Iodine in PDB 3e7a: Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R

All present enzymatic activity of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R:
3.1.3.16;

The structure of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R, PDB code: 3e7a was solved by M.S.Kelker, R.Page, W.Peti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.57 / 1.63
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.354, 77.274, 132.444, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 16.9

The structure of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Chlorine	(Cl)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R (pdb code 3e7a). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 25 binding sites of Iodine where determined in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R, PDB code: 3e7a:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 25 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R


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 Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:27.0 occ:0.20 I A:IOD301 0.0 27.0 0.2 I A:IOD301 1.0 22.5 0.2 O A:HOH681 3.0 40.5 1.0 CG A:LYS260 3.6 21.7 1.0 NE2 A:GLN262 3.6 19.8 1.0 C A:ALA259 3.8 17.7 1.0 CB A:LYS260 4.0 21.6 1.0 O A:ALA259 4.0 17.2 1.0 CA A:ALA259 4.0 16.0 1.0 N A:LYS260 4.1 19.6 1.0 CB A:ALA229 4.2 18.1 1.0 CB A:ALA259 4.3 18.3 1.0 CA A:LYS260 4.7 20.6 1.0 O A:ALA229 4.7 17.0 1.0 CD A:GLN262 4.9 19.2 1.0

Iodine binding site 2 out of 25 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R


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 Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:22.5 occ:0.20 I A:IOD301 0.0 22.5 0.2 I A:IOD301 1.0 27.0 0.2 O A:HOH681 3.5 40.5 1.0 NE2 A:GLN262 3.6 19.8 1.0 CB A:ALA229 3.8 18.1 1.0 O A:ALA229 3.9 17.0 1.0 C A:ALA229 4.2 17.0 1.0 CB A:ALA259 4.3 18.3 1.0 CB A:ALA233 4.3 15.9 1.0 CA A:ALA259 4.3 16.0 1.0 C A:ALA259 4.4 17.7 1.0 O A:ALA259 4.4 17.2 1.0 CA A:ALA229 4.6 16.5 1.0 CG A:LYS260 4.6 21.7 1.0 N A:GLU230 4.7 18.0 1.0 CD A:GLN262 4.8 19.2 1.0 CB A:LYS260 4.9 21.6 1.0 N A:LYS260 4.9 19.6 1.0

Iodine binding site 3 out of 25 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R


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 Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:14.1 occ:0.38 I A:IOD302 0.0 14.1 0.4 I A:IOD302 0.6 9.7 0.4 O A:HOH591 3.0 33.3 1.0 NH1 A:ARG132 3.6 17.3 1.0 CG A:ARG132 4.0 16.6 1.0 CB A:ARG132 4.0 16.8 1.0 CA A:SER129 4.1 13.5 0.5 CH2 A:TRP149 4.2 13.1 1.0 CD A:ARG132 4.2 19.2 1.0 O A:ALA128 4.2 14.5 1.0 CA A:SER129 4.3 14.0 0.5 C A:ALA128 4.4 12.8 1.0 N A:SER129 4.4 12.4 1.0 CZ A:ARG132 4.5 14.0 1.0 O A:HOH431 4.5 20.7 1.0 O A:HOH665 4.5 42.7 1.0 NE A:ARG132 4.7 18.4 1.0 CB A:SER129 4.7 14.4 0.5 CB A:ALA128 4.8 12.0 1.0 CZ2 A:TRP149 4.9 13.4 1.0 OG A:SER129 4.9 20.5 0.5

Iodine binding site 4 out of 25 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R


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 Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:9.7 occ:0.38 I A:IOD302 0.0 9.7 0.4 I A:IOD302 0.6 14.1 0.4 O A:HOH591 3.4 33.3 1.0 NH1 A:ARG132 3.8 17.3 1.0 CH2 A:TRP149 4.1 13.1 1.0 CA A:SER129 4.2 13.5 0.5 O A:ALA128 4.2 14.5 1.0 C A:ALA128 4.3 12.8 1.0 CA A:SER129 4.3 14.0 0.5 N A:SER129 4.3 12.4 1.0 CB A:ALA128 4.4 12.0 1.0 CB A:ARG132 4.4 16.8 1.0 CG A:ARG132 4.5 16.6 1.0 CD A:ARG132 4.6 19.2 1.0 CB A:SER129 4.7 14.4 0.5 CZ2 A:TRP149 4.8 13.4 1.0 CZ A:ARG132 4.8 14.0 1.0 OG A:SER129 4.8 20.5 0.5 O A:HOH431 4.9 20.7 1.0

