Iodine in PDB 2h9a: Corrinoid Iron-Sulfur Protein

The structure of Corrinoid Iron-Sulfur Protein, PDB code: 2h9a was solved by H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	158.030, 44.270, 100.660, 90.00, 118.63, 90.00
R / Rfree (%)	20.3 / 26

The structure of Corrinoid Iron-Sulfur Protein also contains other interesting chemical elements:

Cobalt	(Co)	1 atom
Iron	(Fe)	4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iodine atom in the Corrinoid Iron-Sulfur Protein (pdb code 2h9a). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 16 binding sites of Iodine where determined in the Corrinoid Iron-Sulfur Protein, PDB code: 2h9a:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 16 in the Corrinoid Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Corrinoid Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I1445 b:13.8 occ:0.50 O A:HOH1509 3.3 10.7 1.0 O A:HOH1462 3.5 9.3 1.0 CE A:LYS253 3.6 23.4 1.0 CE1 A:PHE82 3.9 13.5 1.0 OE2 B:GLU8 4.1 39.4 1.0 CD B:GLU8 4.1 36.1 1.0 CD1 A:LEU81 4.2 14.0 1.0 CG B:GLU8 4.2 32.5 1.0 CH2 B:TRP10 4.3 7.8 1.0 NZ A:LYS253 4.3 27.0 1.0 NE A:ARG249 4.5 8.9 1.0 NH1 A:ARG249 4.5 7.2 1.0 CZ A:PHE82 4.5 12.3 1.0 CZ2 B:TRP10 4.6 10.0 1.0 CZ A:ARG249 4.7 8.3 1.0 OE1 B:GLU8 4.8 40.3 1.0 CD1 B:LEU34 4.8 3.2 1.0 CD A:LYS253 4.8 22.6 1.0 CD1 A:PHE82 5.0 11.2 1.0

Iodine binding site 2 out of 16 in the Corrinoid Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Corrinoid Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I1448 b:24.3 occ:0.50 OG1 A:THR221 3.3 20.1 1.0 CG A:PRO258 3.7 17.2 1.0 O A:HOH1597 3.8 29.3 1.0 N A:PRO258 3.9 16.4 1.0 CB A:ARG257 3.9 24.1 1.0 CD A:PRO258 4.0 16.6 1.0 CG A:GLN218 4.0 26.4 1.0 CA A:PRO258 4.0 14.3 1.0 CG2 A:THR221 4.2 17.0 1.0 C A:ARG257 4.2 16.9 1.0 CB A:THR221 4.2 17.6 1.0 CA A:GLN218 4.3 20.4 1.0 CB A:PRO258 4.4 17.5 1.0 O A:ARG257 4.5 15.7 1.0 CG1 A:VAL217 4.6 12.8 1.0 CB A:GLN218 4.7 23.0 1.0 CA A:ARG257 4.8 19.3 1.0 N A:GLN218 4.8 17.4 1.0 O A:VAL217 4.8 14.1 1.0 C A:VAL217 5.0 16.0 1.0

Iodine binding site 3 out of 16 in the Corrinoid Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Corrinoid Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I1449 b:16.1 occ:1.00 O A:HOH1463 3.5 7.2 1.0 O A:HOH1485 3.5 13.1 1.0 CG A:PRO91 3.8 10.9 1.0 CA A:LEU308 3.8 6.0 1.0 CB A:PRO91 3.9 10.9 1.0 CE1 A:HIS126 4.0 15.7 1.0 ND1 A:HIS126 4.1 15.9 1.0 NE A:ARG307 4.1 10.0 1.0 N A:LEU308 4.1 4.8 1.0 CG A:ARG307 4.4 6.3 1.0 C A:ARG307 4.5 3.1 1.0 CB A:LEU308 4.5 5.2 1.0 O A:ARG307 4.6 2.5 1.0 CD A:ARG307 4.6 9.7 1.0 CG A:LEU308 4.7 9.6 1.0 CZ A:ARG307 4.8 12.5 1.0 NE2 A:HIS126 4.8 13.0 1.0 CD2 A:LEU308 4.9 8.6 1.0 CB A:TYR311 4.9 6.6 1.0 NH2 A:ARG307 5.0 10.9 1.0 CG A:HIS126 5.0 14.6 1.0 O A:HOH1694 5.0 31.5 1.0 C A:LEU308 5.0 6.9 1.0

