Sodium in PDB 8t7i: Structure of the S1CE Variant of Fab F1 (FABS1CE-F1)

The structure of Structure of the S1CE Variant of Fab F1 (FABS1CE-F1), PDB code: 8t7i was solved by A.U.Singer, H.A.Bruce, L.Enderle, L.Blazer, J.J.Adams, F.Sicheri, S.S.Sidhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.32 / 2.60
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	74, 74, 219.13, 90, 90, 90
R / Rfree (%)	20.1 / 25.7

The structure of Structure of the S1CE Variant of Fab F1 (FABS1CE-F1) also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Structure of the S1CE Variant of Fab F1 (FABS1CE-F1) (pdb code 8t7i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Structure of the S1CE Variant of Fab F1 (FABS1CE-F1), PDB code: 8t7i:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Structure of the S1CE Variant of Fab F1 (FABS1CE-F1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the S1CE Variant of Fab F1 (FABS1CE-F1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:53.5 occ:1.00 N A:ASN137 3.4 52.0 1.0 ND2 A:ASN137 3.5 61.8 1.0 CG A:ASN137 3.5 53.6 1.0 CB A:ALA96 3.7 62.8 1.0 O A:VAL135 3.7 55.0 1.0 CB A:ASN137 3.8 53.7 1.0 C A:PHE136 3.9 51.9 1.0 OD1 A:ASN137 4.0 52.0 1.0 CA A:PHE136 4.1 51.0 1.0 CG2 A:VAL135 4.1 59.0 1.0 CZ A:PHE170 4.2 41.5 1.0 CA A:ASN137 4.2 51.3 1.0 C A:VAL135 4.2 52.5 1.0 CA A:ALA96 4.2 65.7 1.0 N A:PHE136 4.4 53.5 1.0 CG A:PRO15 4.4 59.7 1.0 CE1 A:PHE170 4.5 44.9 1.0 O A:PHE136 4.6 52.0 1.0 O A:HOH423 4.9 47.2 1.0 N A:ALA96 4.9 68.3 1.0

Sodium binding site 2 out of 7 in the Structure of the S1CE Variant of Fab F1 (FABS1CE-F1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the S1CE Variant of Fab F1 (FABS1CE-F1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:70.8 occ:1.00 OG A:SER152 3.1 76.4 1.0 CL A:CL306 3.2 81.3 1.0 OG A:SER156 3.5 72.2 1.0 CB A:SER156 3.6 72.6 1.0 CB A:SER152 3.9 73.0 1.0 O A:SER151 4.0 69.8 1.0 CA A:SER152 4.2 70.4 1.0 C A:SER151 4.8 68.6 1.0 N A:SER152 4.9 62.2 1.0 CA A:SER156 5.0 68.9 1.0

Sodium binding site 3 out of 7 in the Structure of the S1CE Variant of Fab F1 (FABS1CE-F1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the S1CE Variant of Fab F1 (FABS1CE-F1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:49.0 occ:1.00 O A:HOH422 2.7 43.0 1.0 OG1 A:THR175 3.1 41.6 1.0 O A:THR175 3.4 38.9 1.0 O A:ASN221 3.4 34.8 1.0 OG A:SER177 3.7 34.2 1.0 C A:THR175 3.8 39.6 1.0 CB A:ASN223 3.9 41.3 1.0 N A:SER177 4.0 33.7 1.0 C A:VAL176 4.1 35.9 1.0 N A:VAL176 4.1 36.0 1.0 CB A:THR175 4.1 43.6 1.0 CA A:VAL176 4.2 35.1 1.0 CB A:SER177 4.2 32.0 1.0 C A:ASN221 4.2 34.4 1.0 N A:ASN223 4.3 33.0 1.0 CA A:THR175 4.6 41.3 1.0 O A:VAL176 4.6 37.4 1.0 CB A:ASN221 4.6 34.8 1.0 C A:VAL222 4.7 35.2 1.0 CA A:ASN223 4.7 36.9 1.0 CA A:SER177 4.7 31.2 1.0 N A:VAL222 4.8 33.9 1.0 CA A:VAL222 4.8 32.7 1.0