Iodine binding site 5 out of 25 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:17.6 occ:0.37 O A:HOH483 2.3 22.4 1.0 OE1 A:GLU139 3.0 25.8 1.0 OG A:SER100 3.0 14.8 1.0 C A:GLY135 3.4 12.3 1.0 O A:GLY135 3.5 13.2 1.0 O A:GLY97 3.5 15.0 1.0 N A:PHE136 3.6 10.7 1.0 O A:HOH508 3.7 31.4 1.0 CA A:ASP95 3.7 11.5 1.0 CB A:SER100 3.8 13.4 1.0 CA A:PHE136 3.8 10.8 1.0 O A:HOH720 3.8 24.0 1.0 CA A:GLY135 3.8 13.3 1.0 N A:ASP95 3.9 10.8 1.0 C A:ASP95 4.1 12.7 1.0 N A:ARG96 4.1 11.6 1.0 CD A:GLU139 4.1 21.5 1.0 CB A:GLU139 4.1 15.7 1.0 CB A:PHE136 4.5 10.3 1.0 C A:GLY97 4.6 12.2 1.0 N A:GLY97 4.6 13.6 1.0 CG A:GLU139 4.7 18.4 1.0 O A:TYR134 4.7 12.1 1.0 CD1 A:PHE136 4.7 11.9 1.0 OD1 A:ASP95 4.8 12.1 1.0 O A:ASP95 4.8 11.9 1.0 N A:SER100 4.8 12.8 1.0 C A:ARG96 4.9 15.5 1.0 CA A:SER100 4.9 12.8 1.0 N A:GLY135 4.9 12.3 1.0 O A:HOH627 5.0 40.4 1.0

Iodine binding site 6 out of 25 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range: probe atom residue distance (Å) B Occ A:I404 b:21.3 occ:0.19 I A:IOD404 0.0 21.3 0.2 I A:IOD404 0.8 20.0 0.2 O B:HOH548 2.7 30.5 1.0 NH2 A:ARG261 3.4 15.6 0.5 N B:ILE295 3.4 11.9 1.0 O B:ILE295 3.8 14.4 1.0 CE2 A:PHE293 3.8 12.2 1.0 CA B:GLN294 3.9 11.5 1.0 NH2 A:ARG261 4.0 30.7 0.5 CE2 B:TYR78 4.0 23.8 0.7 CD2 A:PHE293 4.1 13.2 1.0 CE2 A:PHE257 4.2 19.1 1.0 C B:GLN294 4.2 12.6 1.0 CD2 B:TYR78 4.3 20.2 0.7 OH A:TYR255 4.3 18.5 1.0 CB B:GLN294 4.3 12.6 1.0 CE2 A:TYR255 4.4 16.4 1.0 CA B:ILE295 4.4 12.8 0.5 CA B:ILE295 4.4 12.9 0.5 C B:ILE295 4.5 12.0 1.0 CZ A:TYR255 4.7 18.2 1.0 CZ A:ARG261 4.7 14.9 0.5 CB B:ILE295 4.7 13.5 0.5 CG B:GLN294 4.7 14.0 1.0 CB B:ILE295 4.7 13.8 0.5 CZ A:PHE257 4.8 16.5 1.0 O B:PHE293 4.9 10.3 1.0 CZ A:PHE293 4.9 13.6 1.0

Iodine binding site 7 out of 25 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range: probe atom residue distance (Å) B Occ A:I404 b:20.0 occ:0.19 I A:IOD404 0.0 20.0 0.2 I A:IOD404 0.8 21.3 0.2 NH2 A:ARG261 3.3 15.6 0.5 O B:HOH548 3.4 30.5 1.0 NH2 A:ARG261 3.6 30.7 0.5 N B:ILE295 3.8 11.9 1.0 CE2 B:TYR78 3.8 23.8 0.7 CD2 B:TYR78 3.8 20.2 0.7 CA B:GLN294 3.9 11.5 1.0 CE2 A:PHE293 3.9 12.2 1.0 CB B:GLN294 4.0 12.6 1.0 O B:ILE295 4.2 14.4 1.0 CG B:GLN294 4.2 14.0 1.0 CE2 A:PHE257 4.3 19.1 1.0 C B:GLN294 4.3 12.6 1.0 CD2 A:PHE293 4.3 13.2 1.0 O A:HOH525 4.4 0.3 1.0 O A:CYS291 4.5 12.3 1.0 CZ A:ARG261 4.6 14.9 0.5 CZ A:PHE257 4.7 16.5 1.0 CA B:ILE295 4.8 12.8 0.5 CA B:ILE295 4.8 12.9 0.5 CZ A:ARG261 4.8 28.7 0.5 C B:ILE295 4.9 12.0 1.0 CZ B:TYR78 5.0 26.9 0.7

