3 22.3 1.0
O B:HOH583 4.3 34.2 1.0
O B:HOH704 4.4 50.1 1.0
N B:LYS215 4.5 18.9 1.0
CA B:LYS215 4.7 19.8 1.0
OG B:SER214 4.8 23.4 1.0
OH A:TYR286 4.8 26.0 1.0
CG B:LYS215 5.0 26.1 1.0

Calcium binding site 2 out of 10 in 4mbx

Go back to Calcium Binding Sites List in 4mbx
Calcium binding site 2 out of 10 in the Structure of Unliganded B-Lymphotropic Polyomavirus VP1


Mono view


Stereo pair view

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

b:23.8
occ:0.50
 O C:HOH671 2.0 28.4 1.0
O B:HOH660 2.2 47.0 1.0
O C:SER214 2.3 20.2 1.0
OE1 B:GLU46 2.5 31.1 0.5
OE2 B:GLU46 2.6 33.6 0.5
OE2 B:GLU46 2.6 36.6 0.5
OE1 B:GLU46 2.7 33.6 0.5
CD B:GLU46 2.9 31.3 0.5
CD B:GLU46 2.9 33.4 0.5
C C:SER214 3.4 20.7 1.0
OE2 C:GLU217 3.7 26.7 0.5
O C:HOH574 4.1 28.7 1.0
CA C:SER214 4.1 20.6 1.0
CB C:SER214 4.3 21.2 1.0
CG B:GLU46 4.4 30.6 0.5
CG B:GLU46 4.4 28.8 0.5
N C:LYS215 4.5 19.0 1.0
CA C:LYS215 4.7 20.8 1.0
OH B:TYR286 4.8 28.3 1.0
CD C:GLU217 4.9 23.7 0.5
OG C:SER214 4.9 22.2 1.0
CG C:LYS215 5.0 24.6 1.0

Calcium binding site 3 out of 10 in 4mbx

Go back to Calcium Binding Sites List in 4mbx
Calcium binding site 3 out of 10 in the Structure of Unliganded B-Lymphotropic Polyomavirus VP1


Mono view


Stereo pair view

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

b:24.8
occ:0.50
 O C:HOH679 2.0 28.3 1.0
O D:HOH683 2.1 47.1 1.0
OE1 C:GLU46 2.3 55.1 1.0
O D:SER214 2.3 24.4 1.0
OE2 C:GLU46 2.7 50.4 1.0
CD C:GLU46 2.8 49.8 1.0
C D:SER214 3.5 23.9 1.0
OE2 D:GLU217 3.8 59.4 1.0
O D:HOH591 4.1 50.2 1.0
CG C:GLU46 4.2 45.7 1.0
CA D:SER214 4.2 24.5 1.0
O D:HOH550 4.3 28.4 1.0
CB D:SER214 4.3 26.4 1.0
N D:LYS215 4.6 22.2 1.0
CA D:LYS215 4.7 23.6 1.0
OG D:SER214 4.9 26.7 1.0

Calcium binding site 4 out of 10 in 4mbx

Go back to Calcium Binding Sites List in 4mbx
Calcium binding site 4 out of 10 in the Structure of Unliganded B-Lymphotropic Polyomavirus VP1


Mono view


Stereo pair view

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

b:29.2
occ:0.50
 O E:HOH702 2.1 45.1 1.0
O D:HOH663 2.3 38.7 1.0
O E:SER214 2.4 23.1 1.0
OE2 D:GLU46 2.4 51.2 1.0
OE1 D:GLU46 2.8 52.8 1.0
CD D:GLU46 2.8 48.5 1.0
C E:SER214 3.5 22.8 1.0
OE2 E:GLU217 3.9 34.9 0.5
CA E:SER214 4.2 21.9 1.0
CG D:GLU46 4.2 40.8 1.0
CB E:SER214 4.2 22.9 1.0
O E:HOH622 4.4 37.3 1.0
N E:LYS215 4.6 21.8 1.0
OH D:TYR286 4.8 27.1 1.0
CA E:LYS215 4.8 22.5 0.5
CA E:LYS215 4.8 22.4 0.5
OE2 E:GLU217 4.8 40.9 0.5
OG E:SER214 4.8 23.2 1.0

