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Calcium in PDB 4poq: Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9

Protein crystallography data

The structure of Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9, PDB code: 4poq was solved by Z.M.Khan, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 133.65 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.330, 180.090, 199.390, 90.00, 90.00, 90.00
R / Rfree (%) 19.6 / 23.6

Calcium Binding Sites:

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

Calcium binding site 1 out of 10 in 4poq

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Calcium binding site 1 out of 10 in the Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9


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 VP1 Pentamer of Human Polyomavirus 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:44.0
occ:1.00
 O B:HOH674 2.2 29.0 1.0
O B:SER217 2.4 23.4 1.0
OE2 A:GLU49 2.5 35.7 1.0
O A:HOH689 2.6 32.1 1.0
OE1 A:GLU49 2.7 32.1 1.0
O A:HOH588 2.7 35.3 1.0
CD A:GLU49 3.0 33.0 1.0
C B:SER217 3.5 22.3 1.0
OE2 B:GLU220 4.0 41.8 1.0
CA B:SER217 4.2 21.6 1.0
O B:HOH577 4.2 26.9 1.0
CB B:SER217 4.3 22.2 1.0
O B:HOH637 4.4 31.7 1.0
CG A:GLU49 4.5 30.3 1.0
N B:LYS218 4.6 21.1 1.0
OH A:TYR289 4.7 21.6 1.0
CA B:LYS218 4.8 21.8 1.0
OG B:SER217 4.9 21.9 1.0

Calcium binding site 2 out of 10 in 4poq

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Calcium binding site 2 out of 10 in the Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9


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 VP1 Pentamer of Human Polyomavirus 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:39.8
occ:1.00
 O C:HOH501 2.3 48.1 1.0
O C:HOH575 2.3 32.6 1.0
O C:SER217 2.3 25.1 1.0
OE2 B:GLU49 2.5 40.3 1.0
O B:HOH695 2.8 36.2 1.0
OE1 B:GLU49 2.9 33.7 1.0
CD B:GLU49 3.1 35.3 1.0
C C:SER217 3.5 24.3 1.0
OE2 C:GLU220 3.9 27.9 0.5
CA C:SER217 4.2 23.2 1.0
CB C:SER217 4.3 23.7 1.0
O C:HOH607 4.3 27.9 1.0
CG B:GLU49 4.5 32.0 1.0
O C:HOH631 4.5 35.5 1.0
N C:LYS218 4.6 23.6 1.0
OH B:TYR289 4.7 24.2 1.0
CA C:LYS218 4.8 24.4 1.0
OE1 C:GLU220 4.8 26.0 0.5
OG C:SER217 4.9 23.8 1.0

Calcium binding site 3 out of 10 in 4poq

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Calcium binding site 3 out of 10 in the Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9


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 VP1 Pentamer of Human Polyomavirus 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:45.3
occ:1.00
 O D:HOH652 2.3 44.4 1.0
OE2 C:GLU49 2.3 41.5 1.0
O D:HOH639 2.4 35.3 1.0
O D:SER217 2.4 29.5 1.0
OE1 C:GLU49 2.9 38.3 1.0
CD C:GLU49 3.0 39.5 1.0
C D:SER217 3.6 28.3 1.0
OE2 D:GLU220 3.9 47.1 1.0
O D:HOH653 4.1 38.5 1.0
O D:HOH650 4.3 31.3 1.0
CA D:SER217 4.4 28.2 1.0
CG C:GLU49 4.4 36.5 1.0
CB D:SER217 4.5 28.4 1.0
N D:LYS218 4.6 28.3 1.0
CA D:LYS218 4.8 28.9 1.0
OH C:TYR289 4.9 26.1 1.0
CD D:GLU220 4.9 42.7 1.0

Calcium binding site 4 out of 10 in 4poq

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Calcium binding site 4 out of 10 in the Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9