Iodine binding site 4 out of 16 in the Corrinoid Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Corrinoid Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I1450 b:17.6 occ:0.70 OE2 B:GLU263 3.1 52.8 1.0 N A:ASP120 3.4 13.1 1.0 O B:HOH1462 3.6 3.4 1.0 CB B:GLU263 3.8 34.7 1.0 CD B:GLU263 3.8 48.4 1.0 CA A:PHE119 3.9 12.9 1.0 O A:HOH1543 4.1 20.7 1.0 CB A:ASP120 4.1 20.1 1.0 C A:PHE119 4.2 12.2 1.0 O A:HOH1740 4.2 21.7 1.0 CG B:GLU263 4.3 43.1 1.0 CG A:ASP120 4.3 25.2 1.0 O A:VAL118 4.4 11.9 1.0 CA A:ASP120 4.4 15.8 1.0 CD2 A:PHE119 4.5 9.4 1.0 OD1 A:ASP120 4.5 28.7 1.0 O B:GLU263 4.5 22.8 1.0 CB A:PHE119 4.5 10.5 1.0 NE1 B:TRP264 4.5 16.1 1.0 CD1 B:TRP264 4.6 15.8 1.0 OE1 B:GLU263 4.7 50.2 1.0 OD2 A:ASP120 4.8 26.3 1.0 O A:ASP120 4.8 16.3 1.0 CA B:GLU263 4.9 27.2 1.0 C B:GLU263 4.9 24.7 1.0 N A:PHE119 4.9 12.6 1.0 CG A:PHE119 5.0 10.5 1.0

Iodine binding site 5 out of 16 in the Corrinoid Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Corrinoid Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I1451 b:11.1 occ:0.60 O A:HOH1588 3.2 17.8 1.0 NH2 A:ARG110 3.9 7.1 1.0 CG A:ARG110 4.0 6.2 1.0 CB A:ARG110 4.0 7.8 1.0 CA A:ARG110 4.1 8.5 1.0 CD A:LYS113 4.3 20.4 1.0 CD A:ARG110 4.3 3.5 1.0 CG2 A:VAL295 4.3 7.7 1.0 N A:ARG110 4.6 10.1 1.0 O A:HOH1742 4.7 22.0 1.0 OE1 A:GLU109 4.7 38.2 1.0 O A:HOH1763 4.8 25.4 1.0 CG A:GLU109 4.9 29.5 1.0 CE A:LYS113 4.9 23.8 1.0 CD A:GLU109 4.9 35.0 1.0 O A:HOH1688 5.0 20.8 1.0 CZ A:ARG110 5.0 6.7 1.0

Iodine binding site 6 out of 16 in the Corrinoid Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Corrinoid Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I1452 b:21.8 occ:0.50 O A:HOH1701 3.1 30.7 1.0 O A:HOH1555 3.1 13.4 1.0 N A:ALA176 3.8 12.5 1.0 CA A:ALA176 4.1 12.0 1.0 CD2 A:TYR199 4.1 15.2 1.0 CE2 A:TYR199 4.2 15.5 1.0 C A:GLY175 4.3 12.6 1.0 CB A:ALA176 4.4 14.8 1.0 CA A:GLY175 4.7 12.2 1.0 O A:GLY175 4.8 11.4 1.0

