Iodine in PDB 5a11: The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21)

The structure of The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21), PDB code: 5a11 was solved by J.Krausze, F.Gumz, U.Wittstock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.031 / 2.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.367, 89.613, 83.842, 90.00, 101.08, 90.00
R / Rfree (%)	26.01 / 28.76

The binding sites of Iodine atom in the The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21) (pdb code 5a11). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21), PDB code: 5a11:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1349 b:46.9 occ:1.00 NE A:ARG157 3.5 19.5 1.0 NH2 A:ARG157 3.7 15.8 1.0 CA A:GLY185 3.9 21.6 1.0 CZ A:ARG157 4.1 16.2 1.0 CD2 A:PHE202 4.2 19.0 1.0 CB A:PHE130 4.2 20.0 1.0 C A:GLY185 4.3 20.1 1.0 N A:GLY185 4.4 22.5 1.0 CD A:ARG157 4.6 22.6 1.0 CG A:PHE130 4.6 23.3 1.0 CD2 A:PHE130 4.6 25.8 1.0 CB A:PHE202 4.7 13.6 1.0 CG A:MET186 4.7 20.2 1.0 O A:GLY185 4.7 18.9 1.0 CG1 A:VAL146 4.8 28.0 1.0 N A:MET186 4.8 21.2 1.0 CG A:PHE202 4.8 18.4 1.0 CB A:VAL146 5.0 27.7 1.0 CE2 A:PHE202 5.0 21.4 1.0

Iodine binding site 2 out of 7 in the The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1350 b:80.3 occ:1.00 O A:HOH2013 3.2 6.6 1.0 CD A:ARG80 3.5 39.1 1.0 NE A:ARG80 3.6 43.0 1.0 N A:MET133 3.8 24.4 1.0 CE1 A:HIS253 4.0 24.7 1.0 CA A:SER132 4.1 20.6 1.0 O A:MET133 4.1 21.1 1.0 NE2 A:HIS253 4.1 24.3 1.0 CB A:SER132 4.2 18.7 1.0 OG A:SER132 4.4 17.4 1.0 C A:SER132 4.5 22.9 1.0 CG A:ARG80 4.5 35.9 1.0 CA A:MET133 4.8 24.3 1.0 CZ A:ARG80 4.8 47.9 1.0 C A:MET133 4.9 23.1 1.0 O A:HIS131 4.9 17.8 1.0

Iodine binding site 3 out of 7 in the The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21) within 5.0Å range: probe atom residue distance (Å) B Occ A:I1351 b:73.9 occ:1.00 CE A:MET10 3.6 65.6 1.0 CG2 A:ILE317 4.2 23.6 1.0 CG2 A:VAL12 4.2 31.9 1.0 CA A:VAL12 4.3 30.6 1.0 CG1 A:VAL12 4.4 31.7 1.0 CE1 A:HIS60 4.4 52.0 1.0 CB A:VAL12 4.5 31.4 1.0 ND2 A:ASN318 4.6 36.2 1.0 SD A:MET10 4.6 0.6 1.0 O A:LYS11 4.7 29.1 1.0 CB A:MET10 4.8 21.6 1.0

Iodine binding site 4 out of 7 in the The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21) within 5.0Å range: probe atom residue distance (Å) B Occ B:I1349 b:43.4 occ:1.00 NE B:ARG157 3.4 28.8 1.0 NH2 B:ARG157 3.8 24.4 1.0 CA B:GLY185 3.8 20.6 1.0 CZ B:ARG157 4.1 27.5 1.0 CD2 B:PHE202 4.1 22.6 1.0 N B:GLY185 4.3 21.7 1.0 CG1 B:VAL146 4.3 18.5 1.0 CB B:PHE130 4.4 17.4 1.0 C B:GLY185 4.4 19.7 1.0 CD B:ARG157 4.4 30.6 1.0 CB B:VAL146 4.7 18.6 1.0 CB B:PHE202 4.7 23.8 1.0 CG B:PHE130 4.8 18.4 1.0 O B:GLY185 4.8 19.6 1.0 CG B:PHE202 4.9 23.3 1.0 CD2 B:PHE130 4.9 18.5 1.0 O B:PHE202 4.9 17.8 1.0 CE2 B:PHE202 4.9 25.4 1.0 N B:MET186 4.9 17.9 1.0 CG B:MET186 5.0 22.7 1.0

