Iodine in PDB 3fgw: One Chain Form of the 66.3 kDa Protein

The structure of One Chain Form of the 66.3 kDa Protein, PDB code: 3fgw was solved by K.Lakomek, A.Dickmanns, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.07 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	146.690, 88.110, 73.550, 90.00, 111.10, 90.00
R / Rfree (%)	22.3 / 24.9

The structure of One Chain Form of the 66.3 kDa Protein also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iodine atom in the One Chain Form of the 66.3 kDa Protein (pdb code 3fgw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the One Chain Form of the 66.3 kDa Protein, PDB code: 3fgw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the One Chain Form of the 66.3 kDa Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of One Chain Form of the 66.3 kDa Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I607 b:64.2 occ:1.00 O A:HOH28 2.6 10.5 1.0 O A:HOH648 3.8 14.7 1.0 CG2 A:THR426 4.0 19.9 1.0 CA A:PRO257 4.2 19.7 1.0 I A:IOD20 4.6 74.4 0.5 CB A:PRO257 4.6 17.9 1.0 N A:GLY258 4.8 24.2 1.0 CB A:THR426 4.9 21.8 1.0 OG1 A:THR426 5.0 22.4 1.0

Iodine binding site 2 out of 7 in the One Chain Form of the 66.3 kDa Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of One Chain Form of the 66.3 kDa Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I15 b:62.1 occ:0.50 OG A:SER117 2.9 26.5 1.0 N A:SER117 3.7 32.6 1.0 CB A:SER117 3.8 29.3 1.0 CB A:ASN115 3.8 41.2 1.0 N A:ASP116 4.0 36.9 1.0 CE1 A:HIS185 4.1 15.6 1.0 OD1 A:ASP116 4.2 44.8 1.0 CA A:SER117 4.4 30.5 1.0 C7 A:NAG11 4.4 42.1 1.0 CB A:ASP116 4.4 39.7 1.0 CA A:ASP116 4.6 37.0 1.0 O7 A:NAG11 4.6 42.3 1.0 C A:ASN115 4.6 38.2 1.0 N2 A:NAG11 4.6 44.1 1.0 O A:PRO290 4.6 41.2 1.0 CG A:ASP116 4.6 42.8 1.0 C A:ASP116 4.6 35.0 1.0 C8 A:NAG11 4.6 42.5 1.0 CG A:ASN115 4.6 45.5 1.0 CA A:ASN115 4.7 39.2 1.0 ND1 A:HIS185 4.8 15.8 1.0 ND2 A:ASN115 4.8 47.8 1.0

Iodine binding site 3 out of 7 in the One Chain Form of the 66.3 kDa Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of One Chain Form of the 66.3 kDa Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I16 b:45.2 occ:0.50 NZ A:LYS161 3.4 40.0 1.0 CG A:LYS215 3.6 41.0 1.0 N A:LEU217 3.6 31.3 1.0 CE A:LYS161 3.6 40.9 1.0 CD A:PRO216 3.8 32.7 1.0 CE A:LYS215 3.9 40.9 1.0 CB A:LEU217 3.9 31.0 1.0 CD A:LYS215 4.1 40.6 1.0 N A:PRO216 4.2 33.4 1.0 CA A:LEU217 4.2 31.3 1.0 CG A:PRO216 4.3 32.9 1.0 CB A:PRO216 4.4 33.1 1.0 NZ A:LYS215 4.5 39.3 1.0 CD A:LYS161 4.6 40.7 1.0 CB A:LYS215 4.6 37.7 1.0 C A:PRO216 4.6 32.1 1.0 C A:LEU217 4.6 32.2 1.0 CA A:PRO216 4.6 33.4 1.0 C A:LYS215 4.7 34.1 1.0 N A:GLY218 4.9 33.4 1.0 CA A:LYS215 4.9 34.8 1.0 CG A:LEU217 5.0 31.0 1.0

