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Sodium in PDB 4pcg: Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer

Protein crystallography data

The structure of Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer, PDB code: 4pcg was solved by L.J.Stroh, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.900, 89.440, 125.270, 90.00, 131.26, 90.00
R / Rfree (%) 14.8 / 17.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer (pdb code 4pcg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer, PDB code: 4pcg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4pcg

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Sodium binding site 1 out of 7 in the Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:31.9
occ:1.00
 OG1 A:THR65 2.4 30.1 1.0
O A:HOH528 2.4 29.0 1.0
OD2 A:ASP69 2.4 32.0 1.0
O A:THR67 2.5 29.5 1.0
OG1 A:THR63 2.5 31.6 1.0
O A:THR63 3.0 31.6 1.0
CG A:ASP69 3.5 31.9 1.0
C A:THR63 3.6 29.1 1.0
CB A:THR65 3.6 37.8 1.0
C A:THR67 3.7 30.7 1.0
O A:HOH517 3.7 33.7 1.0
N A:THR65 3.7 36.3 1.0
O A:HOH482 3.8 25.8 1.0
CB A:THR63 3.8 29.4 1.0
O A:THR65 4.0 41.4 1.0
OD1 A:ASP69 4.0 31.6 1.0
O A:HOH575 4.0 41.6 1.0
CA A:THR65 4.1 37.1 1.0
CA A:THR63 4.1 25.3 1.0
C A:THR65 4.2 37.7 1.0
O A:HOH503 4.2 33.2 1.0
CG2 A:THR65 4.2 40.7 1.0
N A:THR67 4.2 34.7 1.0
N A:THR63 4.3 23.4 1.0
O A:HOH470 4.4 22.7 1.0
CA A:THR67 4.5 33.7 1.0
N A:PHE64 4.5 31.1 1.0
CB A:ASP69 4.6 28.2 1.0
N A:ASP69 4.7 24.6 1.0
C A:PHE64 4.7 36.5 1.0
N A:LEU68 4.7 28.4 1.0
CB A:THR67 4.8 34.6 1.0
CA A:LEU68 4.8 27.0 1.0
CG2 A:THR63 4.8 30.7 1.0
CA A:PHE64 4.9 34.3 1.0

Sodium binding site 2 out of 7 in 4pcg

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Sodium binding site 2 out of 7 in the Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:27.4
occ:1.00
 O B:HOH590 2.3 26.0 1.0
OD2 B:ASP69 2.4 27.5 1.0
O B:THR67 2.5 25.0 1.0
OG1 B:THR65 2.5 27.7 1.0
OG1 B:THR63 2.6 25.7 1.0
O B:THR63 3.0 29.0 1.0
CG B:ASP69 3.5 29.8 1.0
C B:THR63 3.6 26.5 1.0
C B:THR67 3.7 27.5 1.0
N B:THR65 3.7 33.6 1.0
CB B:THR65 3.7 32.1 1.0
O B:HOH591 3.8 31.0 1.0
O B:HOH472 3.8 23.4 1.0
CB B:THR63 3.8 27.0 1.0
O B:HOH612 3.9 46.2 1.0
O B:HOH594 4.0 40.0 1.0
OD1 B:ASP69 4.0 27.7 1.0
O B:THR65 4.1 35.2 1.0
CA B:THR63 4.1 23.8 1.0
CA B:THR65 4.1 30.4 1.0
O B:HOH515 4.2 29.8 1.0
N B:THR63 4.2 21.8 1.0
C B:THR65 4.3 34.0 1.0
N B:THR67 4.3 31.0 1.0
O B:HOH479 4.3 23.3 1.0
CG2 B:THR65 4.3 36.5 1.0
N B:PHE64 4.5 27.4 1.0
CA B:THR67 4.5 31.0 1.0
CB B:ASP69 4.6 25.9 1.0
N B:ASP69 4.6 22.3 1.0
N B:LEU68 4.6 24.8 1.0
C B:PHE64 4.7 33.8 1.0
CA B:LEU68 4.7 23.6 1.0
CB B:THR67 4.9 29.5 1.0
CA B:PHE64 4.9 32.5 1.0
CG2 B:THR63 5.0 29.6 1.0

