Chlorine in PDB 9fyt: Mabs in Complex with Cobratoxin at pH 4.5

The structure of Mabs in Complex with Cobratoxin at pH 4.5, PDB code: 9fyt was solved by J.Wade, M.F.Bohn, A.H.Laustsen, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.52 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.86, 83.86, 98.65, 90, 90, 90
R / Rfree (%)	18.6 / 23.7

The structure of Mabs in Complex with Cobratoxin at pH 4.5 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Mabs in Complex with Cobratoxin at pH 4.5 (pdb code 9fyt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Mabs in Complex with Cobratoxin at pH 4.5, PDB code: 9fyt:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Mabs in Complex with Cobratoxin at pH 4.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Mabs in Complex with Cobratoxin at pH 4.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:65.4 occ:1.00 H A:LYS49 2.4 58.0 1.0 HA A:VAL48 3.0 54.7 1.0 HB2 A:LYS49 3.2 63.0 1.0 N A:LYS49 3.2 48.3 1.0 HG21 A:VAL52 3.3 39.6 1.0 HD2 A:LYS49 3.3 71.1 1.0 HB A:VAL48 3.4 56.5 1.0 HG12 A:VAL48 3.7 57.5 1.0 CA A:VAL48 3.7 45.5 1.0 HD3 A:LYS49 3.7 71.1 1.0 HG11 A:VAL52 3.8 37.0 1.0 CD A:LYS49 3.9 59.2 1.0 CB A:LYS49 3.9 52.5 1.0 CB A:VAL48 4.0 47.0 1.0 C A:VAL48 4.0 46.3 1.0 HB A:VAL52 4.1 38.4 1.0 CG2 A:VAL52 4.1 33.0 1.0 O A:HOH245 4.1 61.0 1.0 CA A:LYS49 4.2 49.0 1.0 HG3 A:LYS49 4.2 68.1 1.0 CG A:LYS49 4.3 56.7 1.0 HG23 A:VAL52 4.3 39.6 1.0 CG1 A:VAL48 4.3 47.9 1.0 CB A:VAL52 4.5 32.0 1.0 CG1 A:VAL52 4.6 30.8 1.0 O A:THR47 4.7 44.4 1.0 HB3 A:LYS49 4.7 63.0 1.0 HG11 A:VAL48 4.8 57.5 1.0 HG22 A:VAL52 4.9 39.6 1.0 HA A:LYS49 4.9 58.9 1.0 O A:LYS49 4.9 44.6 1.0 HD3 A:LYS23 5.0 44.0 1.0 N A:VAL48 5.0 45.4 1.0 HG12 A:VAL52 5.0 37.0 1.0 C A:LYS49 5.0 46.5 1.0

Chlorine binding site 2 out of 4 in the Mabs in Complex with Cobratoxin at pH 4.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Mabs in Complex with Cobratoxin at pH 4.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl102 b:93.5 occ:1.00 HE1 D:TRP91 2.0 29.7 1.0 HH22 A:ARG70 2.2 62.6 1.0 HH12 A:ARG70 2.4 64.0 1.0 HB2 D:SER93 2.8 42.4 1.0 NE1 D:TRP91 2.9 24.7 1.0 O C:TYR100I 2.9 26.4 1.0 NH2 A:ARG70 3.0 52.1 1.0 HB3 D:SER93 3.0 42.4 1.0 HD2 C:TYR100J 3.0 43.2 1.0 NH1 A:ARG70 3.1 53.3 1.0 O A:HOH201 3.3 41.8 1.0 CB D:SER93 3.3 35.3 1.0 HA C:TYR100J 3.4 29.1 1.0 CL A:CL103 3.4 44.2 0.4 CZ A:ARG70 3.5 53.4 1.0 HZ2 D:TRP91 3.5 29.6 1.0 HA D:SER93 3.6 40.0 1.0 HH21 A:ARG70 3.6 62.6 1.0 HB2 C:TYR100J 3.6 32.2 1.0 CD2 C:TYR100J 3.7 36.0 1.0 CE2 D:TRP91 3.8 23.5 1.0 HH11 A:ARG70 3.9 64.0 1.0 CD1 D:TRP91 3.9 24.3 1.0 HD1 D:TRP91 4.0 29.2 1.0 CZ2 D:TRP91 4.0 24.6 1.0 C C:TYR100I 4.0 24.5 1.0 CA D:SER93 4.0 33.3 1.0 CA C:TYR100J 4.1 24.2 1.0 CB C:TYR100J 4.2 26.8 1.0 CG C:TYR100J 4.3 32.5 1.0 CL A:CL103 4.4 65.9 0.6 OG D:SER93 4.5 36.6 1.0 N C:TYR100J 4.5 24.1 1.0 CE2 C:TYR100J 4.6 38.7 1.0 HE2 C:TYR100J 4.6 46.5 1.0 OD1 D:ASP95A 4.7 39.9 1.0 HD1 C:TYR100I 4.8 26.8 1.0 NE A:ARG70 4.8 53.8 1.0 CD1 C:TYR100I 4.9 22.3 1.0 O D:SER93 4.9 38.5 1.0 CE1 C:TYR100I 5.0 23.4 1.0 HE1 C:TYR100I 5.0 28.2 1.0 O A:ILE32 5.0 22.2 1.0 C D:SER93 5.0 35.1 1.0

Chlorine binding site 3 out of 4 in the Mabs in Complex with Cobratoxin at pH 4.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Mabs in Complex with Cobratoxin at pH 4.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl103 b:65.9 occ:0.64 CL A:CL103 0.0 65.9 0.6 HD2 A:PRO71 2.9 89.8 1.0 HA A:ARG70 3.0 72.5 1.0 HG2 A:ARG70 3.3 69.2 1.0 HG3 B:PRO71 3.4 91.6 1.0 HH12 A:ARG70 3.4 64.0 1.0 CL A:CL103 3.5 44.2 0.4 NH1 A:ARG70 3.5 53.3 1.0 OD2 C:ASP100H 3.6 33.9 1.0 HB3 A:ARG70 3.7 71.8 1.0 CZ A:ARG70 3.7 53.4 1.0 HH11 A:ARG70 3.8 64.0 1.0 CA A:ARG70 3.9 60.4 1.0 CD A:PRO71 3.9 74.8 1.0 HH22 A:ARG70 3.9 62.6 1.0 NH2 A:ARG70 3.9 52.1 1.0 HG2 B:PRO71 4.0 91.6 1.0 CB A:ARG70 4.1 59.8 1.0 CG A:ARG70 4.1 57.6 1.0 CG B:PRO71 4.2 76.3 1.0 HB2 D:SER93 4.2 42.4 1.0 HH21 A:ARG68 4.2 46.6 1.0 O A:HOH201 4.3 41.8 1.0 N A:PRO71 4.3 72.7 1.0 HD3 A:PRO71 4.4 89.8 1.0 NE A:ARG70 4.4 53.8 1.0 HH21 A:ARG70 4.4 62.6 1.0 CL A:CL102 4.4 93.5 1.0 HE A:ARG68 4.4 43.8 1.0 C A:ARG70 4.5 66.8 1.0 HG2 A:PRO71 4.5 90.9 1.0 CG C:ASP100H 4.6 31.8 1.0 OD1 C:ASP100H 4.7 31.9 1.0 CG A:PRO71 4.8 75.7 1.0 NH2 A:ARG68 4.8 38.8 1.0 HG3 A:ARG70 4.8 69.2 1.0 HE A:ARG70 4.8 64.6 1.0 O A:LYS69 4.8 49.5 1.0 CD A:ARG70 4.9 55.0 1.0 HG2 A:ARG68 5.0 45.2 1.0 N A:ARG70 5.0 55.1 1.0 HB2 A:PRO71 5.0 90.7 1.0 NE A:ARG68 5.0 36.5 1.0

Chlorine binding site 4 out of 4 in the Mabs in Complex with Cobratoxin at pH 4.5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Mabs in Complex with Cobratoxin at pH 4.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl103 b:44.2 occ:0.36 CL A:CL103 0.0 44.2 0.4 O A:HOH201 2.7 41.8 1.0 HD2 C:TYR100J 3.2 43.2 1.0 O A:HOH247 3.4 48.7 1.0 HH21 A:ARG68 3.4 46.6 1.0 HB2 D:SER93 3.4 42.4 1.0 CL A:CL102 3.4 93.5 1.0 CL A:CL103 3.5 65.9 0.6 HB3 D:SER93 3.6 42.4 1.0 HH22 A:ARG68 3.6 46.6 1.0 NH2 A:ARG68 3.8 38.8 1.0 CB D:SER93 3.8 35.3 1.0 HE2 C:TYR100J 3.9 46.5 1.0 OG D:SER93 3.9 36.6 1.0 CD2 C:TYR100J 4.0 36.0 1.0 HA A:ILE32 4.1 25.7 1.0 HH12 A:ARG70 4.2 64.0 1.0 HG3 B:PRO71 4.3 91.6 1.0 O A:ILE32 4.3 22.2 1.0 CE2 C:TYR100J 4.4 38.7 1.0 HG D:SER93 4.5 44.0 1.0 OD2 C:ASP100H 4.5 33.9 1.0 HH22 A:ARG70 4.5 62.6 1.0 O A:SER31 4.7 29.5 1.0 HE1 D:TRP91 4.8 29.7 1.0 HB2 C:TYR100J 4.8 32.2 1.0 CZ A:ARG68 4.9 36.1 1.0 NH1 A:ARG70 4.9 53.3 1.0 CA A:ILE32 4.9 21.4 1.0 HD3 B:PRO71 5.0 90.4 1.0

J.Wade, J.Wade, M.F.Bohn, A.H.Laustsen, J.P.Morth. N/A N/A.