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 VP1 Pentamer of Human Polyomavirus 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:51.1
occ:1.00
 O E:SER217 2.4 28.1 1.0
OE2 D:GLU49 2.7 42.1 1.0
O E:HOH670 2.8 51.4 1.0
O D:HOH659 3.1 43.3 1.0
OE1 D:GLU49 3.1 39.7 1.0
CD D:GLU49 3.3 40.7 1.0
C E:SER217 3.6 28.4 1.0
CA E:SER217 4.3 27.5 1.0
O E:HOH672 4.4 28.0 1.0
CB E:SER217 4.4 27.3 1.0
N E:LYS218 4.6 28.8 1.0
OE2 E:GLU220 4.7 54.4 1.0
CG D:GLU49 4.8 37.5 1.0
CA E:LYS218 4.8 29.2 1.0
O E:HOH651 4.8 42.0 1.0
OH D:TYR289 4.9 26.8 1.0
OG E:SER217 4.9 27.4 1.0

Calcium binding site 5 out of 10 in 4poq

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Calcium binding site 5 out of 10 in the Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9


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 VP1 Pentamer of Human Polyomavirus 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:36.9
occ:1.00
 O A:SER217 2.3 25.2 1.0
O A:HOH695 2.3 47.5 1.0
O E:HOH681 2.5 38.1 1.0
OE1 E:GLU49 2.7 37.7 1.0
OE2 E:GLU49 2.8 41.3 1.0
CD E:GLU49 3.1 39.1 1.0
C A:SER217 3.5 24.2 1.0
OE2 A:GLU220 3.9 37.0 1.0
CA A:SER217 4.2 23.6 1.0
O A:HOH674 4.3 32.3 1.0
CB A:SER217 4.4 24.7 1.0
N A:LYS218 4.5 22.9 1.0
CG E:GLU49 4.5 35.7 1.0
O A:HOH694 4.6 36.0 1.0
CD A:GLU220 4.7 34.6 1.0
CA A:LYS218 4.7 23.2 1.0
OH E:TYR289 4.8 24.5 1.0
OG A:SER217 4.8 25.2 1.0

Calcium binding site 6 out of 10 in 4poq

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Calcium binding site 6 out of 10 in the Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9


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 VP1 Pentamer of Human Polyomavirus 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca401

b:55.5
occ:1.00
 O F:HOH637 2.1 33.0 1.0
O G:SER217 2.3 29.3 1.0
O G:HOH659 2.6 47.1 1.0
OE2 F:GLU49 2.6 46.6 1.0
O F:HOH638 2.6 40.2 1.0
OE1 F:GLU49 2.8 41.6 1.0
CD F:GLU49 3.1 42.7 1.0
OE2 G:GLU220 3.5 44.3 1.0
C G:SER217 3.5 28.4 1.0
O G:HOH626 4.2 33.0 1.0
CA G:SER217 4.3 27.8 1.0
CB G:SER217 4.5 27.5 1.0
N G:LYS218 4.5 27.8 1.0
CG F:GLU49 4.6 38.7 1.0
CA G:LYS218 4.6 28.0 1.0
CD G:GLU220 4.7 41.5 1.0
OH F:TYR289 4.7 24.8 1.0

Calcium binding site 7 out of 10 in 4poq

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Calcium binding site 7 out of 10 in the Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9


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 VP1 Pentamer of Human Polyomavirus 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca401

b:39.3
occ:1.00
 O H:HOH681 2.1 45.4 1.0
O H:HOH682 2.1 48.4 1.0
O H:SER217 2.4 23.8 1.0
OE2 G:GLU49 2.5 39.6 1.0
OE1 G:GLU49 3.0 35.9 1.0
CD G:GLU49 3.1 36.5 1.0
C H:SER217 3.6 22.9 1.0
OE2 H:GLU220 3.8 44.5 1.0
CA H:SER217 4.3 22.8 1.0
O H:HOH519 4.4 22.1 1.0
CB H:SER217 4.4 24.1 1.0
O H:HOH617 4.4 26.6 1.0
N H:LYS218 4.6 22.4 1.0
CG G:GLU49 4.6 33.1 1.0
CA H:LYS218 4.8 22.3 1.0
OH G:TYR289 4.8 23.1 1.0
OG H:SER217 5.0 25.1 1.0
CD H:GLU220 5.0 37.9 1.0

