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

Protein crystallography data

The structure of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine, PDB code: 4mbz 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) 48.75 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.160, 97.240, 234.220, 90.00, 96.21, 90.00
R / Rfree (%) 16.5 / 19.5

Other elements in 4mbz:

The structure of Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine 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'- Sialyllactosamine (pdb code 4mbz). 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'- Sialyllactosamine, PDB code: 4mbz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 4mbz

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Calcium binding site 1 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


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'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:19.4
occ:0.60
 O B:HOH510 1.9 14.5 1.0
O B:HOH817 2.0 34.0 1.0
O B:HOH819 2.3 47.4 1.0
OE1 A:GLU46 2.3 41.2 1.0
O B:SER214 2.4 13.8 1.0
OE2 A:GLU46 2.8 34.6 1.0
CD A:GLU46 2.9 35.2 1.0
O A:HOH784 3.3 46.7 1.0
OE2 B:GLU217 3.5 33.1 1.0
C B:SER214 3.5 14.1 1.0
O A:HOH790 3.9 36.9 1.0
O B:HOH545 4.2 18.1 1.0
CA B:SER214 4.3 13.7 1.0
CG A:GLU46 4.4 27.4 1.0
CB B:SER214 4.4 16.9 1.0
O B:HOH808 4.5 42.7 1.0
N B:LYS215 4.6 12.5 1.0
O B:HOH742 4.6 35.4 1.0
CA B:LYS215 4.7 13.6 1.0
CD B:GLU217 4.8 33.4 1.0
OG B:SER214 4.9 18.9 1.0

Calcium binding site 2 out of 10 in 4mbz

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Calcium binding site 2 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


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'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:20.8
occ:0.60
 O C:HOH507 2.0 12.9 1.0
O C:HOH816 2.1 35.8 1.0
O C:SER214 2.3 14.2 1.0
OE1 B:GLU46 2.4 39.3 1.0
O C:HOH766 2.4 50.1 1.0
O B:HOH828 2.7 41.2 1.0
OE2 B:GLU46 2.7 28.8 1.0
O B:HOH666 2.9 42.3 1.0
CD B:GLU46 2.9 34.7 1.0
C C:SER214 3.5 14.3 1.0
OE2 C:GLU217 3.6 35.8 1.0
O B:HOH774 4.0 38.8 1.0
O C:HOH549 4.2 17.6 1.0
CA C:SER214 4.2 13.7 1.0
CB C:SER214 4.4 16.3 1.0
CG B:GLU46 4.4 29.5 1.0
N C:LYS215 4.5 13.2 1.0
O C:HOH736 4.6 30.7 1.0
CA C:LYS215 4.7 14.8 1.0
O C:HOH829 4.8 43.0 1.0
CD C:GLU217 4.8 31.4 1.0
OG C:SER214 4.9 17.4 1.0

Calcium binding site 3 out of 10 in 4mbz

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Calcium binding site 3 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


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'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:23.6
occ:0.60
 O D:HOH519 2.0 16.1 1.0
O D:HOH689 2.3 45.4 1.0
OE1 C:GLU46 2.3 42.8 1.0
O D:SER214 2.3 17.7 1.0
O D:HOH773 2.4 45.6 1.0
O C:HOH800 2.5 50.4 1.0
OE2 C:GLU46 2.9 33.2 1.0
CD C:GLU46 2.9 37.9 1.0
O C:HOH771 2.9 49.4 1.0
C D:SER214 3.5 18.7 1.0
OE2 D:GLU217 3.6 29.0 0.8
O D:HOH542 4.2 23.5 1.0
CA D:SER214 4.2 18.1 1.0
CG C:GLU46 4.4 31.2 1.0
CB D:SER214 4.4 20.2 1.0
N D:LYS215 4.5 17.5 1.0
O D:HOH649 4.6 37.1 1.0
CA D:LYS215 4.7 17.8 1.0
CD D:GLU217 4.8 24.3 0.5
OG D:SER214 4.9 21.4 1.0

Calcium binding site 4 out of 10 in 4mbz

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Calcium binding site 4 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


