Iodine in PDB 1c3x: Purine Nucleoside Phosphorylase From Cellulomonas Sp. in Complex with 8-Iodo-Guanine

The structure of Purine Nucleoside Phosphorylase From Cellulomonas Sp. in Complex with 8-Iodo-Guanine, PDB code: 1c3x was solved by J.Tebbe, A.Bzowska, B.Wielgus-Kutrowska, W.Schroeder, Z.Kazimierczuk, D.Shugar, W.Saenger, G.Koellner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.319, 108.340, 117.562, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 25.1

The structure of Purine Nucleoside Phosphorylase From Cellulomonas Sp. in Complex with 8-Iodo-Guanine also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iodine atom in the Purine Nucleoside Phosphorylase From Cellulomonas Sp. in Complex with 8-Iodo-Guanine (pdb code 1c3x). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Purine Nucleoside Phosphorylase From Cellulomonas Sp. in Complex with 8-Iodo-Guanine, PDB code: 1c3x:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Purine Nucleoside Phosphorylase From Cellulomonas Sp. in Complex with 8-Iodo-Guanine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Purine Nucleoside Phosphorylase From Cellulomonas Sp. in Complex with 8-Iodo-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:25.3 occ:0.28 I A:8IG306 0.0 25.3 0.3 C8 A:8IG306 2.1 26.1 0.8 OG1 A:THR245 2.7 36.0 1.0 N7 A:8IG306 3.0 27.8 0.8 N9 A:8IG306 3.1 26.1 0.8 CB A:THR245 3.6 27.6 1.0 O A:HOH322 3.6 16.0 1.0 CG2 A:THR245 3.8 29.3 1.0 C A:GLY135 3.8 24.6 1.0 O A:GLY135 3.9 24.1 1.0 CA A:GLY135 4.1 21.4 1.0 N A:CYS136 4.2 23.4 1.0 O A:HOH401 4.2 18.6 1.0 C4 A:8IG306 4.2 26.7 0.8 C5 A:8IG306 4.2 29.1 0.8 CB A:SER46 4.2 25.0 1.0 CA A:CYS136 4.6 22.6 1.0 OH A:TYR203 4.7 38.5 1.0 OG A:SER46 4.7 27.6 1.0 O A:CYS136 4.8 23.3 1.0 C A:CYS136 5.0 22.3 1.0 CA A:THR245 5.0 23.9 1.0

Iodine binding site 2 out of 3 in the Purine Nucleoside Phosphorylase From Cellulomonas Sp. in Complex with 8-Iodo-Guanine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Purine Nucleoside Phosphorylase From Cellulomonas Sp. in Complex with 8-Iodo-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ B:I305 b:48.7 occ:0.28 I B:8IG305 0.0 48.7 0.3 C8 B:8IG305 2.1 38.1 0.8 N7 B:8IG305 3.0 36.2 0.8 N9 B:8IG305 3.0 34.5 0.8 OG1 B:THR245 3.1 25.5 1.0 O B:HOH337 3.2 46.2 1.0 C B:GLY135 3.5 18.4 1.0 O B:HOH553 3.7 53.4 1.0 CB B:THR245 3.7 27.2 1.0 O B:GLY135 3.7 22.9 1.0 CA B:GLY135 3.8 17.8 1.0 N B:CYS136 3.8 16.6 1.0 CG2 B:THR245 3.9 31.6 1.0 C4 B:8IG305 4.1 32.6 0.8 O B:HOH512 4.1 34.4 1.0 CB B:SER46 4.1 33.3 1.0 C5 B:8IG305 4.1 32.0 0.8 CA B:CYS136 4.4 13.8 1.0 O2 B:PO4302 4.5 36.9 0.7 OG B:SER46 4.6 43.4 1.0 OH B:TYR203 4.6 50.2 1.0 N B:GLY135 4.7 21.4 1.0 O B:CYS136 4.9 18.8 1.0 C B:CYS136 5.0 16.5 1.0

Iodine binding site 3 out of 3 in the Purine Nucleoside Phosphorylase From Cellulomonas Sp. in Complex with 8-Iodo-Guanine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Purine Nucleoside Phosphorylase From Cellulomonas Sp. in Complex with 8-Iodo-Guanine within 5.0Å range: probe atom residue distance (Å) B Occ C:I304 b:33.7 occ:0.28 I C:8IG304 0.0 33.7 0.3 C8 C:8IG304 2.1 18.7 0.8 OG1 C:THR245 2.8 30.6 1.0 N9 C:8IG304 3.0 19.1 0.8 N7 C:8IG304 3.0 16.6 0.8 O C:HOH314 3.6 24.1 1.0 CG2 C:THR245 3.8 32.5 1.0 CB C:THR245 3.8 31.7 1.0 C C:GLY135 3.9 17.2 1.0 O C:GLY135 4.0 18.4 1.0 C4 C:8IG304 4.1 18.3 0.8 CB C:SER46 4.1 23.8 1.0 OH C:TYR203 4.1 49.0 1.0 C5 C:8IG304 4.1 14.7 0.8 CA C:GLY135 4.3 17.9 1.0 N C:CYS136 4.3 17.9 1.0 OG C:SER46 4.5 23.8 1.0 O C:HOH531 4.5 31.8 1.0 CA C:CYS136 4.7 20.8 1.0

J.Tebbe, A.Bzowska, B.Wielgus-Kutrowska, W.Schroder, Z.Kazimierczuk, D.Shugar, W.Saenger, G.Koellner. Crystal Structure of the Purine Nucleoside Phosphorylase (Pnp) From Cellulomonas Sp. and Its Implication For the Mechanism of Trimeric Pnps. J.Mol.Biol. V. 294 1239 1999.
ISSN: ISSN 0022-2836
PubMed: 10600382
DOI: 10.1006/JMBI.1999.3327