Iodine binding site 4 out of 7 in the One Chain Form of the 66.3 kDa Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of One Chain Form of the 66.3 kDa Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I17 b:63.5 occ:0.50 N A:HIS577 3.2 37.8 1.0 CA A:LEU576 3.8 40.7 1.0 ND1 A:HIS577 3.8 33.7 1.0 CE1 A:HIS577 3.8 33.2 1.0 NE2 A:HIS577 4.0 33.5 1.0 CG A:HIS577 4.0 34.1 1.0 C A:HIS577 4.0 31.4 1.0 C A:LEU576 4.0 39.8 1.0 CD2 A:HIS577 4.1 34.7 1.0 CA A:HIS577 4.1 33.9 1.0 CB A:LEU576 4.2 40.9 1.0 N A:MET578 4.3 29.9 1.0 O A:HIS577 4.3 30.4 1.0 O A:MET575 4.5 43.5 1.0 CB A:HIS577 4.7 33.3 1.0 CA A:MET578 4.8 28.4 1.0 N A:LEU576 4.9 40.6 1.0 CG A:MET578 5.0 31.0 1.0

Iodine binding site 5 out of 7 in the One Chain Form of the 66.3 kDa Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of One Chain Form of the 66.3 kDa Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I20 b:74.4 occ:0.50 O A:HOH28 3.2 10.5 1.0 I A:IOD607 4.6 64.2 1.0

Iodine binding site 6 out of 7 in the One Chain Form of the 66.3 kDa Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of One Chain Form of the 66.3 kDa Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I608 b:38.4 occ:1.00 O A:HOH630 2.9 21.3 1.0 NE A:ARG373 3.6 13.2 1.0 O A:HOH693 3.6 27.8 1.0 O A:HOH697 3.8 18.5 1.0 CB A:TYR183 4.1 14.8 1.0 NH2 A:ARG373 4.1 15.1 1.0 CD1 A:TYR183 4.2 10.2 1.0 CZ A:ARG373 4.2 15.1 1.0 CD1 A:LEU360 4.3 18.3 1.0 CD A:ARG373 4.4 16.4 1.0 CG2 A:VAL370 4.4 6.4 1.0 O A:HOH715 4.5 18.6 1.0 O3 A:GOL606 4.5 47.8 1.0 CG A:TYR183 4.6 11.6 1.0 CG1 A:VAL370 4.6 6.4 1.0 CA A:TYR183 4.7 17.0 1.0 N A:TYR183 4.9 17.7 1.0

Iodine binding site 7 out of 7 in the One Chain Form of the 66.3 kDa Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of One Chain Form of the 66.3 kDa Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I609 b:45.0 occ:0.50 CD2 A:LEU78 3.6 57.0 1.0 N A:PHE207 3.6 28.6 1.0 N A:LEU78 3.7 59.9 1.0 CA A:THR206 3.9 27.9 1.0 N A:THR206 3.9 29.6 1.0 O A:LEU205 4.0 30.9 1.0 C A:LEU205 4.0 30.6 1.0 CB A:LEU78 4.0 57.7 1.0 CB A:PHE207 4.3 28.6 1.0 C A:THR206 4.3 28.2 1.0 CB A:LEU205 4.4 27.3 1.0 CG A:LEU78 4.4 57.0 1.0 CA A:GLN77 4.4 61.6 1.0 CA A:LEU78 4.4 58.4 1.0 C A:GLN77 4.5 60.8 1.0 CA A:PHE207 4.6 28.1 1.0 OE1 A:GLN77 4.6 66.4 1.0 CA A:LEU205 4.9 31.1 1.0 CB A:GLN77 4.9 62.6 1.0 CD A:GLN77 4.9 66.1 1.0 C8 A:NAG12 4.9 49.7 1.0 O A:LEU78 4.9 56.0 1.0

K.Lakomek, A.Dickmanns, M.Kettwig, H.Urlaub, R.Ficner, T.Luebke. Initial Insight Into the Function of the Lysosomal 66.3 kDa Protein From Mouse By Means of X-Ray Crystallography Bmc Struct.Biol. V. 9 56 2009.
ISSN: ESSN 1472-6807
PubMed: 19706171
DOI: 10.1186/1472-6807-9-56