Chlorine in PDB 5c2b: Anti-CXCL13 Parental Scfv - 3B4

The structure of Anti-CXCL13 Parental Scfv - 3B4, PDB code: 5c2b was solved by C.Tu, J.Bard, L.Mosyak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.98 / 1.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	131.900, 133.500, 44.900, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 19.4

The binding sites of Chlorine atom in the Anti-CXCL13 Parental Scfv - 3B4 (pdb code 5c2b). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Anti-CXCL13 Parental Scfv - 3B4, PDB code: 5c2b:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Anti-CXCL13 Parental Scfv - 3B4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Anti-CXCL13 Parental Scfv - 3B4 within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl201 b:29.8 occ:1.00 OG H:SER16 3.1 22.0 0.5 N H:LYS13 3.2 15.9 1.0 O H:HOH388 3.3 26.1 1.0 O H:HOH447 3.4 39.6 1.0 CB H:SER16 3.8 16.6 0.5 CB H:SER16 3.8 17.5 0.5 CA H:LYS12 3.8 16.9 1.0 OG H:SER16 3.8 17.8 0.5 CB H:LYS13 4.0 16.9 1.0 C H:LYS12 4.0 15.6 1.0 CD H:LYS12 4.1 25.5 1.0 CA H:LYS13 4.1 15.7 1.0 CG H:LYS13 4.1 19.2 1.0 CB H:LYS12 4.3 19.4 1.0 O H:LYS13 4.5 17.4 1.0 CD H:LYS13 4.5 21.0 1.0 O H:VAL11 4.8 21.2 1.0 C H:LYS13 4.8 16.5 1.0 O H:HOH360 4.9 27.5 1.0 CG H:LYS12 4.9 21.1 1.0

Chlorine binding site 2 out of 3 in the Anti-CXCL13 Parental Scfv - 3B4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Anti-CXCL13 Parental Scfv - 3B4 within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl601 b:27.9 occ:1.00 O L:HOH841 3.1 29.4 1.0 N L:SER61 3.2 19.1 1.0 O L:HOH772 3.3 26.8 1.0 O L:HOH834 3.4 49.0 1.0 NZ L:LYS47 3.6 30.2 1.0 CA L:VAL60 3.8 19.8 1.0 CB L:SER61 3.9 21.8 1.0 C L:VAL60 4.0 21.3 1.0 CG1 L:VAL60 4.1 16.3 1.0 CE1 L:PHE64 4.1 18.8 1.0 CA L:SER61 4.2 20.0 1.0 O L:HOH795 4.2 38.2 1.0 O L:GLY59 4.3 28.4 1.0 CE L:LYS47 4.3 26.3 1.0 CB L:VAL60 4.3 16.7 1.0 CD1 L:PHE64 4.5 17.5 1.0 CG2 L:VAL60 4.5 18.8 1.0 CD2 L:LEU49 4.6 19.4 1.0 N L:VAL60 4.9 19.0 1.0

Chlorine binding site 3 out of 3 in the Anti-CXCL13 Parental Scfv - 3B4


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Anti-CXCL13 Parental Scfv - 3B4 within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl602 b:24.1 occ:1.00 O H:HOH322 3.0 27.6 1.0 O H:HOH380 3.1 23.8 1.0 O L:HOH870 3.1 40.6 1.0 N L:ALA45 3.3 19.6 1.0 CB L:ALA45 3.8 20.1 1.0 CA H:GLN119 4.0 14.7 1.0 CA L:LYS44 4.0 23.1 1.0 CB H:GLN119 4.1 16.0 1.0 C L:LYS44 4.1 18.6 1.0 CA L:ALA45 4.2 17.9 1.0 CB L:LYS44 4.4 23.9 1.0 O H:GLN119 4.6 17.3 1.0 O L:HOH759 4.6 33.0 1.0 O H:GLY118 4.6 14.7 1.0 C H:GLN119 4.7 13.9 1.0 O L:GLY43 4.9 29.4 1.0 CG L:LYS44 4.9 30.7 1.0 O H:HOH456 4.9 31.8 1.0 N H:GLN119 4.9 14.0 1.0 O L:HOH703 4.9 33.9 1.0

C.Tu, V.Terrabube, A.Tam, W.Stochaj, B.Fennell, L.Lin, M.Stahl, E.Lavallie, W.Somers, W.Finlay, L.Mosyak, J.Bard, O.Cunningham. Optimization of A Scfv-Based Biotherapeutic By Cdr Side-Chain Clash Repair To Be Published.