Sodium in PDB 8v13: Crystal Structure of Black Mamba Toxin in Complex with Centi-Snx-B03 Antibody

The structure of Crystal Structure of Black Mamba Toxin in Complex with Centi-Snx-B03 Antibody, PDB code: 8v13 was solved by S.Pletnev, J.Glanville, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.01 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	103.539, 72.252, 179.656, 90, 91.99, 90
R / Rfree (%)	18.1 / 22.9

The binding sites of Sodium atom in the Crystal Structure of Black Mamba Toxin in Complex with Centi-Snx-B03 Antibody (pdb code 8v13). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Black Mamba Toxin in Complex with Centi-Snx-B03 Antibody, PDB code: 8v13:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Black Mamba Toxin in Complex with Centi-Snx-B03 Antibody


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 Black Mamba Toxin in Complex with Centi-Snx-B03 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Na301 b:25.4 occ:1.00 O L:ASP92 2.3 20.5 1.0 O H:HOH326 2.3 22.8 1.0 O L:SER95 2.3 23.9 1.0 O L:HOH545 2.4 21.1 1.0 O T:HOH103 2.4 22.7 1.0 NE1 L:TRP91 3.2 23.1 1.0 CD1 L:TRP91 3.4 21.3 1.0 C L:ASP92 3.4 20.8 1.0 C L:SER95 3.5 25.5 1.0 O L:HOH454 3.8 23.2 1.0 CE2 L:TRP91 3.9 21.5 1.0 N L:ASP92 4.0 23.3 1.0 O T:ARG28 4.0 25.1 1.0 O H:HOH344 4.2 27.6 1.0 CG L:TRP91 4.2 23.6 1.0 N L:SER95 4.2 25.1 1.0 N L:ASN93 4.3 24.6 1.0 CA L:ASN93 4.3 24.5 1.0 C L:ASN93 4.3 25.1 1.0 CA L:ASP92 4.3 22.6 1.0 N L:ASP95A 4.4 25.5 1.0 OD2 H:ASP99 4.4 22.0 1.0 O L:ASN93 4.4 24.5 1.0 CA L:ASP95A 4.4 26.1 1.0 CD2 L:TRP91 4.5 22.0 1.0 CA L:SER95 4.5 24.8 1.0 O L:HOH441 4.5 33.5 1.0 CZ2 L:TRP91 4.6 23.9 1.0 N L:ASN94 4.7 24.8 1.0 C L:ASP95A 4.7 26.1 1.0 O L:ASP95A 4.9 26.2 1.0 CB L:ASP92 4.9 24.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Black Mamba Toxin in Complex with Centi-Snx-B03 Antibody


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 Black Mamba Toxin in Complex with Centi-Snx-B03 Antibody within 5.0Å range: probe atom residue distance (Å) B Occ l:Na301 b:27.3 occ:1.00 O l:SER95 2.2 23.9 1.0 O l:ASP92 2.3 24.8 1.0 O t:HOH113 2.3 24.5 1.0 O h:HOH342 2.4 24.1 1.0 O l:HOH513 2.4 23.2 1.0 NE1 l:TRP91 3.1 22.9 1.0 CD1 l:TRP91 3.4 25.4 1.0 C l:ASP92 3.4 24.3 1.0 C l:SER95 3.5 26.0 1.0 CE2 l:TRP91 3.8 22.1 1.0 N l:ASP92 4.0 25.8 1.0 O l:HOH487 4.0 28.6 1.0 N l:SER95 4.1 25.4 1.0 O h:HOH317 4.2 27.1 1.0 CG l:TRP91 4.2 23.1 1.0 N l:ASN93 4.2 25.2 1.0 O t:ARG28 4.2 22.7 1.0 CA l:ASN93 4.3 25.7 1.0 CA l:ASP92 4.3 29.1 1.0 CA l:SER95 4.3 26.0 1.0 O l:HOH413 4.3 26.9 1.0 C l:ASN93 4.3 21.7 1.0 O l:ASN93 4.4 24.5 1.0 N l:ASP95A 4.4 24.0 1.0 OD2 h:ASP99 4.4 24.9 1.0 CD2 l:TRP91 4.4 20.4 1.0 CA l:ASP95A 4.5 26.4 1.0 CZ2 l:TRP91 4.6 23.4 1.0 N l:ASN94 4.9 23.5 1.0 C l:TRP91 4.9 22.4 1.0 CB l:SER95 5.0 29.9 1.0 C l:ASP95A 5.0 27.0 1.0 CB l:ASP92 5.0 29.3 1.0

J.Glanville, J.Andrade, M.Bellin, S.Kim, S.Pletnev, D.Tsao, R.Verardi, R.Bedi, T.Friede, E.Tully, B.Zhang, T.Bylund, T.Liu, P.D.Kwong. Venom Protection By Broadly Neutralizing Antibody From A Snakebite Subject To Be Published.