Iodine binding site 8 out of 25 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:15.9 occ:0.25 I A:IOD405 0.0 15.9 0.2 I A:IOD405 1.0 20.6 0.2 N A:LYS260 3.5 19.6 1.0 C A:PHE258 3.8 14.9 1.0 CA A:PHE258 3.8 12.3 1.0 N A:ARG261 3.8 18.3 1.0 N A:PHE258 3.9 13.9 1.0 O A:HOH682 3.9 38.5 1.0 N A:ALA259 3.9 15.6 1.0 O A:PHE257 3.9 15.1 1.0 CA A:LYS260 3.9 20.6 1.0 C A:PHE257 4.0 12.1 1.0 O A:PHE258 4.3 12.8 1.0 CB A:PHE257 4.4 11.0 1.0 C A:LYS260 4.4 19.7 1.0 C A:ALA259 4.4 17.7 1.0 O A:HOH470 4.5 29.9 1.0 O A:HOH531 4.5 42.2 1.0 CG A:ARG261 4.7 20.6 0.5 CG A:ARG261 4.7 23.1 0.5 CA A:ALA259 4.7 16.0 1.0 CA A:ARG261 4.8 18.3 0.5 CA A:ARG261 4.8 18.7 0.5 CA A:PHE257 4.8 12.9 1.0

Iodine binding site 9 out of 25 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:20.6 occ:0.23 I A:IOD405 0.0 20.6 0.2 I A:IOD405 1.0 15.9 0.2 N A:ARG261 3.7 18.3 1.0 CB A:PHE257 3.9 11.0 1.0 CG A:ARG261 3.9 20.6 0.5 CG A:ARG261 3.9 23.1 0.5 C A:PHE257 4.0 12.1 1.0 O A:PHE257 4.0 15.1 1.0 N A:LYS260 4.1 19.6 1.0 N A:PHE258 4.1 13.9 1.0 CA A:LYS260 4.1 20.6 1.0 O A:HOH531 4.3 42.2 1.0 C A:LYS260 4.4 19.7 1.0 CA A:PHE258 4.4 12.3 1.0 C A:PHE258 4.4 14.9 1.0 CA A:ARG261 4.5 18.7 0.5 CA A:ARG261 4.5 18.3 0.5 CA A:PHE257 4.6 12.9 1.0 O A:PHE258 4.7 12.8 1.0 N A:ALA259 4.7 15.6 1.0 O A:HOH682 4.7 38.5 1.0 CB A:ARG261 4.8 19.6 0.5 CB A:ARG261 4.8 20.3 0.5 NH1 A:ARG261 4.9 15.4 0.5

Iodine binding site 10 out of 25 in the Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of Protein Phosphatase-1 Bound to the Natural Toxin Nodularin-R within 5.0Å range: probe atom residue distance (Å) B Occ A:I406 b:15.0 occ:0.25 I A:IOD406 0.0 15.0 0.2 I A:IOD406 0.8 10.9 0.2 CL A:CL304 3.2 32.9 1.0 O A:HOH659 3.4 45.8 1.0 N A:TYR70 3.7 13.7 1.0 CA A:GLN68 3.7 12.3 1.0 N A:TYR69 3.8 12.9 1.0 C A:GLN68 3.8 12.9 1.0 CB A:TYR70 4.0 15.3 1.0 CB A:GLN68 4.2 12.8 1.0 CD1 A:TYR70 4.2 14.9 1.0 O A:HOH754 4.3 39.0 1.0 CA A:TYR70 4.4 13.6 1.0 OE1 A:GLN99 4.4 30.0 1.0 O A:GLN68 4.5 11.2 1.0 O A:GLY67 4.6 12.1 1.0 N A:ASP71 4.6 12.6 1.0 CG A:TYR70 4.6 16.6 1.0 C A:TYR69 4.7 12.8 1.0 CB A:PRO24 4.7 33.4 1.0 O A:HOH539 4.7 38.5 1.0 CA A:TYR69 4.7 12.1 1.0 OD2 A:ASP71 4.8 14.2 1.0 CG A:GLN68 4.8 11.7 1.0 N A:GLN68 5.0 11.1 1.0

M.S.Kelker, R.Page, W.Peti. Crystal Structures of Protein Phosphatase-1 Bound to Nodularin-R and Tautomycin: A Novel Scaffold For Structure-Based Drug Design of Serine/Threonine Phosphatase Inhibitors J.Mol.Biol. V. 385 11 2009.
ISSN: ISSN 0022-2836
PubMed: 18992256
DOI: 10.1016/J.JMB.2008.10.053