Iodine in PDB 5ma2: Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol, PDB code: 5ma2 was solved by C.Kunze, M.Bommer, W.R.Hagen, M.Uksa, H.Dobbek, T.Schubert, G.Diekert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.27 / 1.88
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	73.765, 73.765, 184.711, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 16.6

The structure of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol also contains other interesting chemical elements:

Cobalt	(Co)	2 atoms
Iron	(Fe)	16 atoms

Pages:

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

Binding sites:

The binding sites of Iodine atom in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol (pdb code 5ma2). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol, PDB code: 5ma2:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 11 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:I509 b:36.9 occ:0.66 I1 A:IOL509 0.0 36.9 0.7 C1 A:IOL509 2.1 18.8 0.7 C2 A:IOL509 3.0 24.6 0.7 C6 A:IOL509 3.0 25.4 0.7 CG A:TYR102 3.5 29.6 1.0 CD1 A:TYR102 3.6 30.8 1.0 CH2 A:TRP56 3.6 43.0 1.0 CE1 A:TYR382 3.6 27.6 1.0 CD2 A:TYR102 3.8 28.7 1.0 CE1 A:TYR102 3.9 34.2 1.0 O A:HOH828 4.0 28.5 1.0 CD1 A:TYR382 4.0 29.3 1.0 CB A:TYR102 4.0 23.7 1.0 CZ3 A:TRP56 4.1 34.0 1.0 CE2 A:TYR102 4.1 24.4 1.0 CZ A:TYR102 4.2 32.0 1.0 CZ A:TYR382 4.2 24.7 1.0 C3 A:IOL509 4.3 24.6 0.7 C5 A:IOL509 4.3 22.8 0.7 CZ2 A:TRP96 4.3 22.5 1.0 I A:IOD512 4.4 69.3 0.4 CZ3 A:TRP376 4.4 25.1 1.0 OH A:TYR382 4.5 26.1 1.0 CZ2 A:TRP56 4.6 41.7 1.0 CH2 A:TRP96 4.7 23.0 1.0 CE3 A:TRP376 4.8 19.3 1.0 C4 A:IOL509 4.9 32.1 0.7 CG A:TYR382 4.9 24.0 1.0

Iodine binding site 2 out of 11 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:I510 b:78.3 occ:0.51 I1 A:IOL510 0.0 78.3 0.5 C1 A:IOL510 2.1 48.7 0.5 C2 A:IOL510 3.0 49.2 0.5 C6 A:IOL510 3.0 45.9 0.5 CG2 A:VAL34 4.0 32.6 1.0 CB A:GLU189 4.0 28.3 1.0 C A:GLU189 4.1 32.8 1.0 O A:GLU189 4.1 30.9 1.0 O A:ILE190 4.1 29.7 1.0 N1 A:BEN504 4.1 45.9 1.0 C A:ILE190 4.2 26.4 1.0 N A:ILE190 4.2 28.9 1.0 CG1 A:VAL174 4.2 29.0 1.0 C3 A:IOL510 4.3 53.6 0.5 C5 A:IOL510 4.3 49.8 0.5 CA A:ILE190 4.4 28.8 1.0 C A:BEN504 4.4 52.8 1.0 CG2 A:VAL174 4.4 29.6 1.0 N2 A:BEN504 4.6 39.5 1.0 CG A:GLU191 4.6 33.6 1.0 OE1 A:GLU189 4.6 34.0 1.0 CA A:GLU189 4.7 27.0 1.0 N A:GLU191 4.7 26.6 1.0 CB A:VAL174 4.9 28.2 1.0 C4 A:IOL510 4.9 55.4 0.5 CB A:VAL34 5.0 27.2 1.0

Iodine binding site 3 out of 11 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:I511 b:38.1 occ:0.43 I1 A:IOL511 0.0 38.1 0.4 C1 A:IOL511 2.1 54.0 0.4 C2 A:IOL511 3.0 57.7 0.4 C6 A:IOL511 3.0 57.5 0.4 O B:LEU124 3.2 27.2 1.0 C5 A:IOL511 3.4 57.9 0.6 O4 A:IOL511 3.7 59.1 0.6 CG B:PRO127 3.9 35.3 1.0 CD B:PRO127 3.9 24.4 1.0 C B:LEU124 4.0 24.5 1.0 C4 A:IOL511 4.0 59.1 0.6 O B:GLN123 4.1 26.2 1.0 CA B:LEU124 4.1 23.1 1.0 CD2 A:LEU58 4.3 32.0 1.0 CE2 A:TYR61 4.3 24.3 1.0 C3 A:IOL511 4.3 58.6 0.4 C5 A:IOL511 4.3 59.9 0.4 CD1 A:LEU186 4.4 37.2 1.0 CD1 B:LEU124 4.4 25.7 1.0 C6 A:IOL511 4.5 60.3 0.6 CE2 A:PHE57 4.6 36.4 1.0 C4 A:IOL511 4.9 60.1 0.4 OH A:TYR61 4.9 26.3 1.0 C B:GLN123 5.0 25.9 1.0

Iodine binding site 4 out of 11 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:I511 b:0.1 occ:0.57 I1 A:IOL511 0.0 0.1 0.6 C1 A:IOL511 2.1 54.4 0.6 C6 A:IOL511 3.0 60.3 0.6 C2 A:IOL511 3.0 58.3 0.6 C3 A:IOL511 3.7 58.6 0.4 O A:LEU186 3.8 39.3 1.0 CZ A:PHE44 4.1 38.0 1.0 CB A:LEU186 4.3 35.1 1.0 CG A:PRO55 4.3 32.2 1.0 C5 A:IOL511 4.3 57.9 0.6 C3 A:IOL511 4.3 60.8 0.6 O4 A:IOL511 4.3 61.9 0.4 CZ A:PHE57 4.3 34.7 1.0 C A:LEU186 4.4 34.3 1.0 C4 A:IOL511 4.5 60.1 0.4 C2 A:IOL511 4.6 57.7 0.4 CE2 A:PHE44 4.7 35.2 1.0 CB A:PRO55 4.7 31.2 1.0 C4 A:IOL511 4.9 59.1 0.6 CA A:LEU186 4.9 27.8 1.0 CD2 A:HIS187 4.9 72.0 1.0 CE1 A:PHE57 5.0 34.9 1.0

Iodine binding site 5 out of 11 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ A:I512 b:69.3 occ:0.44 CE1 A:TYR382 3.3 27.6 1.0 CB A:ALA60 3.4 26.2 1.0 NZ A:LYS64 3.4 25.3 1.0 O A:GLY381 3.5 31.6 1.0 CD1 A:TYR382 3.5 29.3 1.0 O A:HOH828 3.6 28.5 1.0 C A:GLY381 3.9 27.8 1.0 CE A:LYS64 3.9 28.2 1.0 CA A:GLY381 4.1 25.4 1.0 N A:GLY381 4.3 23.1 1.0 CZ3 A:TRP56 4.3 34.0 1.0 I1 A:IOL509 4.4 36.9 0.7 CZ A:TYR382 4.5 24.7 1.0 C A:GLY380 4.5 29.9 1.0 O A:GLY380 4.6 28.7 1.0 CE3 A:TRP376 4.6 19.3 1.0 N A:TYR382 4.8 24.1 1.0 CA A:ALA60 4.8 24.5 1.0 CB A:TRP376 4.8 21.2 1.0 CG A:TYR382 4.8 24.0 1.0 OH A:TYR382 4.9 26.1 1.0 O A:TRP376 4.9 26.5 1.0 CE3 A:TRP56 5.0 41.2 1.0

Iodine binding site 6 out of 11 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:I506 b:55.4 occ:0.51 I1 B:IOL506 0.0 55.4 0.5 C1 B:IOL506 2.1 58.6 0.5 C6 B:IOL506 3.0 61.9 0.5 C2 B:IOL506 3.0 63.9 0.5 O B:GLU189 3.9 31.1 1.0 CB B:GLU189 4.0 28.9 1.0 C B:GLU189 4.0 29.4 1.0 CG2 B:VAL34 4.1 35.4 1.0 N B:ILE190 4.2 27.0 1.0 CG1 B:VAL174 4.3 29.8 1.0 C B:ILE190 4.3 25.3 1.0 O B:ILE190 4.3 27.9 1.0 C5 B:IOL506 4.3 65.2 0.5 C3 B:IOL506 4.3 70.2 0.5 CG2 B:VAL174 4.4 24.6 1.0 CA B:ILE190 4.4 26.1 1.0 OE1 B:GLU189 4.5 34.6 1.0 CG B:GLU191 4.6 43.3 1.0 O B:HOH833 4.6 42.3 1.0 CA B:GLU189 4.7 27.2 1.0 N B:GLU191 4.8 27.9 1.0 C4 B:IOL506 4.9 65.6 0.5 CB B:VAL34 4.9 27.4 1.0 CB B:VAL174 4.9 32.5 1.0

Iodine binding site 7 out of 11 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:I507 b:0.9 occ:0.68 I1 B:IOL507 0.0 0.9 0.7 C1 B:IOL507 2.1 52.2 0.7 C2 B:IOL507 3.0 49.9 0.7 C6 B:IOL507 3.0 52.5 0.7 C3 B:IOL508 3.8 33.4 0.6 ND1 B:HIS187 3.9 59.8 1.0 CE1 B:HIS187 4.0 65.6 1.0 O B:LEU186 4.0 37.5 1.0 CG B:PRO55 4.1 27.7 1.0 C3 B:IOL507 4.3 59.4 0.7 C5 B:IOL507 4.3 57.2 0.7 CB B:LEU186 4.3 28.5 1.0 C B:LEU186 4.4 36.2 1.0 O4 B:IOL508 4.4 38.8 0.6 CZ B:PHE44 4.5 37.7 1.0 CZ B:PHE57 4.6 32.5 1.0 CE2 B:PHE44 4.6 39.5 1.0 C4 B:IOL508 4.6 32.0 0.6 C2 B:IOL508 4.7 31.4 0.6 CB B:PRO55 4.7 29.5 1.0 CG B:HIS187 4.8 53.7 1.0 NE2 B:HIS187 4.8 69.2 1.0 C4 B:IOL507 4.9 63.2 0.7 N B:HIS187 4.9 31.6 1.0 CA B:HIS187 4.9 32.6 1.0

Iodine binding site 8 out of 11 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:I508 b:31.3 occ:0.60 I1 B:IOL508 0.0 31.3 0.6 C1 B:IOL508 2.1 20.5 0.6 C2 B:IOL508 3.0 31.4 0.6 C6 B:IOL508 3.0 29.8 0.6 O A:LEU124 3.1 25.1 1.0 CG A:PRO127 3.8 29.9 1.0 CD A:PRO127 3.9 28.5 1.0 C A:LEU124 3.9 22.8 1.0 O A:GLN123 4.1 23.5 1.0 CD2 B:LEU58 4.1 29.1 1.0 CA A:LEU124 4.1 28.0 1.0 O B:HOH878 4.2 40.1 1.0 CE2 B:TYR61 4.3 23.1 1.0 CD1 B:LEU186 4.3 37.7 1.0 C3 B:IOL508 4.3 33.4 0.6 C5 B:IOL508 4.3 35.5 0.6 CD1 A:LEU124 4.4 22.7 1.0 CE2 B:PHE57 4.7 35.2 1.0 O A:HOH989 4.9 70.7 1.0 C4 B:IOL508 4.9 32.0 0.6 OH B:TYR61 4.9 26.4 1.0 C A:GLN123 5.0 22.5 1.0

Iodine binding site 9 out of 11 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:I509 b:38.2 occ:0.70 I1 B:IOL509 0.0 38.2 0.7 C1 B:IOL509 2.1 22.1 0.7 C2 B:IOL509 3.0 28.6 0.7 C6 B:IOL509 3.0 35.9 0.7 CD1 B:TYR102 3.5 34.0 1.0 CG B:TYR102 3.6 32.3 1.0 CH2 B:TRP56 3.7 41.4 1.0 CE1 B:TYR382 3.7 34.2 1.0 CE1 B:TYR102 3.8 33.7 1.0 CD2 B:TYR102 3.9 25.8 1.0 O B:HOH693 4.0 25.9 1.0 CD1 B:TYR382 4.1 35.8 1.0 I B:IOD511 4.1 89.1 0.5 CZ B:TYR102 4.1 35.1 1.0 CZ3 B:TRP56 4.1 36.8 1.0 CB B:TYR102 4.1 28.6 1.0 CE2 B:TYR102 4.2 25.6 1.0 CZ B:TYR382 4.3 27.2 1.0 C3 B:IOL509 4.3 30.1 0.7 C5 B:IOL509 4.3 27.3 0.7 CZ3 B:TRP376 4.4 28.2 1.0 CZ2 B:TRP96 4.5 27.6 1.0 OH B:TYR382 4.6 27.9 1.0 CZ2 B:TRP56 4.7 42.5 1.0 CE3 B:TRP376 4.8 25.5 1.0 C4 B:IOL509 4.9 37.8 0.7 CH2 B:TRP96 4.9 23.5 1.0 CG B:TYR382 5.0 27.4 1.0 OH B:TYR102 5.0 30.8 1.0

Iodine binding site 10 out of 11 in the Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Pce Reductive Dehalogenase From S. Multivorans in Complex with 4- Iodophenol within 5.0Å range: probe atom residue distance (Å) B Occ B:I510 b:65.3 occ:0.36 O B:PRO391 3.8 33.8 1.0 C B:PRO391 3.8 37.2 1.0 CB B:PRO391 3.9 36.4 1.0 N B:PHE392 4.0 29.4 1.0 CD1 B:PHE392 4.0 30.7 1.0 NZ B:LYS394 4.1 75.3 1.0 CA B:PHE392 4.2 30.3 1.0 CE1 B:PHE392 4.2 32.6 1.0 CG B:PHE392 4.3 29.7 1.0 CA B:PRO391 4.5 32.0 1.0 CZ B:PHE392 4.6 34.5 1.0 CZ B:PHE328 4.6 61.9 1.0 CE2 B:PHE328 4.6 62.3 1.0 CD2 B:PHE392 4.6 33.3 1.0 CE2 B:PHE392 4.8 35.7 1.0 CB B:PHE392 4.9 29.4 1.0

C.Kunze, M.Bommer, W.R.Hagen, M.Uksa, H.Dobbek, T.Schubert, G.Diekert. Cobamide-Mediated Enzymatic Reductive Dehalogenation Via Long-Range Electron Transfer. Nat Commun V. 8 15858 2017.
ISSN: ESSN 2041-1723
PubMed: 28671181
DOI: 10.1038/NCOMMS15858