Calcium binding site 5 out of 10 in 4mbx

Go back to Calcium Binding Sites List in 4mbx
Calcium binding site 5 out of 10 in the Structure of Unliganded B-Lymphotropic Polyomavirus VP1


Mono view


Stereo pair view

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

b:25.9
occ:0.50
 O A:HOH726 2.0 33.6 1.0
O A:HOH732 2.0 42.5 1.0
O E:HOH652 2.4 48.5 1.0
O A:SER214 2.4 21.6 1.0
OE2 E:GLU46 2.6 51.1 1.0
OE1 E:GLU46 2.7 44.4 1.0
CD E:GLU46 3.0 46.0 1.0
C A:SER214 3.5 21.5 1.0
OE2 A:GLU217 3.6 56.8 1.0
O A:HOH593 4.2 30.3 1.0
CA A:SER214 4.2 21.2 1.0
CB A:SER214 4.3 22.0 1.0
CG E:GLU46 4.5 36.9 1.0
N A:LYS215 4.6 20.4 1.0
CA A:LYS215 4.8 20.7 1.0
OH E:TYR286 4.8 23.0 1.0
CD A:GLU217 4.8 49.3 1.0
OG A:SER214 5.0 23.6 1.0

Calcium binding site 6 out of 10 in 4mbx

Go back to Calcium Binding Sites List in 4mbx
Calcium binding site 6 out of 10 in the Structure of Unliganded B-Lymphotropic Polyomavirus VP1


Mono view


Stereo pair view

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

b:25.9
occ:0.50
 O F:HOH630 2.1 37.0 1.0
O G:HOH634 2.1 47.2 1.0
O G:SER214 2.3 24.5 1.0
OE1 F:GLU46 2.6 54.7 1.0
OE2 F:GLU46 2.6 49.0 1.0
CD F:GLU46 2.9 50.3 1.0
C G:SER214 3.5 24.1 1.0
OE2 G:GLU217 3.7 54.4 1.0
CA G:SER214 4.2 22.9 1.0
O G:HOH543 4.3 30.0 1.0
CG F:GLU46 4.3 43.9 1.0
CB G:SER214 4.3 24.1 1.0
N G:LYS215 4.5 21.8 1.0
CA G:LYS215 4.7 22.9 1.0
OG G:SER214 4.9 24.5 1.0
OH F:TYR286 4.9 27.3 1.0
CG G:LYS215 4.9 28.7 1.0
CD G:GLU217 4.9 45.1 1.0

Calcium binding site 7 out of 10 in 4mbx

Go back to Calcium Binding Sites List in 4mbx
Calcium binding site 7 out of 10 in the Structure of Unliganded B-Lymphotropic Polyomavirus VP1


Mono view


Stereo pair view

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

b:24.4
occ:0.50
 O H:HOH649 2.0 29.7 1.0
O H:SER214 2.3 24.8 1.0
O H:HOH501 2.4 40.3 1.0
OE2 G:GLU46 2.5 50.2 1.0
OE1 G:GLU46 2.7 41.1 1.0
CD G:GLU46 2.9 43.0 1.0
C H:SER214 3.5 25.1 1.0
OE2 H:GLU217 3.7 59.5 1.0
CA H:SER214 4.2 25.6 1.0
O H:HOH548 4.2 32.5 1.0
CB H:SER214 4.4 26.9 1.0
CG G:GLU46 4.4 36.3 1.0
N H:LYS215 4.5 24.2 1.0
CA H:LYS215 4.7 24.6 1.0
OH G:TYR286 4.7 29.6 1.0
OG H:SER214 4.9 28.6 1.0
CD H:GLU217 4.9 46.0 1.0

Calcium binding site 8 out of 10 in 4mbx

Go back to Calcium Binding Sites List in 4mbx
Calcium binding site 8 out of 10 in the Structure of Unliganded B-Lymphotropic Polyomavirus VP1


