Sodium in PDB 7bbg: Crystal Structure of Hla-A2-WT1-Rmf and Fab 11D06

The structure of Crystal Structure of Hla-A2-WT1-Rmf and Fab 11D06, PDB code: 7bbg was solved by A.Bujotzek, G.Georges, L.J.Hanisch, C.Klein, J.Benz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.30 / 2.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.111, 67.009, 139.361, 90, 90.57, 90
R / Rfree (%)	16.8 / 23

The binding sites of Sodium atom in the Crystal Structure of Hla-A2-WT1-Rmf and Fab 11D06 (pdb code 7bbg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Hla-A2-WT1-Rmf and Fab 11D06, PDB code: 7bbg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of Hla-A2-WT1-Rmf and Fab 11D06


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 Hla-A2-WT1-Rmf and Fab 11D06 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:65.8 occ:1.00 O A:ASP37 2.4 56.3 1.0 O A:HOH516 2.5 32.9 1.0 N A:GLN43 3.0 51.0 1.0 CB A:ALA40 3.2 53.4 1.0 CA A:GLN43 3.3 50.3 1.0 NE2 A:GLN43 3.3 35.9 1.0 C A:ASP37 3.6 55.4 1.0 OG A:SER42 3.6 66.8 1.0 O A:ALA40 3.6 59.2 1.0 C A:ALA40 3.7 58.9 1.0 CA A:ALA40 3.7 54.2 1.0 N A:ALA40 3.8 55.1 1.0 N A:ARG44 3.9 49.8 1.0 C A:GLN43 4.1 54.4 1.0 C A:SER42 4.1 55.9 1.0 CD A:GLN43 4.1 49.9 1.0 N A:SER42 4.2 53.2 1.0 N A:ASP37 4.2 48.3 1.0 CE1 A:PHE36 4.2 42.8 1.0 CA A:ASP37 4.4 49.8 1.0 CA A:SER42 4.4 52.6 1.0 N A:SER38 4.5 51.7 1.0 O A:ARG44 4.5 51.0 1.0 C A:SER38 4.5 60.8 1.0 N A:ALA41 4.5 55.4 1.0 CD1 A:PHE36 4.6 42.5 1.0 CB A:GLN43 4.6 51.8 1.0 CZ A:PHE36 4.6 42.5 1.0 CB A:SER42 4.6 54.4 1.0 CA A:SER38 4.6 52.5 1.0 O A:SER38 4.6 62.5 1.0 CG A:GLN43 4.7 40.0 1.0 C A:ALA41 4.7 57.7 1.0 CB A:ASP37 4.8 52.2 1.0 OE1 A:GLN43 4.8 50.6 1.0 OE1 A:GLU46 4.9 83.7 1.0 N A:ASP39 4.9 58.3 1.0 C A:ASP39 4.9 61.6 1.0 O A:HOH524 5.0 56.6 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of Hla-A2-WT1-Rmf and Fab 11D06


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 Hla-A2-WT1-Rmf and Fab 11D06 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:62.1 occ:1.00 O A:ASP29 2.5 54.2 1.0 OG A:SER4 3.0 58.5 1.0 CG A:ARG6 3.4 59.1 1.0 C A:ASP29 3.4 52.3 1.0 N A:ASP29 3.4 46.2 1.0 CA A:ASP29 3.6 45.5 1.0 CB A:TYR27 3.7 49.4 1.0 O A:TYR27 3.9 47.8 1.0 CB A:ARG6 3.9 44.7 1.0 O A:SER4 3.9 45.2 1.0 C A:TYR27 4.0 49.8 1.0 N A:ARG6 4.2 44.5 1.0 C A:VAL28 4.3 50.2 1.0 CB A:SER4 4.3 53.1 1.0 C A:SER4 4.4 48.0 1.0 CD A:ARG6 4.4 65.8 1.0 N A:VAL28 4.4 47.8 1.0 NE A:ARG6 4.5 80.9 1.0 CA A:TYR27 4.5 47.1 1.0 CA A:VAL28 4.6 46.9 1.0 C A:MET5 4.6 48.6 1.0 O B:HOH225 4.7 49.7 1.0 CA A:ARG6 4.7 43.5 1.0 N A:ASP30 4.7 49.1 1.0 CA A:MET5 4.8 45.4 1.0 N A:MET5 4.8 45.6 1.0 CG A:TYR27 4.8 53.1 1.0 CE1 A:PHE8 5.0 43.6 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of Hla-A2-WT1-Rmf and Fab 11D06


