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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Sun Jul 14 10:18:46 2024

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