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Calcium in PDB 4pot: Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine

Protein crystallography data

The structure of Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine, PDB code: 4pot 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) 132.42 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 103.400, 177.650, 198.650, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine (pdb code 4pot). 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 Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine, PDB code: 4pot:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 4pot

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Calcium binding site 1 out of 10 in the Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 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 Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:49.2
occ:1.00
 O B:HOH621 2.4 36.1 1.0
O B:SER217 2.4 22.8 1.0
OE2 A:GLU49 2.7 42.1 1.0
OE1 A:GLU49 2.9 37.2 1.0
CD A:GLU49 3.1 37.8 1.0
C B:SER217 3.6 22.3 1.0
OE2 B:GLU220 3.9 25.5 0.5
CA B:SER217 4.4 22.3 1.0
O B:HOH709 4.4 39.4 1.0
CB B:SER217 4.5 22.9 1.0
O B:HOH635 4.5 33.2 1.0
CG A:GLU49 4.6 33.3 1.0
N B:LYS218 4.6 22.1 1.0
CA B:LYS218 4.8 22.9 1.0
OH A:TYR289 4.8 23.4 1.0
OE1 B:GLU220 5.0 28.4 0.5

Calcium binding site 2 out of 10 in 4pot

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Calcium binding site 2 out of 10 in the Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 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 Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:44.7
occ:1.00
 O C:SER217 2.3 23.7 1.0
O C:HOH549 2.4 29.1 1.0
OE2 B:GLU49 2.6 37.1 1.0
O B:HOH640 2.6 41.7 1.0
O C:HOH574 2.7 49.7 1.0
O B:HOH698 2.7 42.0 1.0
OE1 B:GLU49 2.8 34.3 1.0
CD B:GLU49 3.1 35.1 1.0
C C:SER217 3.5 23.1 1.0
CA C:SER217 4.3 22.6 1.0
O C:HOH585 4.3 24.9 1.0
CB C:SER217 4.5 22.8 1.0
N C:LYS218 4.5 22.7 1.0
CG B:GLU49 4.6 30.9 1.0
CA C:LYS218 4.7 22.8 1.0
OH B:TYR289 4.8 24.0 1.0
OG C:SER217 5.0 22.6 1.0

Calcium binding site 3 out of 10 in 4pot

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Calcium binding site 3 out of 10 in the Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 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 Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:41.3
occ:1.00
 O D:HOH599 2.1 31.1 1.0
O D:SER217 2.3 27.0 1.0
O C:HOH623 2.5 42.5 1.0
O D:HOH682 2.6 41.5 1.0
OE2 C:GLU49 2.7 42.3 1.0
OE1 C:GLU49 2.8 39.8 1.0
CD C:GLU49 3.2 39.5 1.0
C D:SER217 3.5 26.1 1.0
OE2 D:GLU220 3.8 42.7 1.0
O C:HOH693 4.0 42.6 1.0
CA D:SER217 4.2 25.6 1.0
CB D:SER217 4.4 26.0 1.0
O D:HOH685 4.5 37.3 1.0
N D:LYS218 4.5 25.8 1.0
CA D:LYS218 4.7 25.6 1.0
CG C:GLU49 4.7 35.0 1.0
OH C:TYR289 4.8 26.3 1.0
OG D:SER217 4.8 26.8 1.0
CG D:LYS218 4.9 27.8 1.0
O C:HOH621 4.9 42.4 1.0
CD D:GLU220 5.0 37.6 1.0

Calcium binding site 4 out of 10 in 4pot

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Calcium binding site 4 out of 10 in the Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 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 Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:43.3
occ:1.00
 O E:HOH582 2.3 36.6 1.0
O E:SER217 2.5 24.3 1.0
OE2 D:GLU49 2.6 33.6 1.0
OE1 D:GLU49 2.8 32.1 1.0
CD D:GLU49 3.0 31.9 1.0
O D:HOH547 3.2 43.2 1.0
C E:SER217 3.6 23.7 1.0
CA E:SER217 4.3 23.6 1.0
CB E:SER217 4.5 23.9 1.0
O E:HOH589 4.5 34.5 1.0
CG D:GLU49 4.6 29.2 1.0
OE2 E:GLU220 4.7 41.6 1.0
N E:LYS218 4.7 23.8 1.0
OH D:TYR289 4.8 24.9 1.0
O E:HOH731 4.8 35.9 1.0
CA E:LYS218 4.9 24.3 1.0

Calcium binding site 5 out of 10 in 4pot

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Calcium binding site 5 out of 10 in the Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 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 Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca401

b:40.1
occ:1.00
 O A:HOH524 2.2 32.5 1.0
O A:SER217 2.4 22.9 1.0
O A:HOH658 2.6 40.1 1.0
OE2 E:GLU49 2.6 48.3 1.0
O E:HOH501 2.6 44.0 1.0
OE1 E:GLU49 2.7 45.3 1.0
CD E:GLU49 3.0 44.4 1.0
C A:SER217 3.6 23.2 1.0
OE1 A:GLU220 4.1 45.8 1.0
CA A:SER217 4.2 23.1 1.0
O A:HOH612 4.4 36.3 1.0
CB A:SER217 4.4 23.3 1.0
CG E:GLU49 4.5 38.6 1.0
O A:HOH701 4.6 32.7 1.0
N A:LYS218 4.6 22.9 1.0
OH E:TYR289 4.7 23.9 1.0
CA A:LYS218 4.8 23.6 1.0
CD A:GLU220 5.0 40.2 1.0

