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Iodine in PDB 3q1e: Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4

Enzymatic activity of Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4

All present enzymatic activity of Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4:
3.5.2.17;

Protein crystallography data

The structure of Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4, PDB code: 3q1e was solved by L.Cendron, I.Ramazzina, R.Percudani, G.Zanotti, R.Berni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.73 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.771, 103.462, 53.490, 90.00, 109.47, 90.00
R / Rfree (%) 22.2 / 27.1

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4 (pdb code 3q1e). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4, PDB code: 3q1e:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 3q1e

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Iodine binding site 1 out of 8 in the Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4


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 Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I128

b:80.6
occ:0.40
 CD2 A:LEU14 3.8 44.4 1.0
ND1 C:HIS103 4.1 41.4 1.0
CG C:PRO105 4.3 39.2 1.0
CE1 A:HIS12 4.3 50.4 1.0
CG2 C:THR116 4.4 38.5 1.0
ND1 A:HIS12 4.4 47.0 1.0
CE1 C:HIS103 4.5 39.1 1.0
O A:HOH125 4.5 30.7 1.0
CD1 A:LEU14 4.9 45.5 1.0
CG A:LEU14 4.9 43.7 1.0

Iodine binding site 2 out of 8 in 3q1e

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Iodine binding site 2 out of 8 in the Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4


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 Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I128

b:48.8
occ:0.40
 I3' C:T44128 0.0 48.8 0.4
O4' C:T44128 3.5 31.4 0.4
O A:SER114 3.5 36.0 1.0
CG A:PRO105 3.6 42.9 1.0
N A:LEU107 3.7 36.6 1.0
CB A:LEU107 3.8 37.9 1.0
CA A:THR115 4.1 36.7 1.0
C A:SER114 4.1 36.1 1.0
OG A:SER114 4.1 39.2 1.0
CB A:PRO105 4.2 42.9 1.0
C A:LEU106 4.2 37.5 1.0
C A:PRO105 4.2 40.6 1.0
O A:PRO105 4.2 41.5 1.0
N A:LEU106 4.3 39.1 1.0
N A:THR116 4.3 39.2 1.0
CA A:LEU107 4.4 36.6 1.0
CA A:LEU106 4.4 37.7 1.0
N A:THR115 4.4 36.6 1.0
O A:HOH125 4.4 30.7 1.0
C A:THR115 4.5 38.4 1.0
OG1 A:THR116 4.8 47.2 1.0
CA A:PRO105 4.8 41.6 1.0
O A:LEU106 4.9 37.0 1.0
CD A:PRO105 4.9 43.5 1.0

Iodine binding site 3 out of 8 in 3q1e

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Iodine binding site 3 out of 8 in the Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4


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 Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I128

b:90.7
occ:0.40
 CD1 C:LEU14 3.5 50.7 1.0
ND1 C:HIS12 4.1 49.9 1.0
CG C:LEU14 4.2 45.0 1.0
CE1 C:HIS12 4.2 51.9 1.0
ND1 A:HIS103 4.3 44.4 1.0
CE1 A:HIS103 4.6 40.9 1.0
CG A:PRO105 4.8 42.9 1.0
CD2 C:LEU14 4.8 49.6 1.0

Iodine binding site 4 out of 8 in 3q1e

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Iodine binding site 4 out of 8 in the Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4


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 Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I128

b:53.5
occ:0.40
 I5' C:T44128 0.0 53.5 0.4
O4' C:T44128 3.4 31.4 0.4
N C:LEU107 3.6 33.8 1.0
CB C:LEU107 3.6 38.5 1.0
O C:SER114 3.6 31.3 1.0
CG C:PRO105 3.9 39.2 1.0
CB C:PRO105 3.9 37.0 1.0
OG C:SER114 4.1 40.9 1.0
C C:PRO105 4.1 36.7 1.0
C C:LEU106 4.1 34.8 1.0
N C:LEU106 4.2 35.7 1.0
CA C:THR115 4.2 33.4 1.0
CA C:LEU107 4.2 37.2 1.0
C C:SER114 4.3 32.1 1.0
O C:PRO105 4.3 35.6 1.0
CA C:LEU106 4.4 33.5 1.0
N C:THR116 4.5 34.4 1.0
CG2 C:THR116 4.5 38.5 1.0
N C:THR115 4.6 33.5 1.0
CA C:PRO105 4.6 37.6 1.0
C C:THR115 4.6 34.0 1.0
CD C:PRO105 4.8 37.8 1.0
CG C:LEU107 4.8 43.6 1.0
O C:LEU106 4.9 35.2 1.0
CD2 C:LEU107 4.9 47.3 1.0

