Sodium in PDB 7lsf: Crystal Structure of the Human Neutralizing Antibody Fab Fragment T025 Bound to Tbev Ediii (Western Subtype)

The structure of Crystal Structure of the Human Neutralizing Antibody Fab Fragment T025 Bound to Tbev Ediii (Western Subtype), PDB code: 7lsf was solved by J.R.Keeffe, P.J.Bjorkman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.91 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.542, 66.73, 91.21, 90, 94.64, 90
R / Rfree (%)	18.9 / 22.7

The binding sites of Sodium atom in the Crystal Structure of the Human Neutralizing Antibody Fab Fragment T025 Bound to Tbev Ediii (Western Subtype) (pdb code 7lsf). 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 the Human Neutralizing Antibody Fab Fragment T025 Bound to Tbev Ediii (Western Subtype), PDB code: 7lsf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Human Neutralizing Antibody Fab Fragment T025 Bound to Tbev Ediii (Western Subtype)


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 the Human Neutralizing Antibody Fab Fragment T025 Bound to Tbev Ediii (Western Subtype) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:23.4 occ:1.00 N L:PHE98 3.2 27.6 1.0 N H:TRP47 3.3 24.4 1.0 CA L:ARG97 3.7 32.3 1.0 CD2 L:PHE98 3.7 25.3 1.0 O L:HOH425 3.8 28.8 1.0 CB H:TRP47 3.9 24.0 1.0 O L:PRO96 3.9 30.4 1.0 C L:ARG97 4.0 34.1 1.0 CG L:ARG97 4.0 33.3 1.0 CA H:ASP46 4.0 27.3 1.0 CB L:PHE98 4.0 27.8 1.0 CD L:ARG97 4.0 32.5 1.0 O H:LEU45 4.1 26.6 1.0 C H:ASP46 4.2 27.0 1.0 CA L:PHE98 4.2 28.6 1.0 OD1 H:ASP46 4.2 28.2 1.0 CA H:TRP47 4.2 24.1 1.0 CG L:PHE98 4.3 27.2 1.0 CB L:ARG97 4.5 33.1 1.0 O L:PHE98 4.5 28.8 1.0 N L:ARG97 4.7 33.3 1.0 C L:PRO96 4.7 31.3 1.0 CE2 L:PHE98 4.7 23.1 1.0 NE L:ARG97 4.7 33.8 1.0 N H:ASP46 4.8 28.0 1.0 C H:LEU45 4.8 26.4 1.0 C L:PHE98 4.9 29.3 1.0 O H:TRP47 4.9 24.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Human Neutralizing Antibody Fab Fragment T025 Bound to Tbev Ediii (Western Subtype)


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 the Human Neutralizing Antibody Fab Fragment T025 Bound to Tbev Ediii (Western Subtype) within 5.0Å range: probe atom residue distance (Å) B Occ E:Na501 b:28.3 occ:1.00 OD1 H:ASP100 2.7 27.7 1.0 O E:HOH603 2.7 26.4 1.0 O E:THR335 2.9 25.6 1.0 N E:ASP308 3.1 26.2 1.0 CZ E:PHE332 3.3 26.2 1.0 CG H:ASP100 3.6 27.1 1.0 CA E:CYS307 3.7 29.2 1.0 OD2 H:ASP100 3.7 27.2 1.0 CB E:ASP308 3.8 25.5 1.0 C E:CYS307 3.8 28.3 1.0 C E:THR335 3.9 27.4 1.0 N E:THR335 3.9 25.1 1.0 SG E:CYS338 4.0 32.0 1.0 CG2 H:ILE99 4.0 26.4 1.0 CE2 E:PHE332 4.0 27.8 1.0 CA E:ASP308 4.0 25.8 1.0 NE1 L:TRP94 4.1 26.9 1.0 CA E:THR335 4.2 27.1 1.0 CB E:THR335 4.2 27.8 1.0 CZ2 L:TRP94 4.2 22.4 1.0 O E:MET306 4.2 29.8 1.0 CB E:CYS338 4.3 32.2 1.0 CE1 E:PHE332 4.4 26.2 1.0 CE2 L:TRP94 4.5 25.4 1.0 CB E:CYS307 4.5 29.9 1.0 N E:CYS307 4.7 29.5 1.0 C E:GLY334 4.7 26.6 1.0 OG1 E:THR335 4.8 27.5 1.0 C E:MET306 4.8 29.5 1.0 CB H:ASP100 5.0 24.9 1.0

M.A.Agudelo, M.Palus, J.R.Keeffe. Broad and Potent Neutralizing Human Antibodies to Tick-Borne Flaviviruses Protect Against and Treat Infection in Mice To Be Published.