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

Protein crystallography data

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

Iodine Binding Sites:

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 5a11

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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 5a11

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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 5a11

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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 5a11

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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 5a11

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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 5a11

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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 5a11

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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

Reference:

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
Page generated: Sun Dec 13 19:38:22 2020

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