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'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:21.7
occ:0.60
 O E:HOH833 2.0 15.8 1.0
O E:HOH723 2.1 39.8 1.0
OE1 D:GLU46 2.3 51.8 1.0
O E:SER214 2.4 17.9 1.0
OE2 D:GLU46 2.7 35.9 1.0
CD D:GLU46 2.8 40.3 1.0
C E:SER214 3.5 17.6 1.0
OE1 E:GLU217 3.8 25.7 0.5
CA E:SER214 4.2 17.5 1.0
CG D:GLU46 4.3 34.2 1.0
O E:HOH545 4.3 24.2 1.0
CB E:SER214 4.3 18.1 1.0
N E:LYS215 4.6 16.7 1.0
O E:HOH655 4.6 36.5 1.0
OE1 E:GLU217 4.8 26.9 0.5
CA E:LYS215 4.8 18.2 1.0
OG E:SER214 4.9 21.3 1.0
CD E:GLU217 4.9 21.7 0.5
OH D:TYR286 5.0 23.9 1.0

Calcium binding site 5 out of 10 in 4mbz

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Calcium binding site 5 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


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'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:20.4
occ:0.60
 O A:HOH503 1.9 15.0 1.0
O A:HOH846 2.1 33.0 1.0
O A:HOH519 2.2 42.5 1.0
O A:SER214 2.3 15.2 1.0
OE1 E:GLU46 2.4 46.5 1.0
O E:HOH799 2.7 44.7 1.0
OE2 E:GLU46 2.7 35.8 1.0
CD E:GLU46 2.9 36.8 1.0
C A:SER214 3.5 16.6 1.0
OE2 A:GLU217 3.6 36.6 1.0
CA A:SER214 4.2 16.7 1.0
O A:HOH561 4.2 19.4 1.0
CG E:GLU46 4.4 30.9 1.0
CB A:SER214 4.4 17.9 1.0
N A:LYS215 4.6 14.5 1.0
O A:HOH678 4.7 30.2 1.0
CA A:LYS215 4.8 15.6 1.0
CD A:GLU217 4.8 32.7 1.0
OG A:SER214 4.9 19.0 1.0
OH E:TYR286 4.9 20.7 1.0

Calcium binding site 6 out of 10 in 4mbz

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Calcium binding site 6 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


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'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca401

b:23.1
occ:0.60
 O G:HOH718 2.0 37.4 1.0
O G:HOH710 2.0 24.5 1.0
O G:HOH719 2.1 37.6 1.0
OE1 F:GLU46 2.3 50.3 1.0
O G:SER214 2.4 22.3 1.0
O F:HOH608 2.4 38.7 1.0
OE2 F:GLU46 2.8 35.9 1.0
CD F:GLU46 2.9 39.1 1.0
C G:SER214 3.5 22.2 1.0
OE2 G:GLU217 3.8 26.7 0.5
CA G:SER214 4.3 22.6 1.0
O G:HOH543 4.3 27.2 1.0
CG F:GLU46 4.4 34.7 1.0
CB G:SER214 4.5 25.1 1.0
N G:LYS215 4.6 20.6 1.0
OE2 G:GLU217 4.6 28.7 0.5
CA G:LYS215 4.8 21.5 1.0
OG G:SER214 4.9 27.0 1.0
CD G:GLU217 4.9 23.6 0.5
O G:HOH704 5.0 46.1 1.0

Calcium binding site 7 out of 10 in 4mbz

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Calcium binding site 7 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


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'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca401

b:24.7
occ:0.60
 O H:HOH526 2.0 18.5 1.0
O H:HOH658 2.1 42.7 1.0
O H:HOH720 2.2 42.1 1.0
O H:SER214 2.3 22.8 1.0
OE1 G:GLU46 2.3 48.8 1.0
OE2 G:GLU46 2.6 39.4 1.0
O G:HOH656 2.7 41.3 1.0
CD G:GLU46 2.8 42.5 1.0
C H:SER214 3.5 23.0 1.0
OE2 H:GLU217 3.8 28.7 0.5
O H:HOH530 4.2 21.7 1.0
CA H:SER214 4.2 23.5 1.0
CG G:GLU46 4.3 38.2 1.0
CB H:SER214 4.5 25.9 1.0
N H:LYS215 4.5 21.5 1.0
CA H:LYS215 4.7 22.2 1.0
O H:HOH653 4.8 36.2 1.0
OE1 H:GLU217 4.8 27.0 0.2
CD H:GLU217 4.9 25.9 0.5
OH G:TYR286 4.9 27.7 1.0

