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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Sun Jul 14 10:18:46 2024

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