Iodine in PDB 1ydo: Crystal Structure of the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181.

The structure of Crystal Structure of the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181., PDB code: 1ydo was solved by F.Forouhar, M.Hussain, W.Edstrom, S.M.Vorobiev, R.Xiao, M.Ciano, L.Shih, T.B.Acton, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structuralgenomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.94 / 2.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.693, 104.666, 97.445, 90.00, 107.43, 90.00
R / Rfree (%)	26.3 / 30.3

The binding sites of Iodine atom in the Crystal Structure of the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181. (pdb code 1ydo). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181., PDB code: 1ydo:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Crystal Structure of the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181.


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 the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181. within 5.0Å range: probe atom residue distance (Å) B Occ A:I501 b:68.9 occ:1.00 CG1 A:VAL51 3.8 43.2 1.0 N A:HIS52 3.8 52.5 1.0 CB A:PRO82 4.0 42.2 1.0 OD1 A:ASN83 4.2 42.6 1.0 CG A:PRO82 4.3 42.4 1.0 CB A:HIS52 4.3 58.2 1.0 CA A:VAL51 4.5 47.6 1.0 C A:VAL51 4.7 50.4 1.0 CA A:HIS52 4.7 54.8 1.0 CB A:VAL51 4.7 46.4 1.0 CD1 A:ILE113 4.7 68.7 1.0 CD1 A:TRP55 4.8 53.4 1.0 NE1 A:TRP55 4.9 53.4 1.0

Iodine binding site 2 out of 4 in the Crystal Structure of the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181.


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 the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181. within 5.0Å range: probe atom residue distance (Å) B Occ B:I502 b:50.9 occ:1.00 O B:HOH564 3.1 22.2 1.0 N B:HIS52 3.3 39.5 1.0 CG1 B:VAL51 3.7 32.6 1.0 CB B:HIS52 3.7 46.9 1.0 CA B:HIS52 4.1 42.7 1.0 CB B:PRO82 4.2 26.8 1.0 C B:VAL51 4.2 36.3 1.0 CA B:VAL51 4.2 34.9 1.0 CG B:PRO82 4.2 27.2 1.0 OD1 B:ASN83 4.5 33.7 1.0 CB B:VAL51 4.6 33.0 1.0 CD1 B:TRP55 4.7 55.7 1.0 NE1 B:TRP55 4.9 56.6 1.0 CG B:HIS52 5.0 49.5 1.0

Iodine binding site 3 out of 4 in the Crystal Structure of the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181.


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 the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181. within 5.0Å range: probe atom residue distance (Å) B Occ C:I503 b:59.7 occ:1.00 N C:HIS52 3.6 31.7 1.0 CG1 C:VAL51 3.7 32.2 1.0 CB C:PRO82 4.0 25.8 1.0 CB C:HIS52 4.1 34.6 1.0 CG C:PRO82 4.2 26.6 1.0 OD1 C:ASN83 4.3 33.9 1.0 CA C:VAL51 4.4 31.4 1.0 C C:VAL51 4.5 32.1 1.0 CA C:HIS52 4.5 32.5 1.0 O C:HOH507 4.6 19.2 1.0 CB C:VAL51 4.6 31.0 1.0 CD1 C:TRP55 4.7 48.0 1.0 CD1 C:ILE113 4.8 66.5 1.0 NE1 C:TRP55 4.9 50.0 1.0

Iodine binding site 4 out of 4 in the Crystal Structure of the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181.


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 the Bacillis Subtilis Hmg-Coa Lyase, Northeast Structural Genomics Target SR181. within 5.0Å range: probe atom residue distance (Å) B Occ D:I504 b:70.9 occ:1.00 O D:HOH584 3.5 48.6 1.0 N D:HIS52 3.6 57.9 1.0 O D:HOH545 3.7 30.3 1.0 CB D:HIS52 3.8 58.5 1.0 CG1 D:VAL51 3.8 54.4 1.0 CA D:HIS52 4.3 59.0 1.0 CB D:PRO82 4.4 48.4 1.0 O D:HOH580 4.5 37.1 1.0 CG D:PRO82 4.5 49.7 1.0 OD1 D:ASN83 4.5 52.9 1.0 CA D:VAL51 4.5 55.3 1.0 C D:VAL51 4.5 56.9 1.0 CD1 D:TRP55 4.6 64.7 1.0 NE1 D:TRP55 4.7 66.1 1.0 CB D:VAL51 4.8 55.1 1.0

F.Forouhar, M.Hussain, R.Farid, J.Benach, M.Abashidze, W.C.Edstrom, S.M.Vorobiev, R.Xiao, T.B.Acton, Z.Fu, J.J.Kim, H.M.Miziorko, G.T.Montelione, J.F.Hunt. Crystal Structures of Two Bacterial 3-Hydroxy-3-Methylglutaryl-Coa Lyases Suggest A Common Catalytic Mechanism Among A Family of Tim Barrel Metalloenzymes Cleaving Carbon-Carbon Bonds. J.Biol.Chem. V. 281 7533 2006.
ISSN: ISSN 0021-9258
PubMed: 16330546
DOI: 10.1074/JBC.M507996200