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Sodium in PDB 3s7x: Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant

Protein crystallography data

The structure of Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant, PDB code: 3s7x was solved by U.Neu, J.Wang, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.36 / 2.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 166.200, 166.200, 127.570, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 25.3

Other elements in 3s7x:

The structure of Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant (pdb code 3s7x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant, PDB code: 3s7x:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 3s7x

Go back to Sodium Binding Sites List in 3s7x
Sodium binding site 1 out of 5 in the Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na297

b:37.1
occ:1.00
 OG E:SER240 3.2 53.1 1.0
OE1 E:GLU125 3.6 52.0 1.0
OE2 E:GLU125 3.7 52.5 1.0
OG E:SER243 4.0 53.6 1.0
N E:SER240 4.1 48.3 1.0
CD E:GLU125 4.1 50.5 1.0
CB E:SER240 4.2 50.4 1.0
CB E:SER243 4.2 51.5 1.0
O E:SER238 4.3 44.5 1.0
CA E:PHE239 4.3 44.0 1.0
C E:PHE239 4.4 45.6 1.0
C E:SER238 4.4 43.8 1.0
N E:PHE239 4.5 43.3 1.0
CB E:SER238 4.7 44.3 1.0
CA E:SER240 4.7 49.6 1.0

Sodium binding site 2 out of 5 in 3s7x

Go back to Sodium Binding Sites List in 3s7x
Sodium binding site 2 out of 5 in the Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na299

b:44.0
occ:1.00
 OG A:SER240 3.1 53.1 1.0
OE1 A:GLU125 3.4 52.1 1.0
OE2 A:GLU125 3.6 52.4 1.0
OG A:SER243 3.9 53.6 1.0
CD A:GLU125 3.9 50.5 1.0
N A:SER240 4.0 48.4 1.0
CB A:SER243 4.1 51.6 1.0
CB A:SER240 4.1 50.5 1.0
O A:SER238 4.3 44.5 1.0
CA A:PHE239 4.3 43.9 1.0
C A:PHE239 4.4 45.6 1.0
C A:SER238 4.5 43.8 1.0
N A:PHE239 4.6 43.2 1.0
CA A:SER240 4.7 49.7 1.0
CB A:SER238 4.9 44.2 1.0

Sodium binding site 3 out of 5 in 3s7x

Go back to Sodium Binding Sites List in 3s7x
Sodium binding site 3 out of 5 in the Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na298

b:48.9
occ:1.00
 OG B:SER240 3.0 53.1 1.0
OE1 B:GLU125 3.8 52.0 1.0
CB B:SER240 3.9 50.4 1.0
N B:SER240 3.9 48.3 1.0
OE2 B:GLU125 4.0 52.5 1.0
C B:PHE239 4.1 45.5 1.0
OG B:SER243 4.1 53.6 1.0
CA B:PHE239 4.2 44.0 1.0
CB B:SER243 4.3 51.6 1.0
CD B:GLU125 4.3 50.6 1.0
N B:PHE239 4.3 43.2 1.0
O B:SER238 4.3 44.5 1.0
C B:SER238 4.4 43.8 1.0
CA B:SER240 4.5 49.7 1.0
CB B:SER238 4.5 44.1 1.0
O B:PHE239 4.8 44.4 1.0

Sodium binding site 4 out of 5 in 3s7x

Go back to Sodium Binding Sites List in 3s7x
Sodium binding site 4 out of 5 in the Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na297

b:36.6
occ:1.00
 OE1 C:GLU125 3.4 52.1 1.0
OG C:SER240 3.5 53.1 1.0
OE2 C:GLU125 3.7 52.5 1.0
CD C:GLU125 3.9 50.5 1.0
O C:SER238 4.0 44.6 1.0
OG C:SER243 4.1 53.7 1.0
N C:SER240 4.2 48.2 1.0
CA C:PHE239 4.3 43.9 1.0
C C:SER238 4.3 43.8 1.0
CB C:SER243 4.5 51.6 1.0
N C:PHE239 4.5 43.2 1.0
C C:PHE239 4.5 45.5 1.0
CB C:SER240 4.6 50.5 1.0
CB C:SER238 4.8 44.2 1.0

Sodium binding site 5 out of 5 in 3s7x

Go back to Sodium Binding Sites List in 3s7x
Sodium binding site 5 out of 5 in the Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Unassembled Washington University Polyomavirus VP1 Pentamer R198K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na299

b:38.1
occ:1.00
 OG D:SER240 3.2 52.9 1.0
OE1 D:GLU125 3.4 52.0 1.0
OE2 D:GLU125 3.6 52.6 1.0
CD D:GLU125 3.9 50.5 1.0
N D:SER240 4.0 48.3 1.0
OG D:SER243 4.1 53.6 1.0
O D:SER238 4.1 44.5 1.0
CA D:PHE239 4.1 44.0 1.0
CB D:SER240 4.2 50.4 1.0
C D:PHE239 4.3 45.5 1.0
CB D:SER243 4.3 51.5 1.0
C D:SER238 4.3 43.7 1.0
N D:PHE239 4.4 43.2 1.0
CA D:SER240 4.7 49.6 1.0
CB D:SER238 4.7 44.3 1.0

Reference:

U.Neu, J.Wang, D.Macejak, R.L.Garcea, T.Stehle. Structures of the Major Capsid Proteins of the Human Ki and Wu Polyomaviruses. J.Virol. V. 85 7384 2011.
ISSN: ISSN 0022-538X
PubMed: 21543504
DOI: 10.1128/JVI.00382-11
Page generated: Mon Oct 7 12:54:45 2024

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