Atomistry » Sodium » PDB 4owe-4pd7 » 4pcg
Atomistry »
  Sodium »
    PDB 4owe-4pd7 »
      4pcg »

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

Go back to Sodium Binding Sites List in 4pcg
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

Go back to Sodium Binding Sites List in 4pcg
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

Go back to Sodium Binding Sites List in 4pcg
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

Go back to Sodium Binding Sites List in 4pcg
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

Go back to Sodium Binding Sites List in 4pcg
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

Go back to Sodium Binding Sites List in 4pcg
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

Go back to Sodium Binding Sites List in 4pcg
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy