Iodine in PDB 4p9t: Crystal Structure

The structure of Crystal Structure, PDB code: 4p9t was solved by T.Shibahara, Y.Hirano, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.18 / 2.50
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	68.777, 68.777, 207.965, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 23.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure (pdb code 4p9t). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 20 binding sites of Iodine where determined in the Crystal Structure, PDB code: 4p9t:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 20 in the Crystal Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:61.5 occ:0.73 C1 A:EDO308 3.7 65.3 1.0 CB A:ASN187 3.8 60.4 1.0 O2 A:EDO308 3.8 75.8 1.0 CG A:ASN187 3.9 54.8 1.0 CE A:LYS214 3.9 72.4 1.0 CE A:MET183 4.0 60.7 1.0 CG A:MET183 4.0 43.5 1.0 O1 A:EDO308 4.0 69.4 1.0 CD A:LYS214 4.1 74.3 1.0 OD1 A:ASN187 4.2 64.3 1.0 ND2 A:ASN187 4.2 69.6 1.0 C2 A:EDO308 4.2 56.1 1.0 O A:MET183 4.4 57.1 1.0 CA A:VAL184 4.8 64.5 1.0 C A:MET183 4.8 58.0 1.0 SD A:MET183 4.9 55.0 1.0 N A:VAL184 5.0 58.5 1.0

Iodine binding site 2 out of 20 in the Crystal Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:55.6 occ:0.66 NE A:ARG210 3.3 71.5 1.0 CE A:MET183 3.4 60.7 1.0 NH2 A:ARG210 3.8 56.0 1.0 CB A:ARG210 4.0 56.7 1.0 CZ A:ARG210 4.0 69.2 1.0 CB A:ALA190 4.0 55.7 1.0 CE A:LYS214 4.0 72.4 1.0 CG A:ARG210 4.0 62.7 1.0 CA A:ASN187 4.0 63.8 1.0 CG A:LEU186 4.2 58.6 1.0 OD1 A:ASN187 4.2 64.3 1.0 CD A:ARG210 4.3 60.6 1.0 CD2 A:LEU186 4.3 58.3 1.0 CA A:ARG210 4.5 50.2 1.0 CD2 A:LEU213 4.5 52.7 1.0 NZ A:LYS214 4.5 63.9 1.0 O A:LEU186 4.5 65.7 1.0 CB A:ASN187 4.5 60.4 1.0 N A:ASN187 4.6 66.1 1.0 O A:ARG210 4.6 54.2 1.0 CD1 A:ILE254 4.7 35.4 1.0 C A:LEU186 4.7 61.9 1.0 SD A:MET183 4.8 55.0 1.0 CG A:ASN187 4.9 54.8 1.0 CD1 A:LEU186 4.9 48.6 1.0 O A:ASN187 4.9 60.9 1.0 C A:ARG210 4.9 63.3 1.0 CG A:LYS214 4.9 64.3 1.0

Iodine binding site 3 out of 20 in the Crystal Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:67.7 occ:0.37 O2 A:EDO307 3.9 34.2 1.0 CB A:ARG229 3.9 43.2 1.0 O A:GLN225 4.2 58.3 1.0 CA A:ALA226 4.3 58.5 1.0 C A:GLN225 4.5 51.8 1.0 N A:ALA226 4.5 44.7 1.0 CB A:GLN225 4.9 45.1 1.0

Iodine binding site 4 out of 20 in the Crystal Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:94.4 occ:0.38 NZ A:LYS214 3.2 63.9 1.0 N A:GLY211 3.9 49.9 1.0 NH1 A:ARG210 3.9 43.5 1.0 O A:ALA207 4.0 68.1 1.0 CA A:GLY211 4.1 61.8 1.0 CB A:ARG210 4.2 56.7 1.0 CZ A:ARG210 4.4 69.2 1.0 C A:ARG210 4.4 63.3 1.0 CE A:LYS214 4.6 72.4 1.0 O1 A:PEG309 4.7 74.4 1.0 NH2 A:ARG210 4.7 56.0 1.0 O A:ARG210 4.9 54.2 1.0 CA A:ARG210 5.0 50.2 1.0

Iodine binding site 5 out of 20 in the Crystal Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:94.6 occ:0.33 CA A:ALA250 3.7 51.0 1.0 N A:ALA250 4.1 59.0 1.0 CB A:ALA212 4.2 40.8 1.0 CA A:ALA209 4.2 42.8 1.0 O A:GLU249 4.2 54.7 1.0 CB A:ALA250 4.3 35.6 1.0 C A:GLU249 4.3 64.4 1.0 CB A:ALA209 4.5 61.9 1.0 C A:ALA250 4.8 57.6 1.0 O A:ALA250 4.8 54.0 1.0 CB A:GLU249 5.0 63.1 1.0

