Sodium in PDB 2x7a: Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain

The structure of Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain, PDB code: 2x7a was solved by G.Natrajan, A.A.Mccarthy, W.Weissenhorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.880 / 2.77
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.890, 85.930, 123.310, 90.00, 126.94, 90.00
R / Rfree (%)	23.64 / 27.28

The structure of Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	7 atoms

The binding sites of Sodium atom in the Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain (pdb code 2x7a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain, PDB code: 2x7a:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1148 b:98.5 occ:1.00 NZ B:LYS106 3.4 84.5 1.0 OG1 G:THR90 3.4 49.4 1.0 CL B:CL1149 3.5 0.4 1.0 CE B:LYS106 3.8 70.3 1.0 CA G:THR90 4.0 44.9 1.0 CD2 B:LEU102 4.1 56.9 1.0 CB G:THR90 4.2 44.1 1.0 CD B:LYS106 4.2 62.1 1.0 ND1 G:HIS93 4.2 0.3 1.0 CG2 G:THR90 4.4 37.6 1.0 N G:THR90 4.4 53.1 1.0 CG B:LEU102 4.7 49.4 1.0 CG G:HIS93 4.7 0.4 1.0 C G:ALA89 4.8 44.9 1.0 O G:ALA89 4.8 42.9 1.0 CB G:HIS93 4.8 82.9 1.0 CE1 G:HIS93 4.9 0.3 1.0

Sodium binding site 2 out of 7 in the Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1143 b:0.9 occ:1.00 CL F:CL1149 3.9 0.6 1.0 NE2 D:GLN110 4.9 0.8 1.0

Sodium binding site 3 out of 7 in the Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ F:Na1148 b:86.4 occ:1.00 O F:LYS106 3.4 45.4 1.0 CL E:CL1147 3.6 0.5 1.0 OE2 E:GLU105 3.9 47.0 1.0 CB F:LYS106 3.9 63.6 1.0 CA F:LYS106 4.0 40.3 1.0 CG F:LYS106 4.0 73.5 1.0 C F:LYS106 4.0 42.1 1.0 CB F:GLN110 4.3 0.1 1.0 NE2 E:GLN108 4.5 78.1 1.0 N F:GLN110 4.8 48.9 1.0 NE2 F:GLN110 4.8 0.5 1.0 CG F:GLN110 4.8 0.2 1.0 CD E:GLU105 4.9 53.4 1.0

Sodium binding site 4 out of 7 in the Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1145 b:81.3 occ:1.00 O G:ASP103 3.1 53.8 1.0 O G:HOH2005 3.4 56.4 1.0 CL G:CL1144 3.6 93.1 1.0 C G:ASP103 3.8 53.0 1.0 CB G:ALA107 3.9 35.5 1.0 CA G:ASP103 4.0 39.4 1.0 CB G:ASP103 4.0 51.9 1.0 N G:ALA107 4.1 37.1 1.0 O G:HOH2008 4.1 52.6 1.0 OD1 G:ASP103 4.2 37.7 1.0 CA G:ALA107 4.3 42.5 1.0 CG G:ASP103 4.4 44.4 1.0 CB G:LYS106 4.5 56.9 1.0 C G:LYS106 4.9 59.2 1.0 CE G:LYS106 5.0 54.2 1.0

Sodium binding site 5 out of 7 in the Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1144 b:83.1 occ:1.00 CL H:CL1145 3.7 97.3 1.0 OG E:SER101 4.1 55.6 1.0 CB H:HIS93 4.2 59.5 1.0 CG H:HIS93 4.7 70.3 1.0 CB E:SER101 4.9 39.1 1.0 ND1 H:HIS93 5.0 77.2 1.0

Sodium binding site 6 out of 7 in the Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ I:Na1149 b:93.2 occ:1.00 O I:LYS106 3.4 43.7 1.0 C I:LYS106 4.1 43.7 1.0 CB I:GLN110 4.1 79.9 1.0 CB I:LYS106 4.1 44.6 1.0 N I:GLN110 4.2 47.9 1.0 CA I:LYS106 4.2 44.2 1.0 OE1 I:GLN110 4.2 0.3 1.0 OE2 J:GLU105 4.2 68.5 1.0 CG I:LYS106 4.3 42.0 1.0 CA I:GLN110 4.4 49.8 1.0 CG I:GLN110 4.8 89.7 1.0 C I:GLY109 4.9 45.9 1.0 CD I:GLN110 5.0 0.8 1.0 CE I:LYS106 5.0 65.5 1.0

Sodium binding site 7 out of 7 in the Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structural Basis of Hiv-1 Tethering to Membranes By the BST2-Tetherin Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ J:Na1148 b:86.2 occ:1.00 CL J:CL1149 3.2 98.2 1.0 OG I:SER101 3.8 55.1 1.0 CB I:SER101 4.4 44.7 1.0 CD2 J:LEU102 4.5 41.1 1.0

A.Hinz, N.Miguet, G.Natrajan, Y.Usami, H.Yamanaka, P.Renesto, B.Hartlieb, A.A.Mccarthy, J.P.Simorre, H.Gottlinger, W.Weissenhorn. Structural Basis of Hiv-1 Tethering to Membranes By the Bst-2/Tetherin Ectodomain. Cell Host Microbe V. 7 314 2010.
ISSN: ISSN 1931-3128
PubMed: 20399176
DOI: 10.1016/J.CHOM.2010.03.005