Calcium binding site 6 out of 10 in 4pot

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Calcium binding site 6 out of 10 in the Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 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 Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca401

b:41.9
occ:1.00
 O G:HOH596 2.2 33.3 1.0
O G:HOH692 2.4 39.2 1.0
O G:SER217 2.4 25.7 1.0
OE1 F:GLU49 2.7 38.5 1.0
OE2 F:GLU49 2.8 41.1 1.0
CD F:GLU49 3.1 38.3 1.0
C G:SER217 3.6 24.8 1.0
O G:HOH707 4.2 29.4 1.0
CA G:SER217 4.3 23.8 1.0
CB G:SER217 4.4 24.0 1.0
OE2 G:GLU220 4.6 52.7 1.0
N G:LYS218 4.6 24.5 1.0
CG F:GLU49 4.7 32.9 1.0
OH F:TYR289 4.8 23.0 1.0
CA G:LYS218 4.8 24.7 1.0
OG G:SER217 5.0 24.8 1.0

Calcium binding site 7 out of 10 in 4pot

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Calcium binding site 7 out of 10 in the Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 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 Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca401

b:43.0
occ:1.00
 O H:SER217 2.3 24.4 1.0
OE2 G:GLU49 2.4 40.1 1.0
O H:HOH620 2.5 32.3 1.0
O H:HOH658 2.5 46.9 1.0
OE1 G:GLU49 2.9 37.0 1.0
CD G:GLU49 3.0 36.8 1.0
C H:SER217 3.4 23.7 1.0
OE2 H:GLU220 3.9 49.9 1.0
CA H:SER217 4.1 23.1 1.0
CB H:SER217 4.3 23.3 1.0
O H:HOH592 4.3 32.3 1.0
CG G:GLU49 4.5 32.4 1.0
O H:HOH724 4.5 28.4 1.0
N H:LYS218 4.5 23.1 1.0
CA H:LYS218 4.7 23.8 1.0
OH G:TYR289 4.8 21.6 1.0
OG H:SER217 4.9 23.3 1.0

Calcium binding site 8 out of 10 in 4pot

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Calcium binding site 8 out of 10 in the Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 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 Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca401

b:49.4
occ:1.00
 O H:HOH647 2.2 32.8 1.0
O I:SER217 2.4 22.6 1.0
O I:HOH728 2.5 34.8 1.0
O H:HOH732 2.6 51.7 1.0
OE2 H:GLU49 2.7 44.7 1.0
OE1 H:GLU49 3.1 42.0 1.0
CD H:GLU49 3.2 41.7 1.0
OE2 I:GLU220 3.3 40.2 1.0
C I:SER217 3.6 23.3 1.0
O I:HOH670 4.2 30.4 1.0
CA I:SER217 4.5 22.6 1.0
N I:LYS218 4.5 23.5 1.0
CA I:LYS218 4.6 24.4 1.0
CD I:GLU220 4.6 36.1 1.0
CG H:GLU49 4.7 36.5 1.0
CB I:SER217 4.8 22.6 1.0
O I:HOH618 4.9 27.6 1.0

Calcium binding site 9 out of 10 in 4pot

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Calcium binding site 9 out of 10 in the Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 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 Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca401

b:53.8
occ:1.00
 O J:SER217 2.4 25.8 1.0
O J:HOH529 2.5 29.5 1.0
OE2 I:GLU49 2.6 44.5 1.0
OE1 I:GLU49 3.0 39.4 1.0
CD I:GLU49 3.1 39.9 1.0
C J:SER217 3.6 24.6 1.0
OE2 J:GLU220 4.0 46.3 1.0
CA J:SER217 4.4 24.4 1.0
O J:HOH721 4.5 26.5 1.0
CB J:SER217 4.5 25.4 1.0
CG I:GLU49 4.6 35.0 1.0
N J:LYS218 4.6 23.9 1.0
O J:HOH692 4.7 31.4 1.0
OH I:TYR289 4.8 27.7 1.0
CA J:LYS218 4.8 24.5 1.0

Calcium binding site 10 out of 10 in 4pot

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Calcium binding site 10 out of 10 in the Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 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 Human Polyomavirus 9 VP1 Pentamer in Complex with N- Glycolylneuraminic Acid Containing 3'-Sialyllactosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca401

b:37.7
occ:1.00
 O F:HOH627 2.3 40.4 1.0
O F:HOH580 2.4 31.5 1.0
O F:SER217 2.4 27.6 1.0
O F:HOH628 2.4 30.9 1.0
OE2 J:GLU49 2.4 54.8 1.0
OE1 J:GLU49 2.9 51.4 1.0
CD J:GLU49 3.0 50.8 1.0
C F:SER217 3.6 26.2 1.0
CA F:SER217 4.3 25.4 1.0
CG J:GLU49 4.5 45.4 1.0
CB F:SER217 4.5 25.6 1.0
OE1 F:GLU220 4.6 43.2 1.0
N F:LYS218 4.6 25.9 1.0
CA F:LYS218 4.7 26.5 1.0
OH J:TYR289 4.8 23.6 1.0
O F:HOH732 4.8 41.0 1.0
OE2 F:GLU220 4.9 41.4 1.0
CD F:GLU220 4.9 40.5 1.0

Reference:

Z.M.Khan, T.Stehle. Structure of Human Polyomavirus 9 VP1 Pentamer in Complex with N-Glycolylneuraminic Acid Containing 3'-Sialyllactosamine To Be Published.
Page generated: Sun Jul 14 12:13:44 2024

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