Iodine binding site 6 out of 20 in the Crystal Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:I301 b:63.6 occ:0.76 O2 B:EDO308 3.5 76.6 1.0 CB B:ASN187 3.8 59.2 1.0 CG B:ASN187 3.9 53.3 1.0 CE B:LYS214 3.9 72.0 1.0 O1 B:EDO308 3.9 72.8 1.0 C1 B:EDO308 4.0 62.6 1.0 CG B:MET183 4.0 45.5 1.0 CE B:MET183 4.0 57.8 1.0 CD B:LYS214 4.1 74.9 1.0 C2 B:EDO308 4.2 59.1 1.0 OD1 B:ASN187 4.2 63.1 1.0 ND2 B:ASN187 4.2 69.9 1.0 O B:MET183 4.4 57.6 1.0 CA B:VAL184 4.7 65.1 1.0 C B:MET183 4.7 56.6 1.0 SD B:MET183 4.9 54.5 1.0 N B:VAL184 4.9 57.0 1.0

Iodine binding site 7 out of 20 in the Crystal Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:54.9 occ:0.65 NE B:ARG210 3.3 69.8 1.0 CE B:MET183 3.4 57.8 1.0 NH2 B:ARG210 3.8 58.4 1.0 CB B:ARG210 3.9 58.7 1.0 CZ B:ARG210 4.0 69.0 1.0 CG B:ARG210 4.0 62.3 1.0 CB B:ALA190 4.0 52.1 1.0 CE B:LYS214 4.0 72.0 1.0 CA B:ASN187 4.1 63.3 1.0 CG B:LEU186 4.2 59.5 1.0 CD B:ARG210 4.2 63.8 1.0 OD1 B:ASN187 4.2 63.1 1.0 CD2 B:LEU186 4.3 58.2 1.0 CA B:ARG210 4.4 51.5 1.0 NZ B:LYS214 4.4 63.9 1.0 CD2 B:LEU213 4.5 51.1 1.0 O B:LEU186 4.5 64.7 1.0 CB B:ASN187 4.6 59.2 1.0 O B:ARG210 4.6 53.0 1.0 N B:ASN187 4.6 66.6 1.0 CD1 B:ILE254 4.6 34.6 1.0 C B:LEU186 4.7 62.6 1.0 SD B:MET183 4.8 54.5 1.0 CG B:ASN187 4.9 53.3 1.0 C B:ARG210 4.9 63.2 1.0 CD1 B:LEU186 4.9 48.2 1.0 O B:ASN187 4.9 59.9 1.0 CG B:LYS214 4.9 62.8 1.0

Iodine binding site 8 out of 20 in the Crystal Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:I303 b:67.2 occ:0.38 CB B:ARG229 3.9 43.1 1.0 O2 B:EDO307 4.0 33.8 1.0 O B:GLN225 4.3 59.6 1.0 CA B:ALA226 4.3 58.2 1.0 C B:GLN225 4.5 53.1 1.0 N B:ALA226 4.6 47.2 1.0 C2 B:EDO307 4.6 42.6 1.0 CB B:GLN225 4.9 46.8 1.0

Iodine binding site 9 out of 20 in the Crystal Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:I304 b:94.9 occ:0.42 NZ B:LYS214 3.2 63.9 1.0 N B:GLY211 3.8 48.4 1.0 NH1 B:ARG210 4.0 44.8 1.0 CA B:GLY211 4.0 61.0 1.0 O B:ALA207 4.1 65.7 1.0 CB B:ARG210 4.2 58.7 1.0 C B:ARG210 4.4 63.2 1.0 CZ B:ARG210 4.4 69.0 1.0 CE B:LYS214 4.6 72.0 1.0 NH2 B:ARG210 4.7 58.4 1.0 O B:ARG210 4.9 53.0 1.0 CA B:ARG210 5.0 51.5 1.0

Iodine binding site 10 out of 20 in the Crystal Structure


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:I305 b:95.3 occ:0.34 CA B:ALA250 3.6 52.1 1.0 N B:ALA250 4.0 59.8 1.0 CB B:ALA212 4.1 40.5 1.0 O B:GLU249 4.2 54.2 1.0 CB B:ALA250 4.2 35.8 1.0 C B:GLU249 4.2 64.6 1.0 CA B:ALA209 4.3 42.9 1.0 CB B:ALA209 4.5 61.3 1.0 C B:ALA250 4.7 58.3 1.0 O B:ALA250 4.8 51.2 1.0 CB B:GLU249 4.9 63.8 1.0 O B:ALA209 5.0 49.5 1.0

T.Shibahara, Y.Hirano, T.Hakoshima. Crystal Structure To Be Published.