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Zinc in PDB 3ikf: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol, PDB code: 3ikf 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) 19.49 / 2.07
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.010, 67.650, 60.090, 90.00, 96.27, 90.00
R / Rfree (%) 17.5 / 22.1

Other elements in 3ikf:

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol (pdb code 3ikf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol, PDB code: 3ikf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3ikf

Go back to Zinc Binding Sites List in 3ikf
Zinc binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:18.7
occ:1.00
 N2 A:717202 1.9 24.8 1.0
OD2 A:ASP10 2.0 15.8 1.0
NE2 A:HIS12 2.0 12.9 1.0
ND1 A:HIS44 2.0 9.4 1.0
CG A:ASP10 2.8 14.4 1.0
C1 A:717202 2.9 25.7 1.0
C3 A:717202 3.0 26.2 1.0
CE1 A:HIS12 3.0 14.7 1.0
CE1 A:HIS44 3.0 11.0 1.0
OD1 A:ASP10 3.0 15.0 1.0
CD2 A:HIS12 3.0 11.6 1.0
CG A:HIS44 3.1 9.9 1.0
C9 A:717202 3.4 25.5 1.0
CB A:HIS44 3.4 7.6 1.0
S8 A:717202 3.8 24.9 1.0
N4 A:717202 4.1 25.2 1.0
ND1 A:HIS12 4.1 15.3 1.0
C5 A:717202 4.1 25.4 1.0
NE2 A:HIS44 4.1 10.7 1.0
CG A:HIS12 4.2 14.4 1.0
CD2 A:HIS44 4.2 9.1 1.0
CB A:ASP10 4.2 13.3 1.0
O10 A:717202 4.5 29.0 1.0
O A:HOH218 4.5 12.5 1.0
CA A:VAL41 4.6 9.7 1.0
O A:ASP40 4.8 9.9 1.0
CA A:HIS44 4.9 7.9 1.0

Zinc binding site 2 out of 3 in 3ikf

Go back to Zinc Binding Sites List in 3ikf
Zinc binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:28.4
occ:0.75
 NE2 B:HIS12 1.9 26.6 1.0
ND1 B:HIS44 2.0 22.3 1.0
N2 B:717202 2.1 34.4 0.5
OD2 B:ASP10 2.2 26.5 1.0
CE1 B:HIS44 2.7 27.3 1.0
CG B:ASP10 2.9 23.1 1.0
CE1 B:HIS12 2.9 27.7 1.0
OD1 B:ASP10 2.9 20.9 1.0
CD2 B:HIS12 2.9 28.5 1.0
C1 B:717202 3.0 34.4 0.5
CG B:HIS44 3.2 23.3 1.0
C3 B:717202 3.2 35.4 0.5
C9 B:717202 3.3 34.2 0.5
CB B:HIS44 3.7 20.9 1.0
NE2 B:HIS44 3.9 26.0 1.0
ND1 B:HIS12 4.0 26.2 1.0
CG B:HIS12 4.1 26.0 1.0
S8 B:717202 4.1 36.6 0.5
CD2 B:HIS44 4.2 24.6 1.0
C5 B:717202 4.3 35.0 0.5
N4 B:717202 4.3 35.9 0.5
CB B:ASP10 4.3 20.6 1.0
O10 B:717202 4.4 34.8 0.5
NZ C:LYS134 4.5 31.2 1.0
CA B:VAL41 4.7 23.3 1.0
O B:VAL11 4.8 24.0 1.0
O B:ASP40 4.9 22.0 1.0
N B:VAL41 4.9 23.5 1.0

Zinc binding site 3 out of 3 in 3ikf

Go back to Zinc Binding Sites List in 3ikf
Zinc binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 717, Imidazo[2,,1-B][1,3]Thiazol-6-Ylmethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:28.5
occ:1.00
 NE2 C:HIS12 2.0 21.6 1.0
OD2 C:ASP10 2.0 18.2 1.0
ND1 C:HIS44 2.1 16.4 1.0
N2 A:717163 2.2 37.4 0.8
CG C:ASP10 2.8 15.4 1.0
CE1 C:HIS12 3.0 22.5 1.0
CG C:HIS44 3.0 15.3 1.0
OD1 C:ASP10 3.0 14.3 1.0
CD2 C:HIS12 3.0 20.3 1.0
CE1 C:HIS44 3.1 16.1 1.0
C1 A:717163 3.2 38.7 0.8
CB C:HIS44 3.3 13.9 1.0
C3 A:717163 3.3 39.6 0.8
C9 A:717163 3.5 38.1 0.8
ND1 C:HIS12 4.1 23.1 1.0
S8 A:717163 4.1 41.2 0.8
CG C:HIS12 4.1 19.8 1.0
CD2 C:HIS44 4.1 16.0 1.0
NE2 C:HIS44 4.2 17.9 1.0
CB C:ASP10 4.3 14.1 1.0
N4 A:717163 4.4 40.0 0.8
C5 A:717163 4.4 39.0 0.8
CA C:VAL41 4.7 16.7 1.0
O10 A:717163 4.8 39.4 0.8
CA C:HIS44 4.8 13.7 1.0
O C:ASP40 4.9 17.9 1.0
O C:VAL11 5.0 16.9 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: Sat Oct 26 07:08:04 2024

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