Sodium binding site 4 out of 7 in the Structure of the S1CE Variant of Fab F1 (FABS1CE-F1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the S1CE Variant of Fab F1 (FABS1CE-F1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:46.7 occ:1.00 O A:ASP232 3.9 40.4 1.0 CD1 A:ILE219 4.1 43.0 1.0 CB A:ASP232 4.2 37.2 1.0 C A:ASP232 4.4 38.7 1.0 N A:LYS234 4.6 37.1 1.0 CB A:LYS234 4.9 41.5 1.0 CG2 A:ILE219 4.9 33.8 1.0 CG1 A:ILE219 4.9 39.1 1.0

Sodium binding site 5 out of 7 in the Structure of the S1CE Variant of Fab F1 (FABS1CE-F1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the S1CE Variant of Fab F1 (FABS1CE-F1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:44.1 occ:1.00 OE1 B:GLN173 3.2 40.8 1.0 CD2 B:LEU199 3.6 35.6 1.0 CD B:GLN173 4.0 37.5 1.0 NE2 B:GLN173 4.2 36.2 1.0 OD2 B:ASP203 4.5 58.4 1.0 CE1 B:HIS207 4.7 45.8 1.0 ND2 B:ASN176 4.7 34.6 1.0 CG2 B:VAL168 4.7 34.7 1.0 CG1 B:VAL168 4.7 36.6 1.0 CB B:VAL168 4.8 38.0 1.0 CB B:ASP203 4.8 40.9 1.0 CD1 B:LEU199 4.8 36.7 1.0 CG B:LEU199 4.8 37.3 1.0 CG B:ASP203 5.0 51.3 1.0

Sodium binding site 6 out of 7 in the Structure of the S1CE Variant of Fab F1 (FABS1CE-F1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the S1CE Variant of Fab F1 (FABS1CE-F1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:54.5 occ:1.00 CB B:SER141 2.8 47.0 1.0 OG B:SER141 3.3 53.9 1.0 CE1 A:PHE146 4.0 32.5 1.0 CD1 A:PHE146 4.1 34.9 1.0 CA B:SER141 4.2 44.2 1.0 O B:HOH403 4.2 48.8 1.0 C B:SER141 4.6 44.4 1.0 O A:VAL145 4.6 33.1 1.0 CE A:LYS233 4.7 46.9 1.0 O B:SER141 4.9 47.4 1.0

Sodium binding site 7 out of 7 in the Structure of the S1CE Variant of Fab F1 (FABS1CE-F1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the S1CE Variant of Fab F1 (FABS1CE-F1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:48.1 occ:1.00 CG2 B:THR147 2.8 43.6 1.0 NE2 B:GLN142 3.3 35.7 1.0 NZ A:LYS167 3.5 35.1 1.0 OG1 B:THR147 3.7 39.6 1.0 OD2 A:ASP168 3.8 40.9 1.0 CB B:THR147 3.9 39.0 1.0 CD A:LYS167 3.9 34.6 1.0 CG B:GLN142 4.0 37.5 1.0 CD B:GLN142 4.2 36.8 1.0 CE A:LYS167 4.3 35.3 1.0 CE2 A:PHE146 4.5 39.0 1.0 CG A:LYS167 4.7 32.7 1.0 O B:THR147 4.7 44.1 1.0 CZ A:PHE146 4.7 35.3 1.0 CA B:THR147 4.8 40.3 1.0 CB B:SER145 4.8 57.6 1.0 CG A:ASP168 4.9 37.2 1.0 N B:THR147 4.9 42.0 1.0 C B:THR147 4.9 40.0 1.0

H.A.Bruce, A.U.Singer, E.V.Filippova, L.L.Blazer, J.J.Adams, L.Enderle, M.Ben-David, E.H.Radley, D.Y.L.Mao, V.Pau, S.Orlicky, F.Sicheri, I.Kourinov, S.Atwell, A.A.Kossiakoff, S.S.Sidhu. Engineered Antigen-Binding Fragments For Enhanced Crystallization of Antibody:Antigen Complexes. Protein Sci. E4824 2023.
ISSN: ESSN 1469-896X
PubMed: 37945533
DOI: 10.1002/PRO.4824