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Iodine in PDB 3k2x: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine, PDB code: 3k2x was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.18 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.475, 67.673, 60.025, 90.00, 96.13, 90.00
R / Rfree (%) 17 / 20.4

Other elements in 3k2x:

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine (pdb code 3k2x). 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 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine, PDB code: 3k2x:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 3k2x

Go back to Iodine Binding Sites List in 3k2x
Iodine binding site 1 out of 4 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine


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 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I164

b:74.8
occ:1.00
 I A:I5A164 0.0 74.8 1.0
C5' A:I5A164 2.1 58.1 1.0
C4' A:I5A164 3.2 50.4 1.0
C3' A:I5A164 3.4 46.9 1.0
O4' A:I5A164 3.9 45.3 1.0
C6 A:I5A164 4.0 28.4 1.0
N A:THR135 4.1 14.1 1.0
C2' A:I5A164 4.2 43.7 1.0
CA A:LYS134 4.3 15.9 1.0
O A:ALA133 4.3 17.1 1.0
C1' A:I5A164 4.5 39.5 1.0
O3' A:I5A164 4.6 47.4 1.0
NZ A:LYS134 4.6 25.5 1.0
CD A:LYS134 4.7 22.6 1.0
N1 A:I5A164 4.7 31.4 1.0
C A:LYS134 4.7 15.3 1.0
CG2 A:THR135 4.7 15.8 1.0
OG1 A:THR135 4.8 12.7 1.0
CE A:LYS134 4.8 23.3 1.0
C5 A:I5A164 5.0 25.1 1.0

Iodine binding site 2 out of 4 in 3k2x

Go back to Iodine Binding Sites List in 3k2x
Iodine binding site 2 out of 4 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine


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 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I164

b:46.4
occ:0.50
 I B:I5A164 0.0 46.4 0.5
C5' B:I5A164 2.1 33.2 0.5
C5' B:I5A164 2.9 76.8 0.5
C3' B:I5A164 2.9 75.9 0.5
C3' B:I5A164 3.0 24.3 0.5
C4' B:I5A164 3.0 27.0 0.5
C4' B:I5A164 3.4 76.1 0.5
O3' B:I5A164 3.5 23.9 0.5
O3' B:I5A164 3.5 76.2 0.5
N B:THR135 3.8 15.2 1.0
O4' B:I5A164 3.9 22.2 0.5
C6 B:I5A164 4.0 74.1 0.5
C6 B:I5A164 4.0 14.7 0.5
O4' B:I5A164 4.1 75.6 0.5
C2' B:I5A164 4.1 75.4 0.5
CA B:LYS134 4.2 15.6 1.0
CE B:LYS134 4.2 22.9 1.0
C2' B:I5A164 4.3 20.4 0.5
NZ B:LYS134 4.4 26.1 1.0
CG2 B:THR135 4.4 14.8 1.0
O B:ALA133 4.4 16.8 1.0
CD B:LYS134 4.5 20.4 1.0
OG1 B:THR135 4.5 13.4 1.0
C B:LYS134 4.5 15.3 1.0
O B:HOH239 4.6 29.8 1.0
C1' B:I5A164 4.6 19.2 0.5
C1' B:I5A164 4.6 75.1 0.5
O A:HOH222 4.6 44.4 1.0
N1 B:I5A164 4.8 74.3 0.5
I B:I5A164 4.8 78.5 0.5
C5 B:I5A164 4.8 73.6 0.5
N1 B:I5A164 4.8 14.3 0.5
CB B:THR135 4.8 14.7 1.0
C5 B:I5A164 4.8 11.5 0.5
CB B:LYS134 4.9 15.0 1.0
CA B:THR135 4.9 14.3 1.0

Iodine binding site 3 out of 4 in 3k2x

Go back to Iodine Binding Sites List in 3k2x
Iodine binding site 3 out of 4 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine


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 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I164

b:78.5
occ:0.50
 I B:I5A164 0.0 78.5 0.5
C5' B:I5A164 2.1 76.8 0.5
C5' B:I5A164 2.8 33.2 0.5
C4' B:I5A164 3.0 76.1 0.5
C4' B:I5A164 3.3 27.0 0.5
O4' B:I5A164 3.4 75.6 0.5
O4' B:I5A164 3.5 22.2 0.5
CB A:ASP65 3.6 40.1 1.0
C A:ASP65 4.2 40.2 1.0
CA A:ASP65 4.3 39.7 1.0
N A:ASP65 4.4 39.0 1.0
C3' B:I5A164 4.4 75.9 0.5
C1' B:I5A164 4.8 75.1 0.5
I B:I5A164 4.8 46.4 0.5
C3' B:I5A164 4.8 24.3 0.5
C1' B:I5A164 4.9 19.2 0.5
O A:ASP65 4.9 40.8 1.0

Iodine binding site 4 out of 4 in 3k2x

Go back to Iodine Binding Sites List in 3k2x
Iodine binding site 4 out of 4 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine


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 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I164

b:70.6
occ:1.00
 I C:I5A164 0.0 70.6 1.0
C5' C:I5A164 2.1 51.1 1.0
C4' C:I5A164 3.3 42.8 1.0
C3' C:I5A164 3.6 38.1 1.0
O4' C:I5A164 4.0 37.7 1.0
C6 C:I5A164 4.1 27.0 1.0
O C:ALA133 4.1 15.4 1.0
NZ C:LYS134 4.2 25.4 1.0
CA C:LYS134 4.3 15.8 1.0
C2' C:I5A164 4.3 35.8 1.0
CD C:LYS134 4.4 20.5 1.0
N C:THR135 4.4 15.7 1.0
CE C:LYS134 4.6 22.6 1.0
C1' C:I5A164 4.6 34.0 1.0
O C:HOH178 4.8 28.5 1.0
C C:LYS134 4.8 16.1 1.0
N1 C:I5A164 4.8 29.6 1.0
O3' C:I5A164 4.9 34.7 1.0
C C:ALA133 5.0 14.8 1.0
CG2 C:THR135 5.0 15.5 1.0
C5 C:I5A164 5.0 23.9 1.0

Reference:

D.W.Begley, R.C.Hartley, D.R.Davies, T.E.Edwards, J.T.Leonard, J.Abendroth, C.A.Burris, J.Bhandari, P.J.Myler, B.L.Staker, L.J.Stewart. Leveraging Structure Determination with Fragment Screening For Infectious Disease Drug Targets: Mecp Synthase From Burkholderia Pseudomallei. J Struct Funct Genomics V. 12 63 2011.
PubMed: 21359640
DOI: 10.1007/S10969-011-9102-6
Page generated: Fri Aug 8 14:28:31 2025

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