Calcium binding site 8 out of 10 in 4poq

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Calcium binding site 8 out of 10 in the Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9


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 VP1 Pentamer of Human Polyomavirus 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca401

b:33.6
occ:1.00
 O I:HOH656 2.3 30.7 1.0
O I:SER217 2.3 19.6 1.0
O I:HOH652 2.3 36.3 1.0
OE1 H:GLU49 2.5 35.8 1.0
O I:HOH634 2.6 44.3 1.0
OE2 H:GLU49 2.6 30.3 1.0
CD H:GLU49 2.9 31.6 1.0
C I:SER217 3.5 19.5 1.0
OE2 I:GLU220 3.6 39.2 1.0
CA I:SER217 4.2 19.1 1.0
CB I:SER217 4.3 19.8 1.0
CG H:GLU49 4.5 29.4 1.0
O I:HOH605 4.5 29.3 1.0
N I:LYS218 4.5 19.4 1.0
CA I:LYS218 4.7 21.1 1.0
OH H:TYR289 4.8 23.0 1.0
CD I:GLU220 4.8 35.1 1.0
OG I:SER217 4.9 19.2 1.0

Calcium binding site 9 out of 10 in 4poq

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Calcium binding site 9 out of 10 in the Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9


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 VP1 Pentamer of Human Polyomavirus 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca401

b:43.1
occ:1.00
 O J:HOH656 2.3 44.3 1.0
O J:HOH562 2.4 36.1 1.0
O I:HOH664 2.4 41.0 1.0
O J:SER217 2.4 26.0 1.0
OE2 I:GLU49 2.5 40.5 1.0
O J:HOH650 2.5 35.2 1.0
OE1 I:GLU49 2.8 36.9 1.0
CD I:GLU49 3.0 37.6 1.0
C J:SER217 3.6 25.9 1.0
CA J:SER217 4.2 24.9 1.0
O J:HOH590 4.3 28.8 1.0
CB J:SER217 4.4 24.4 1.0
CG I:GLU49 4.5 33.7 1.0
N J:LYS218 4.7 25.3 1.0
OH I:TYR289 4.7 25.7 1.0
OE2 J:GLU220 4.8 28.1 0.5
CA J:LYS218 4.9 26.0 1.0
OE2 J:GLU220 4.9 29.8 0.5
O I:HOH665 4.9 45.4 1.0

Calcium binding site 10 out of 10 in 4poq

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Calcium binding site 10 out of 10 in the Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9


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 VP1 Pentamer of Human Polyomavirus 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca401

b:45.3
occ:1.00
 O F:HOH649 2.3 39.6 1.0
O F:HOH642 2.3 40.0 1.0
OE2 J:GLU49 2.4 47.0 1.0
O F:SER217 2.4 29.9 1.0
OE1 J:GLU49 2.8 43.9 1.0
CD J:GLU49 2.9 44.0 1.0
C F:SER217 3.5 29.1 1.0
CA F:SER217 4.1 28.6 1.0
CB F:SER217 4.2 28.8 1.0
OE2 F:GLU220 4.3 35.4 0.5
CG J:GLU49 4.4 39.5 1.0
O F:HOH641 4.4 32.9 1.0
OE2 F:GLU220 4.5 35.8 0.5
OH J:TYR289 4.6 29.9 1.0
O F:HOH651 4.6 34.8 1.0
N F:LYS218 4.6 28.4 1.0
O F:HOH650 4.8 49.1 1.0
OG F:SER217 4.9 28.9 1.0
CA F:LYS218 4.9 28.9 1.0

Reference:

Z.M.Khan, T.Stehle. Structure of Unliganded VP1 Pentamer of Human Polyomavirus 9 To Be Published.
Page generated: Sun Jul 14 12:11:06 2024

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