Sodium binding site 3 out of 7 in 4pcg

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Sodium binding site 3 out of 7 in the Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na303

b:28.9
occ:1.00
 O C:HOH474 2.3 30.8 1.0
OD2 C:ASP69 2.4 33.2 1.0
O C:THR67 2.4 28.0 1.0
OG1 C:THR65 2.5 30.3 1.0
OG1 C:THR63 2.6 27.3 1.0
O C:THR63 2.9 33.1 1.0
CG C:ASP69 3.5 33.2 1.0
C C:THR63 3.6 32.1 1.0
C C:THR67 3.6 30.5 1.0
O C:HOH477 3.6 34.6 1.0
CB C:THR65 3.7 39.0 1.0
N C:THR65 3.8 39.3 1.0
O C:HOH479 3.8 27.4 1.0
CB C:THR63 3.8 31.6 1.0
OD1 C:ASP69 4.0 33.1 1.0
O C:THR65 4.1 39.1 1.0
O C:HOH557 4.1 39.8 1.0
O C:HOH522 4.1 34.3 1.0
CA C:THR63 4.1 28.1 1.0
CA C:THR65 4.1 38.8 1.0
N C:THR67 4.3 35.2 1.0
CG2 C:THR65 4.3 43.0 1.0
N C:THR63 4.3 27.1 1.0
C C:THR65 4.3 39.2 1.0
O C:HOH441 4.3 25.4 1.0
CA C:THR67 4.4 33.0 1.0
N C:PHE64 4.5 31.7 1.0
N C:LEU68 4.6 27.8 1.0
N C:ASP69 4.6 27.7 1.0
CB C:ASP69 4.6 29.1 1.0
CA C:LEU68 4.7 28.0 1.0
C C:PHE64 4.8 41.9 1.0
CB C:THR67 4.9 34.9 1.0
CG2 C:THR63 4.9 34.2 1.0

Sodium binding site 4 out of 7 in 4pcg

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Sodium binding site 4 out of 7 in the Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na304

b:26.0
occ:1.00
 O C:HOH415 2.2 31.4 1.0
O C:HOH530 2.3 32.3 1.0
OD1 C:ASN82 2.4 30.0 1.0
O C:GLY241 2.4 24.7 1.0
O C:LEU83 2.4 30.4 1.0
O C:HOH414 2.5 32.3 1.0
CG C:ASN82 3.3 29.4 1.0
C C:GLY241 3.4 24.9 1.0
C C:LEU83 3.5 28.0 1.0
N C:LEU83 3.6 23.3 1.0
CA C:GLY241 3.7 26.6 1.0
ND2 C:ASN82 3.8 30.3 1.0
OE1 C:GLU85 4.0 65.0 1.0
CA C:LEU83 4.1 25.9 1.0
C C:ASN82 4.5 26.5 1.0
CB C:ASN82 4.5 27.6 1.0
CB C:LEU83 4.5 25.0 1.0
CA C:ASN82 4.5 25.3 1.0
N C:ALA242 4.6 22.9 1.0
N C:PRO84 4.7 30.6 1.0
C C:PRO84 4.7 34.2 1.0
O C:PHE240 4.7 36.7 1.0
O C:PRO84 4.8 30.0 1.0
N C:GLU85 4.9 33.6 1.0
N C:GLY241 5.0 28.9 1.0

Sodium binding site 5 out of 7 in 4pcg

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Sodium binding site 5 out of 7 in the Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na303

b:29.5
occ:1.00
 O D:HOH505 2.3 27.5 1.0
O D:THR67 2.4 26.5 1.0
OG1 D:THR65 2.5 28.4 1.0
OD2 D:ASP69 2.5 31.7 1.0
OG1 D:THR63 2.5 31.2 1.0
O D:THR63 2.9 34.5 1.0
CG D:ASP69 3.5 31.9 1.0
C D:THR67 3.6 30.1 1.0
C D:THR63 3.6 29.3 1.0
CB D:THR65 3.7 37.8 1.0
O D:HOH465 3.7 30.3 1.0
N D:THR65 3.7 35.5 1.0
O D:HOH462 3.7 27.2 1.0
CB D:THR63 3.8 31.0 1.0
O D:HOH596 3.9 40.1 1.0
O D:THR65 4.0 35.7 1.0
OD1 D:ASP69 4.0 30.0 1.0
CA D:THR65 4.1 34.5 1.0
CA D:THR63 4.1 29.8 1.0
O D:HOH488 4.2 32.6 1.0
C D:THR65 4.2 37.2 1.0
N D:THR67 4.2 32.6 1.0
N D:THR63 4.3 26.4 1.0
CG2 D:THR65 4.3 35.9 1.0
O D:HOH430 4.4 24.3 1.0
CA D:THR67 4.4 32.6 1.0
N D:PHE64 4.5 32.9 1.0
N D:LEU68 4.6 25.8 1.0
CB D:ASP69 4.7 25.1 1.0
N D:ASP69 4.7 25.9 1.0
C D:PHE64 4.7 37.8 1.0
CA D:LEU68 4.7 25.0 1.0
CB D:THR67 4.8 33.9 1.0
CG2 D:THR63 4.9 32.6 1.0
CA D:PHE64 5.0 36.2 1.0