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 Hla-A2-WT1-Rmf and Fab 11D06 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:68.9 occ:1.00 OE1 A:GLU63 2.2 65.0 1.0 OH A:TYR7 2.7 50.1 1.0 OH A:TYR59 2.9 43.5 1.0 CE2 A:TYR7 3.4 45.0 1.0 CD A:GLU63 3.5 63.4 1.0 CZ A:TYR7 3.5 52.6 1.0 CG2 A:VAL34 3.6 45.1 1.0 CE A:MET45 3.7 50.0 1.0 CZ A:TYR59 3.8 41.6 1.0 CG1 A:VAL34 3.8 46.3 1.0 CE2 A:PHE33 3.8 41.7 1.0 CB A:VAL34 4.2 46.4 1.0 N C:ARG1 4.2 47.7 1.0 CG A:GLU63 4.2 51.1 1.0 CA C:ARG1 4.3 47.7 1.0 CZ A:PHE33 4.3 39.9 1.0 CE2 A:TYR59 4.4 36.9 1.0 OE2 A:GLU63 4.4 40.4 1.0 N C:MET2 4.4 47.5 1.0 OH A:TYR171 4.5 49.5 1.0 CG C:MET2 4.6 51.8 1.0 CE1 A:TYR59 4.7 36.0 1.0 CD2 A:TYR7 4.7 44.7 1.0 C C:ARG1 4.7 51.7 1.0 CB A:GLU63 4.8 44.7 1.0 CE1 A:TYR7 4.8 46.7 1.0 CD2 A:PHE33 4.8 40.7 1.0 CG A:MET45 4.9 48.4 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of Hla-A2-WT1-Rmf and Fab 11D06


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 Hla-A2-WT1-Rmf and Fab 11D06 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:72.4 occ:1.00 OG H:SER186 2.8 87.7 1.0 OG L:SER175 2.9 68.3 1.0 CB H:PHE173 3.3 59.0 1.0 O L:HOH335 3.3 56.5 1.0 N H:SER186 3.5 66.7 1.0 CB L:SER161 3.5 57.9 1.0 OG L:SER161 3.8 62.6 1.0 CG H:PHE173 3.9 61.8 1.0 CA H:LEU185 3.9 63.6 1.0 O H:PRO174 3.9 60.9 1.0 C H:LEU185 4.0 70.4 1.0 O L:HOH320 4.0 58.3 1.0 CB H:SER186 4.1 72.5 1.0 CB L:SER175 4.1 61.4 1.0 CA H:SER186 4.3 66.8 1.0 CB H:LEU185 4.4 62.0 1.0 CD1 H:PHE173 4.5 66.3 1.0 O H:SER186 4.5 67.1 1.0 CD2 H:PHE173 4.5 64.7 1.0 CA H:PHE173 4.7 56.4 1.0 C H:PHE173 4.9 58.4 1.0 C H:SER186 4.9 68.6 1.0 CA L:SER161 4.9 56.6 1.0 O H:SER184 4.9 68.0 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of Hla-A2-WT1-Rmf and Fab 11D06


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Hla-A2-WT1-Rmf and Fab 11D06 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:70.5 occ:1.00 OG H:SER84 2.7 71.0 1.0 O H:ARG67 2.9 62.0 1.0 OG1 H:THR69 3.1 63.6 1.0 O H:GLU82 3.2 56.0 1.0 C H:ARG67 3.7 61.0 1.0 CB H:SER84 3.7 56.6 1.0 CB H:THR69 3.9 58.4 1.0 N H:SER84 4.0 52.1 1.0 C H:GLU82 4.0 55.3 1.0 N H:THR69 4.1 53.0 1.0 C H:VAL68 4.1 58.8 1.0 CG H:GLU82 4.3 62.8 1.0 CA H:VAL68 4.3 54.3 1.0 N H:VAL68 4.3 55.4 1.0 CA H:ARG67 4.5 58.6 1.0 CA H:SER84 4.5 53.0 1.0 CB H:GLU82 4.6 55.7 1.0 O H:VAL68 4.6 60.9 1.0 C H:LEU83 4.6 54.6 1.0 CA H:THR69 4.6 52.0 1.0 CA H:LEU83 4.6 47.8 1.0 N H:LEU83 4.7 48.8 1.0 OE2 H:GLU82 4.7 80.1 1.0 CD H:GLU82 4.9 89.2 1.0 CA H:GLU82 4.9 53.2 1.0

C.Augsberger, G.Hanel, W.Xu, V.Pulko, L.J.Hanisch, A.Augustin, J.Challier, K.Hunt, B.Vick, P.E.Rovatti, C.Krupka, M.Rothe, A.Schonle, J.Sam, E.Lezan, A.Ducret, D.Ortiz-Franyuti, A.C.Walz, J.Benz, A.Bujotzek, F.S.Lichtenegger, C.Gassner, A.Carpy, V.Lyamichev, J.Patel, N.P.Konstandin, A.Tunger, M.Schmitz, M.Von Bergwelt-Baildon, K.Spiekermann, L.Vago, I.Jeremias, E.Marrer-Berger, P.Umana, C.Klein, M.Subklewe. Targeting Intracellular WT1 in Aml with A Novel Rmf-Peptide-Mhc Specific T-Cell Bispecific Antibody. Blood 2021.
ISSN: ESSN 1528-0020
PubMed: 34280257
DOI: 10.1182/BLOOD.2020010477