Iodine binding site 5 out of 8 in 3q1e

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Iodine binding site 5 out of 8 in the Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I328

b:86.0
occ:0.36
 CD1 D:LEU14 3.2 52.1 1.0
CG2 B:THR116 4.0 43.7 1.0
CD2 B:HIS103 4.1 46.0 1.0
CG B:PRO105 4.4 40.6 1.0
CG D:LEU14 4.6 47.1 1.0
CE1 D:HIS12 4.7 53.1 1.0
NE2 B:HIS103 4.8 47.1 1.0
ND1 D:HIS12 4.8 52.0 1.0
CA B:GLY118 4.8 51.7 1.0

Iodine binding site 6 out of 8 in 3q1e

Go back to Iodine Binding Sites List in 3q1e
Iodine binding site 6 out of 8 in the Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I328

b:43.7
occ:0.36
 I3' D:T44328 0.0 43.7 0.4
O4' D:T44328 3.2 22.8 0.4
O D:SER114 3.4 33.8 1.0
CA D:THR115 3.8 34.3 1.0
C D:SER114 3.8 35.0 1.0
CB D:LEU107 3.9 37.6 1.0
OG D:SER114 3.9 43.7 1.0
N D:THR115 4.0 34.5 1.0
C D:THR115 4.0 34.8 1.0
N D:THR116 4.1 35.9 1.0
N D:LEU107 4.3 34.8 1.0
CG2 D:THR116 4.3 36.6 1.0
CG D:PRO105 4.5 39.1 1.0
CB D:THR116 4.6 39.2 1.0
O D:PRO105 4.6 36.7 1.0
O D:THR115 4.6 34.3 1.0
CB D:SER114 4.7 36.2 1.0
C D:LEU106 4.7 35.1 1.0
C D:PRO105 4.8 37.8 1.0
CA D:LEU107 4.8 36.5 1.0
CA D:SER114 4.8 34.6 1.0
CA D:LEU106 4.8 35.6 1.0
N D:LEU106 4.8 36.7 1.0
CD2 D:LEU107 4.9 44.1 1.0
CA D:THR116 5.0 36.5 1.0

Iodine binding site 7 out of 8 in 3q1e

Go back to Iodine Binding Sites List in 3q1e
Iodine binding site 7 out of 8 in the Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I328

b:58.3
occ:0.36
 CE1 B:HIS12 3.7 53.4 1.0
ND1 D:HIS103 3.8 42.9 1.0
ND1 B:HIS12 3.9 49.8 1.0
CD2 B:LEU14 3.9 48.4 1.0
CE1 D:HIS103 4.1 38.7 1.0
CG D:PRO105 4.6 39.1 1.0
CA D:GLY118 4.7 53.7 1.0
CD1 B:LEU14 4.7 46.7 1.0
CG B:LEU14 4.8 45.6 1.0
NE2 B:HIS12 5.0 51.0 1.0

Iodine binding site 8 out of 8 in 3q1e

Go back to Iodine Binding Sites List in 3q1e
Iodine binding site 8 out of 8 in the Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of Y116T/I16A Double Mutant of 5-Hydroxyisourate Hydrolase in Complex with T4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I328

b:44.0
occ:0.36
 I5' D:T44328 0.0 44.0 0.4
O4' D:T44328 3.3 22.8 0.4
CG B:PRO105 3.5 40.6 1.0
O B:SER114 3.7 35.4 1.0
N B:LEU107 3.8 36.6 1.0
CB B:LEU107 3.9 39.1 1.0
CA B:THR115 3.9 35.5 1.0
CB B:PRO105 3.9 41.9 1.0
C B:PRO105 4.2 39.0 1.0
N B:LEU106 4.2 38.3 1.0
C B:SER114 4.2 34.9 1.0
C B:LEU106 4.2 37.6 1.0
N B:THR115 4.3 35.9 1.0
CA B:LEU106 4.3 36.5 1.0
O B:PRO105 4.4 38.4 1.0
N B:THR116 4.4 39.1 1.0
C B:THR115 4.4 37.8 1.0
CA B:LEU107 4.4 37.8 1.0
CG2 B:THR116 4.5 43.7 1.0
OG B:SER114 4.5 42.6 1.0
CA B:PRO105 4.7 40.8 1.0
CD1 B:LEU107 4.8 48.2 1.0
CD B:PRO105 4.9 41.6 1.0
CG B:LEU107 4.9 45.3 1.0

Reference:

L.Cendron, I.Ramazzina, R.Percudani, C.Rasore, G.Zanotti, R.Berni. Probing the Evolution of Hydroxyisourate Hydrolase Into Transthyretin Through Active-Site Redesign. J.Mol.Biol. V. 409 504 2011.
ISSN: ESSN 1089-8638
PubMed: 21515285
DOI: 10.1016/J.JMB.2011.04.022
Page generated: Sun Aug 11 16:08:58 2024

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