Iodine binding site 7 out of 16 in the Corrinoid Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Corrinoid Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I1453 b:20.0 occ:0.50 O A:HOH1513 3.3 18.3 1.0 NE1 A:TRP376 3.6 27.1 1.0 CG2 A:THR382 3.8 15.2 1.0 CD2 A:LEU413 4.0 23.5 1.0 CD A:PRO383 4.1 20.8 1.0 O A:HOH1684 4.1 23.0 1.0 CA A:THR382 4.3 16.9 1.0 CB A:THR382 4.3 16.2 1.0 CD1 A:TRP376 4.3 25.4 1.0 CE2 A:TRP376 4.3 28.4 1.0 O A:PHE381 4.7 18.2 1.0 CZ2 A:TRP376 4.7 31.1 1.0 N A:THR382 5.0 17.2 1.0

Iodine binding site 8 out of 16 in the Corrinoid Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Corrinoid Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I1454 b:13.4 occ:0.30 CB A:ASN400 3.9 34.7 1.0 CA A:ASP333 4.0 17.5 1.0 CB A:ASP333 4.1 24.1 1.0 O A:PRO332 4.3 14.1 1.0 N A:HIS401 4.7 19.5 1.0 N A:ASP333 4.7 15.5 1.0 C A:ASN400 4.7 23.6 1.0 C A:PRO332 4.8 14.9 1.0 CA A:ASN400 4.8 25.9 1.0 CB A:HIS401 4.9 17.5 1.0 ND2 A:ASN400 4.9 45.2 1.0 CG A:ASN400 5.0 40.8 1.0 ND1 A:HIS401 5.0 14.3 1.0

Iodine binding site 9 out of 16 in the Corrinoid Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Corrinoid Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I1455 b:22.3 occ:0.50 O A:HOH1550 3.0 18.4 1.0 NZ A:LYS134 3.3 19.7 1.0 O A:HOH1752 3.8 23.5 1.0 C A:GLY135 3.8 11.3 1.0 CG A:LYS134 3.9 15.2 1.0 O A:GLY135 3.9 13.3 1.0 N A:SER136 4.0 12.3 1.0 N A:GLY135 4.1 12.9 1.0 CG2 A:ILE161 4.3 9.5 1.0 CA A:SER136 4.3 11.4 1.0 CE A:LYS134 4.3 19.2 1.0 CA A:GLY135 4.3 11.8 1.0 NE2 A:GLN138 4.5 41.2 1.0 O A:ILE161 4.5 10.6 1.0 CD A:LYS134 4.7 15.0 1.0 CA A:GLY162 4.8 11.6 1.0 C A:LYS134 4.9 11.1 1.0 OG A:SER136 4.9 15.0 1.0 C A:ILE161 5.0 9.7 1.0

Iodine binding site 10 out of 16 in the Corrinoid Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Corrinoid Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:I1456 b:16.3 occ:0.30 N A:SER127 3.4 10.9 1.0 NH2 A:ARG307 3.6 10.9 1.0 ND2 A:ASN129 3.6 11.0 1.0 ND1 A:HIS126 3.7 15.9 1.0 O A:SER127 3.7 11.0 1.0 CA A:HIS126 3.8 12.6 1.0 C A:HIS126 4.1 10.6 1.0 CB A:HIS126 4.2 12.2 1.0 O A:HOH1720 4.3 23.7 1.0 CG A:HIS126 4.4 14.6 1.0 CZ A:ARG307 4.5 12.5 1.0 CA A:SER127 4.5 12.9 1.0 C A:SER127 4.5 10.8 1.0 O A:MET125 4.6 16.9 1.0 OG A:SER127 4.6 19.0 1.0 CE1 A:HIS126 4.8 15.7 1.0 CG A:ASN129 4.8 12.8 1.0 NH1 A:ARG307 4.9 8.3 1.0 O A:HOH1694 4.9 31.5 1.0 O A:HOH1709 4.9 22.6 1.0 N A:HIS126 5.0 14.3 1.0

T.Svetlitchnaia, V.Svetlitchnyi, O.Meyer, H.Dobbek. Structural Insights Into Methyltransfer Reactions of A Corrinoid Iron-Sulfur Protein Involved in Acetyl-Coa Synthesis. Proc.Natl.Acad.Sci.Usa V. 103 14331 2006.
ISSN: ISSN 0027-8424
PubMed: 16983091
DOI: 10.1073/PNAS.0601420103