Iodine binding site 5 out of 7 in the The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21) within 5.0Å range: probe atom residue distance (Å) B Occ B:I1350 b:88.1 occ:1.00 CD B:ARG80 3.6 27.0 1.0 N B:MET133 3.7 17.8 1.0 NE B:ARG80 3.8 28.4 1.0 O B:MET133 4.0 19.6 1.0 NE2 B:HIS253 4.1 16.1 1.0 CE1 B:HIS253 4.1 16.4 1.0 CA B:SER132 4.2 18.0 1.0 CB B:SER132 4.4 16.1 1.0 C B:SER132 4.5 18.2 1.0 CG B:ARG80 4.5 26.3 1.0 OG B:SER132 4.6 18.9 1.0 CA B:MET133 4.7 19.5 1.0 C B:MET133 4.8 19.1 1.0 O B:HIS131 5.0 23.1 1.0 CB B:MET133 5.0 19.5 1.0 CZ B:ARG80 5.0 31.3 1.0 CB B:ARG80 5.0 25.8 1.0

Iodine binding site 6 out of 7 in the The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21) within 5.0Å range: probe atom residue distance (Å) B Occ B:I1351 b:91.1 occ:1.00 NH1 B:ARG94 3.6 41.6 1.0 CB B:LYS148 3.7 77.1 1.0 CG2 B:THR129 3.8 29.7 1.0 CG1 B:VAL146 3.9 18.5 1.0 CG2 B:VAL146 3.9 18.9 1.0 N B:LYS148 4.1 72.9 1.0 CD B:ARG94 4.1 31.5 1.0 O B:VAL146 4.2 47.1 1.0 CA B:LYS148 4.3 74.6 1.0 CB B:VAL146 4.5 18.6 1.0 CZ B:ARG94 4.5 40.6 1.0 C B:VAL146 4.6 49.7 1.0 C B:SER147 4.7 66.7 1.0 NE B:ARG94 4.7 37.4 1.0 CZ B:PHE100 4.8 29.5 1.0 CB B:PRO155 4.9 58.1 1.0

Iodine binding site 7 out of 7 in the The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of The Crystal Structure of Ta-Tfp, A Thiocyanate-Forming Protein Involved in Glucosinolate Breakdown (Space Group P21) within 5.0Å range: probe atom residue distance (Å) B Occ B:I1352 b:70.3 occ:1.00 CG2 B:VAL12 4.2 38.7 1.0 CG2 B:ILE317 4.3 18.4 1.0 CG1 B:VAL12 4.3 33.9 1.0 CA B:VAL12 4.4 36.0 1.0 ND2 B:ASN318 4.5 41.2 1.0 CB B:VAL12 4.5 36.5 1.0 SD B:MET10 4.8 86.2 1.0 CB B:MET10 4.9 26.1 1.0 NE2 B:HIS60 5.0 65.2 1.0 O B:LYS11 5.0 31.8 1.0 CE1 B:HIS60 5.0 63.0 1.0

F.Gumz, J.Krausze, D.Eisenschmidt, A.Backenkohler, L.Barleben, W.Brandt, U.Wittstock. The Crystal Structure of the Thiocyanate-Forming Protein From Thlaspi Arvense, A Kelch Protein Involved in Glucosinolate Breakdown. Plant Mol.Biol. V. 89 67 2015.
ISSN: ISSN 0167-4412
PubMed: 26260516
DOI: 10.1007/S11103-015-0351-9