Sodium binding site 6 out of 7 in 4pcg

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Sodium binding site 6 out of 7 in the Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:30.1
occ:1.00
 O D:HOH555 2.3 35.6 1.0
O D:HOH409 2.4 33.8 1.0
OD1 D:ASN82 2.4 32.7 1.0
O D:HOH414 2.4 35.4 1.0
O D:LEU83 2.5 33.4 1.0
O D:GLY241 2.5 27.6 1.0
CG D:ASN82 3.3 31.4 1.0
C D:GLY241 3.4 28.0 1.0
C D:LEU83 3.5 30.4 1.0
N D:LEU83 3.6 26.5 1.0
ND2 D:ASN82 3.7 33.1 1.0
CA D:GLY241 3.7 30.5 1.0
CA D:LEU83 4.1 29.1 1.0
OE1 D:GLU85 4.3 62.3 1.0
O D:HOH412 4.5 49.1 1.0
C D:ASN82 4.5 27.8 1.0
CB D:LEU83 4.5 28.9 1.0
C D:PRO84 4.6 37.9 1.0
CB D:ASN82 4.6 29.8 1.0
O D:PRO84 4.6 37.3 1.0
CA D:ASN82 4.7 28.5 1.0
N D:PRO84 4.7 34.9 1.0
N D:ALA242 4.7 26.2 1.0
O D:PHE240 4.7 39.9 1.0
N D:GLU85 4.7 36.9 1.0
CA D:PRO84 4.9 36.0 1.0
N D:GLY241 5.0 33.4 1.0

Sodium binding site 7 out of 7 in 4pcg

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Sodium binding site 7 out of 7 in the Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Human Polyomavirus 6 (HPYV6) VP1 Pentamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:40.7
occ:1.00
 O E:HOH467 2.4 33.6 1.0
OG1 E:THR65 2.4 35.2 1.0
OD2 E:ASP69 2.5 36.9 1.0
O E:THR67 2.6 32.8 1.0
OG1 E:THR63 2.6 34.1 1.0
O E:THR63 2.9 38.5 1.0
C E:THR63 3.6 37.6 1.0
CG E:ASP69 3.6 44.1 1.0
CB E:THR65 3.7 45.2 1.0
O E:HOH563 3.7 43.0 1.0
C E:THR67 3.7 35.5 1.0
N E:THR65 3.7 44.3 1.0
O E:HOH459 3.8 34.9 1.0
CB E:THR63 3.9 37.3 1.0
O E:HOH544 4.1 41.0 1.0
O E:THR65 4.1 45.5 1.0
CA E:THR65 4.1 41.6 1.0
CA E:THR63 4.1 34.4 1.0
OD1 E:ASP69 4.2 36.6 1.0
N E:THR67 4.2 42.1 1.0
C E:THR65 4.2 46.1 1.0
N E:THR63 4.3 31.9 1.0
CG2 E:THR65 4.3 46.2 1.0
CA E:THR67 4.5 35.8 1.0
N E:PHE64 4.5 46.0 1.0
O E:HOH433 4.5 31.5 1.0
C E:PHE64 4.7 43.7 1.0
N E:LEU68 4.8 32.6 1.0
CB E:ASP69 4.8 35.2 1.0
N E:ASP69 4.9 33.4 1.0
CB E:THR67 4.9 37.8 1.0
CA E:LEU68 4.9 33.1 1.0
CG2 E:THR63 4.9 39.2 1.0
CA E:PHE64 4.9 49.8 1.0

Reference:

L.J.Stroh, U.Neu, B.S.Blaum, M.H.Buch, R.L.Garcea, T.Stehle. Structure Analysis of the Major Capsid Proteins of Human Polyomaviruses 6 and 7 Reveals An Obstructed Sialic Acid Binding Site. J.Virol. V. 88 10831 2014.
ISSN: ESSN 1098-5514
PubMed: 25008942
DOI: 10.1128/JVI.01084-14
Page generated: Mon Oct 7 17:40:53 2024

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