Calcium binding site 8 out of 10 in 4mbz

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Calcium binding site 8 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


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'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca401

b:40.6
occ:1.00
 O H:HOH716 2.1 26.8 1.0
O I:HOH718 2.3 39.7 1.0
O I:HOH732 2.3 43.9 1.0
O I:SER214 2.4 23.8 1.0
OE1 H:GLU46 2.6 48.9 1.0
OE2 H:GLU46 2.8 43.1 1.0
CD H:GLU46 2.9 44.2 1.0
C I:SER214 3.5 25.1 1.0
OE2 I:GLU217 3.8 32.3 0.5
CG H:GLU46 4.3 39.2 1.0
CA I:SER214 4.3 24.6 1.0
O I:HOH514 4.3 24.6 1.0
CB I:SER214 4.4 24.9 1.0
N I:LYS215 4.6 22.6 1.0
CA I:LYS215 4.8 23.4 1.0
OE2 I:GLU217 4.9 36.0 0.5
CD I:GLU217 5.0 27.8 0.5
OG I:SER214 5.0 26.5 1.0

Calcium binding site 9 out of 10 in 4mbz

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Calcium binding site 9 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


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'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca401

b:23.6
occ:0.60
 O J:HOH763 2.1 42.9 1.0
O I:HOH736 2.1 17.6 1.0
O J:SER214 2.4 19.6 1.0
OE1 I:GLU46 2.4 38.7 0.5
O J:HOH661 2.4 46.1 1.0
OE1 I:GLU46 2.5 31.9 0.5
OE2 I:GLU46 2.7 31.1 0.5
CD I:GLU46 2.9 30.6 0.5
CD I:GLU46 3.0 35.0 0.5
OE2 I:GLU46 3.1 34.1 0.5
O I:HOH502 3.5 45.6 1.0
C J:SER214 3.5 19.8 1.0
OE2 J:GLU217 3.7 47.2 1.0
O I:HOH708 4.1 46.0 1.0
O J:HOH528 4.2 22.8 1.0
CA J:SER214 4.2 19.9 1.0
CB J:SER214 4.4 20.2 1.0
CG I:GLU46 4.4 29.8 0.5
CG I:GLU46 4.4 32.6 0.5
O J:HOH647 4.5 35.2 1.0
N J:LYS215 4.6 18.7 1.0
CA J:LYS215 4.8 20.7 1.0
CD J:GLU217 4.9 34.7 1.0
OG J:SER214 4.9 23.4 1.0

Calcium binding site 10 out of 10 in 4mbz

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Calcium binding site 10 out of 10 in the Structure of B-Lymphotropic Polyomavirus VP1 in Complex with 3'- Sialyllactosamine


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'- Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca401

b:26.8
occ:0.60
 O F:HOH630 2.0 36.1 1.0
O F:HOH503 2.1 19.2 1.0
O F:SER214 2.3 21.5 1.0
OE1 J:GLU46 2.3 46.4 1.0
O F:HOH775 2.6 47.4 1.0
O J:HOH736 2.6 47.4 1.0
OE2 J:GLU46 2.7 42.5 1.0
CD J:GLU46 2.9 41.4 1.0
C F:SER214 3.5 21.6 1.0
OE2 F:GLU217 3.7 28.9 0.7
CA F:SER214 4.2 20.6 1.0
O F:HOH556 4.3 25.9 1.0
OE2 F:GLU217 4.3 30.1 0.3
CB F:SER214 4.4 22.5 1.0
CG J:GLU46 4.4 36.2 1.0
O F:HOH769 4.4 44.6 1.0
O F:HOH601 4.5 43.3 1.0
N F:LYS215 4.5 20.5 1.0
CA F:LYS215 4.7 21.5 1.0
CD F:GLU217 4.9 24.1 0.5
OG F:SER214 4.9 23.3 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: Sun Jul 14 10:18:46 2024

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