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Sodium in PDB 3m8a: Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009

Protein crystallography data

The structure of Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009, PDB code: 3m8a was solved by J.S.Brunzelle, Z.Wawrzak, T.Skarina, A.Savchenko, W.F.Anderson, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.25 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.847, 156.795, 73.523, 90.00, 109.21, 90.00
R / Rfree (%) 17 / 20.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009 (pdb code 3m8a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009, PDB code: 3m8a:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3m8a

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Sodium binding site 1 out of 4 in the Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na101

b:36.1
occ:1.00
O H:ASN25 2.2 29.9 1.0
O C:MET1 2.2 34.6 0.6
O C:MET1 2.2 35.4 0.4
O C:HOH254 2.3 31.6 1.0
O H:HOH106 2.3 27.3 1.0
O H:HOH924 2.5 41.5 1.0
O C:HOH381 2.6 43.1 1.0
C H:ASN25 3.4 28.9 1.0
C C:MET1 3.4 35.5 0.6
C C:MET1 3.4 36.2 0.4
CA H:ASN25 4.1 25.4 1.0
N C:MET1 4.2 37.4 0.6
N C:MET1 4.2 38.0 0.4
O C:HOH158 4.2 33.5 1.0
N C:ASP2 4.2 30.4 1.0
CA C:ASP2 4.2 28.7 1.0
CB H:ASN25 4.3 26.6 1.0
N H:GLY26 4.4 24.6 1.0
CA C:MET1 4.4 36.3 0.4
CA C:MET1 4.4 35.3 0.6
O H:HOH127 4.4 22.0 1.0
O H:HOH82 4.5 31.3 1.0
CB C:ASP2 4.6 30.6 1.0
CA H:GLY26 4.7 24.5 1.0
OD2 C:ASP2 4.8 47.1 1.0
CD2 H:LEU27 4.9 23.6 1.0
OD1 H:ASN25 4.9 41.0 1.0
C H:GLY26 4.9 28.3 1.0
CB C:ALA0 5.0 44.4 1.0

Sodium binding site 2 out of 4 in 3m8a

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Sodium binding site 2 out of 4 in the Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na100

b:50.5
occ:1.00
O I:MET1 2.3 38.3 1.0
O L:HOH1055 2.8 20.5 1.0
C I:MET1 3.0 37.8 1.0
O I:HOH78 3.1 34.0 1.0
CA I:MET1 3.3 36.1 1.0
O L:HOH1054 3.4 40.0 1.0
OG1 I:THR5 3.5 19.8 1.0
CB L:ASP29 3.5 15.2 1.0
CB I:MET1 3.6 38.1 1.0
N I:ASP2 4.1 31.2 1.0
CA L:ASP29 4.3 13.5 1.0
O I:HOH872 4.4 53.9 1.0
OD2 L:ASP29 4.5 23.1 1.0
CG L:ASP29 4.5 20.7 1.0
CB I:ASN4 4.5 15.5 1.0
N I:THR5 4.6 16.1 1.0
CG I:MET1 4.7 41.0 1.0
N I:MET1 4.7 36.5 1.0
CB I:THR5 4.7 20.3 1.0
N L:ALA30 4.8 15.4 1.0
CA I:ASP2 4.8 29.2 1.0

Sodium binding site 3 out of 4 in 3m8a

Go back to Sodium Binding Sites List in 3m8a
Sodium binding site 3 out of 4 in the Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na100

b:40.4
occ:1.00
O J:MET1 2.2 32.5 1.0
O J:HOH1044 2.3 41.0 1.0
C J:MET1 3.3 33.4 1.0
N J:MET1 4.1 36.4 1.0
N J:ASP2 4.1 26.7 1.0
CA J:ASP2 4.2 25.1 1.0
CA J:MET1 4.3 34.7 1.0
O J:HOH1041 4.4 52.3 1.0
CB J:ASP2 4.5 26.4 1.0
O J:HOH733 4.8 22.6 1.0
OD1 J:ASP2 4.8 38.7 1.0

Sodium binding site 4 out of 4 in 3m8a

Go back to Sodium Binding Sites List in 3m8a
Sodium binding site 4 out of 4 in the Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na100

b:52.4
occ:1.00
O L:MET1 2.2 40.6 1.0
O L:HOH517 2.3 41.0 1.0
C L:MET1 3.4 42.0 1.0
N L:MET1 4.1 45.1 1.0
N L:ASP2 4.2 36.3 1.0
CA L:ASP2 4.2 33.7 1.0
CA L:MET1 4.3 43.0 1.0
CB L:ASP2 4.5 36.0 1.0
CB L:ALA0 4.6 52.6 1.0
OD1 L:ASP2 4.7 48.2 1.0

Reference:

J.S.Brunzelle, Z.Wawrzak, T.Skarina, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of Swine Flu Virus NS1 N-Terminal Rna Binding Domain From H1N1 Influenza A/California/07/2009 To Be Published.
Page generated: Tue Dec 15 06:17:16 2020

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