Mono view


Stereo pair view

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

b:30.8
occ:0.50
 OE2 H:GLU46 2.2 36.3 0.5
O I:HOH609 2.3 38.7 1.0
O H:HOH648 2.3 44.6 1.0
O I:SER214 2.5 26.6 1.0
OE1 H:GLU46 2.6 36.9 0.5
OE1 H:GLU46 2.7 34.9 0.5
CD H:GLU46 2.8 34.5 0.5
OE2 H:GLU46 2.8 35.4 0.5
CD H:GLU46 2.9 34.4 0.5
C I:SER214 3.6 25.2 1.0
OE2 I:GLU217 3.9 56.9 1.0
CA I:SER214 4.3 24.7 1.0
CG H:GLU46 4.3 32.1 0.5
O I:HOH555 4.3 35.0 1.0
CG H:GLU46 4.3 31.6 0.5
CB I:SER214 4.3 26.6 1.0
N I:LYS215 4.7 24.9 1.0
OH H:TYR286 4.9 31.6 1.0
CA I:LYS215 4.9 26.3 1.0
OG I:SER214 4.9 29.9 1.0

Calcium binding site 9 out of 10 in 4mbx

Go back to Calcium Binding Sites List in 4mbx
Calcium binding site 9 out of 10 in the Structure of Unliganded B-Lymphotropic Polyomavirus VP1


Mono view


Stereo pair view

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

b:27.5
occ:0.50
 O J:HOH671 2.1 38.4 1.0
O J:SER214 2.3 28.2 1.0
O I:HOH666 2.4 51.2 1.0
OE2 I:GLU46 2.4 37.8 0.5
OE1 I:GLU46 2.5 36.1 0.5
OE2 I:GLU46 2.6 35.2 0.5
CD I:GLU46 2.8 36.3 0.5
OE1 I:GLU46 2.9 35.9 0.5
CD I:GLU46 3.0 34.4 0.5
C J:SER214 3.5 28.8 1.0
OE2 J:GLU217 4.0 35.5 0.5
CA J:SER214 4.2 27.8 1.0
CB J:SER214 4.3 29.1 1.0
CG I:GLU46 4.3 34.2 0.5
O J:HOH618 4.4 38.2 1.0
CG I:GLU46 4.5 32.1 0.5
N J:LYS215 4.6 25.1 1.0
CA J:LYS215 4.8 27.2 1.0
OH I:TYR286 4.8 31.1 1.0
OG J:SER214 4.9 30.9 1.0

Calcium binding site 10 out of 10 in 4mbx

Go back to Calcium Binding Sites List in 4mbx
Calcium binding site 10 out of 10 in the Structure of Unliganded B-Lymphotropic Polyomavirus VP1


Mono view


Stereo pair view

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

b:31.0
occ:0.50
 O J:HOH669 2.1 29.9 1.0
O F:HOH687 2.2 46.2 1.0
O F:SER214 2.3 24.9 1.0
OE2 J:GLU46 2.3 56.4 1.0
OE1 J:GLU46 2.8 52.0 1.0
CD J:GLU46 2.9 50.5 1.0
C F:SER214 3.5 25.3 1.0
OE2 F:GLU217 3.9 32.4 0.5
CA F:SER214 4.1 24.9 1.0
CB F:SER214 4.2 26.1 1.0
CG J:GLU46 4.3 45.3 1.0
O F:HOH589 4.3 32.2 1.0
O F:HOH529 4.5 42.8 1.0
N F:LYS215 4.5 23.2 1.0
OE2 F:GLU217 4.6 39.2 0.5
CA F:LYS215 4.7 24.5 1.0
OG F:SER214 4.9 28.2 1.0
OH J:TYR286 4.9 30.2 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 00:20:16 2025

Last articles

Mg in 4W5O
Mg in 4W5J
Mg in 4W5N
Mg in 4V2I
Mg in 4V3R
Mg in 4V26
Mg in 4V2G
Mg in 4V1T
Mg in 4V25
Mg in 4V1V
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy