Iodine in PDB 5mhe: Crystal Structure of Anti-T4 Fab Fragment with T4

The structure of Crystal Structure of Anti-T4 Fab Fragment with T4, PDB code: 5mhe was solved by T.Parkkinen, J.Rouvinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.84 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.730, 55.330, 61.160, 90.00, 97.77, 90.00
R / Rfree (%)	17.8 / 22.7

The binding sites of Iodine atom in the Crystal Structure of Anti-T4 Fab Fragment with T4 (pdb code 5mhe). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of Anti-T4 Fab Fragment with T4, PDB code: 5mhe:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Crystal Structure of Anti-T4 Fab Fragment with T4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Anti-T4 Fab Fragment with T4 within 5.0Å range: probe atom residue distance (Å) B Occ H:I301 b:40.7 occ:1.00 I3 H:T44301 0.0 40.7 1.0 C3 H:T44301 2.1 36.6 1.0 HG L:LEU95 3.0 28.0 1.0 C2 H:T44301 3.0 32.2 1.0 H2 H:T44301 3.1 38.7 1.0 C4 H:T44301 3.1 29.9 1.0 O4 H:T44301 3.3 31.4 1.0 HD21 L:LEU95 3.5 29.6 1.0 HD1 H:TYR109 3.6 34.0 1.0 HD1 L:TYR93 3.6 34.2 1.0 C1' H:T44301 3.7 30.8 1.0 CD1 L:TYR93 3.7 28.5 1.0 HD11 L:LEU95 3.8 38.0 1.0 CG L:LEU95 3.8 23.3 1.0 H2' H:T44301 3.9 31.1 1.0 HE1 H:TYR109 3.9 36.0 1.0 HD21 H:LEU47 3.9 47.6 1.0 CE1 L:TYR93 3.9 30.8 1.0 C2' H:T44301 4.0 25.9 1.0 HE1 L:TYR93 4.0 36.9 1.0 H L:LEU95 4.0 39.1 1.0 CD2 L:LEU95 4.0 24.7 1.0 HD2 H:TYR59 4.1 36.5 1.0 CD2 H:TYR59 4.1 30.4 1.0 HD23 L:LEU95 4.2 29.6 1.0 HD22 H:LEU47 4.2 47.6 1.0 CD1 H:TYR109 4.2 28.4 1.0 CD1 L:LEU95 4.3 31.7 1.0 CG L:TYR93 4.3 31.7 1.0 HB3 L:TYR93 4.3 36.2 1.0 C1 H:T44301 4.4 35.9 1.0 CE1 H:TYR109 4.4 30.0 1.0 HB3 H:TYR59 4.4 33.6 1.0 C6' H:T44301 4.4 28.2 1.0 CG H:TYR59 4.4 34.9 1.0 CD2 H:LEU47 4.5 39.6 1.0 C5 H:T44301 4.5 34.9 1.0 HD12 L:LEU95 4.5 38.0 1.0 CE2 H:TYR59 4.5 34.0 1.0 HA L:PRO94 4.6 31.2 1.0 HB3 H:ALA50 4.6 31.9 1.0 CZ L:TYR93 4.7 36.1 1.0 HE2 H:TYR59 4.7 40.8 1.0 HD23 H:LEU47 4.7 47.6 1.0 CB H:TYR59 4.8 28.0 1.0 HA L:TYR93 4.8 29.4 1.0 HB2 H:TYR59 4.8 33.6 1.0 N L:LEU95 4.8 32.6 1.0 H6' H:T44301 4.8 33.9 1.0 CB L:TYR93 4.8 30.1 1.0 C3' H:T44301 4.9 28.0 1.0 C6 H:T44301 4.9 28.9 1.0 HD22 L:LEU95 4.9 29.6 1.0 HB2 H:ALA50 5.0 31.9 1.0 CD2 L:TYR93 5.0 28.8 1.0

Iodine binding site 2 out of 4 in the Crystal Structure of Anti-T4 Fab Fragment with T4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Anti-T4 Fab Fragment with T4 within 5.0Å range: probe atom residue distance (Å) B Occ H:I301 b:32.4 occ:1.00 I3' H:T44301 0.0 32.4 1.0 C3' H:T44301 2.1 28.0 1.0 HE2 H:MET111 2.9 33.4 1.0 H2' H:T44301 3.0 31.1 1.0 C2' H:T44301 3.0 25.9 1.0 C4' H:T44301 3.1 29.7 1.0 O4' H:T44301 3.3 33.9 1.0 HA3 H:GLY99 3.4 35.2 1.0 HA H:TYR109 3.5 33.9 1.0 CE H:MET111 3.6 27.8 1.0 HD11 L:LEU95 3.6 38.0 1.0 HE1 H:MET111 3.7 33.4 1.0 SD H:MET111 3.7 49.7 1.0 HG3 H:MET111 3.7 44.4 1.0 HA2 H:GLY99 3.7 35.2 1.0 HB3 H:SER35 3.8 35.4 1.0 HO4' H:T44301 3.9 40.7 1.0 HD12 L:LEU95 4.0 38.0 1.0 CA H:GLY99 4.1 29.3 1.0 HG H:SER35 4.1 43.2 0.0 CD1 L:LEU95 4.2 31.7 1.0 O H:ALA110 4.2 32.2 1.0 C H:TYR109 4.3 26.6 1.0 CG H:MET111 4.3 37.0 1.0 HD13 L:LEU95 4.3 38.0 1.0 CA H:TYR109 4.3 28.3 1.0 C1' H:T44301 4.3 30.8 1.0 C5' H:T44301 4.4 20.5 1.0 HE3 H:MET111 4.4 33.4 1.0 HD1 H:TYR109 4.5 34.0 1.0 N H:ALA110 4.5 27.6 1.0 C H:ALA110 4.5 28.8 1.0 OG H:SER35 4.6 36.0 1.0 CB H:SER35 4.6 29.5 1.0 O H:TYR109 4.6 17.8 1.0 H H:ASP100 4.7 35.2 1.0 HB3 H:TYR109 4.7 36.7 1.0 HA H:MET111 4.7 28.4 1.0 H H:ALA110 4.7 33.1 1.0 N H:GLY99 4.9 27.7 1.0 C6' H:T44301 4.9 28.2 1.0 HB3 H:TYR33 4.9 34.6 1.0 HB2 H:SER35 4.9 35.4 1.0 HG2 H:MET111 4.9 44.4 1.0 HB2 H:ALA50 5.0 31.9 1.0 N H:MET111 5.0 25.4 1.0

Iodine binding site 3 out of 4 in the Crystal Structure of Anti-T4 Fab Fragment with T4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Anti-T4 Fab Fragment with T4 within 5.0Å range: probe atom residue distance (Å) B Occ H:I301 b:40.5 occ:1.00 I5 H:T44301 0.0 40.5 1.0 C5 H:T44301 2.2 34.9 1.0 H6 H:T44301 3.1 34.8 1.0 C6 H:T44301 3.1 28.9 1.0 C4 H:T44301 3.2 29.9 1.0 HE1 H:TYR33 3.2 37.6 1.0 O4 H:T44301 3.4 31.4 1.0 HB3 H:ASN52 3.5 41.0 1.0 HA H:THR58 3.6 33.4 1.0 HA H:ILE51 3.6 35.9 1.0 HD1 H:TYR33 3.6 35.1 1.0 HB2 H:SER57 3.7 44.0 1.0 H H:ASN52 3.8 34.0 1.0 H6' H:T44301 3.8 33.9 1.0 N H:ASN52 3.8 28.3 1.0 CE1 H:TYR33 4.0 31.4 1.0 C H:ILE51 4.0 31.8 1.0 HB2 H:TYR59 4.0 33.6 1.0 O H:SER57 4.0 33.8 1.0 HB3 H:ALA50 4.0 31.9 1.0 C1' H:T44301 4.0 30.8 1.0 O H:ALA50 4.0 28.2 1.0 CA H:ILE51 4.1 29.9 1.0 C6' H:T44301 4.1 28.2 1.0 N H:ILE51 4.1 28.5 1.0 C H:SER57 4.1 38.7 1.0 CA H:THR58 4.1 27.8 1.0 HB1 H:ALA50 4.1 31.9 1.0 CD1 H:TYR33 4.2 29.2 1.0 C H:ALA50 4.2 30.1 1.0 HB3 H:TYR59 4.2 33.6 1.0 N H:THR58 4.2 31.4 1.0 C H:THR58 4.2 36.9 1.0 HB3 H:SER57 4.2 44.0 1.0 H H:TYR59 4.2 33.8 1.0 N H:TYR59 4.3 28.2 1.0 CB H:ASN52 4.3 34.2 1.0 CB H:SER57 4.4 36.6 1.0 C1 H:T44301 4.4 35.9 1.0 HA H:ASN52 4.4 38.7 1.0 CA H:ASN52 4.5 32.3 1.0 C3 H:T44301 4.5 36.6 1.0 H H:ILE51 4.5 34.2 1.0 CB H:TYR59 4.5 28.0 1.0 CB H:ALA50 4.5 26.6 1.0 O H:ILE51 4.6 29.5 1.0 H H:THR58 4.6 37.7 1.0 O H:THR58 4.8 31.7 1.0 O H:HOH403 4.9 51.9 1.0 CA H:SER57 4.9 35.2 1.0 HB2 H:ASN52 4.9 41.0 1.0 C2 H:T44301 4.9 32.2 1.0

Iodine binding site 4 out of 4 in the Crystal Structure of Anti-T4 Fab Fragment with T4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Anti-T4 Fab Fragment with T4 within 5.0Å range: probe atom residue distance (Å) B Occ H:I301 b:31.6 occ:1.00 I5' H:T44301 0.0 31.6 1.0 C5' H:T44301 2.1 20.5 1.0 H6' H:T44301 2.8 33.9 1.0 HO4' H:T44301 3.0 40.7 1.0 C4' H:T44301 3.0 29.7 1.0 C6' H:T44301 3.1 28.2 1.0 O4' H:T44301 3.2 33.9 1.0 HD2 H:TYR107 3.2 43.6 1.0 HB3 H:TYR107 3.3 39.7 1.0 CD2 H:TYR107 3.3 36.3 1.0 HB2 H:ASP100 3.4 41.2 1.0 OD2 H:ASP100 3.5 31.8 1.0 HE1 H:TYR109 3.6 36.0 1.0 CG H:TYR107 3.6 39.3 1.0 CE1 H:TYR109 3.7 30.0 1.0 CZ H:TYR33 3.7 32.4 1.0 CE1 H:TYR33 3.7 31.4 1.0 CE2 H:TYR33 3.8 37.7 1.0 CE2 H:TYR107 3.8 37.5 1.0 CD1 H:TYR33 3.8 29.2 1.0 CD2 H:TYR33 3.9 27.2 1.0 CZ H:TYR109 3.9 29.7 1.0 CG H:TYR33 3.9 29.2 1.0 CB H:TYR107 3.9 33.1 1.0 HE2 H:TYR107 4.1 45.0 1.0 HE1 H:TYR33 4.1 37.6 1.0 CD1 H:TYR109 4.1 28.4 1.0 CB H:ASP100 4.1 34.3 1.0 CG H:ASP100 4.1 34.1 1.0 OH H:TYR109 4.2 33.4 1.0 HE2 H:TYR33 4.2 45.2 1.0 OH H:TYR33 4.3 39.0 1.0 HD1 H:TYR33 4.3 35.1 1.0 C3' H:T44301 4.3 28.0 1.0 CD1 H:TYR107 4.4 38.7 1.0 HD1 H:TYR109 4.4 34.0 1.0 HB2 H:TYR107 4.4 39.7 1.0 HD2 H:TYR33 4.4 32.7 1.0 C1' H:T44301 4.4 30.8 1.0 HB3 H:ASP100 4.5 41.2 1.0 HH H:TYR33 4.5 46.8 0.0 CZ H:TYR107 4.5 39.6 1.0 O H:HOH403 4.5 51.9 1.0 H H:ASP100 4.6 35.2 1.0 CE2 H:TYR109 4.6 26.4 1.0 HB2 H:TYR33 4.6 34.6 1.0 HH H:TYR109 4.6 40.1 0.0 H H:TYR109 4.7 27.9 1.0 CE1 H:TYR107 4.8 39.6 1.0 CB H:TYR33 4.8 28.8 1.0 CG H:TYR109 4.8 25.5 1.0 HB3 H:TYR33 4.8 34.6 1.0 HA H:TYR109 4.8 33.9 1.0 C2' H:T44301 4.8 25.9 1.0 HD1 H:TYR107 4.9 46.5 1.0 CD2 H:TYR109 5.0 30.2 1.0

T.Parkkinen, J.Rouvinen. Crystal Structures of Anti-T4 Fab Fragment To Be Published.