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Zinc in PDB 3mbm: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytosine and 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 Cytosine and 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 Cytosine and 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 Cytosine and Fol Fragment 717, Imidazo[2,1-B][1,3]Thiazol-6-Ylmethanol, PDB code: 3mbm 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) 25.50 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.543, 67.569, 60.030, 90.00, 96.12, 90.00
R / Rfree (%) 18.8 / 21.7

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 Cytosine and Fol Fragment 717, Imidazo[2,1-B][1,3]Thiazol-6-Ylmethanol (pdb code 3mbm). 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 Cytosine and Fol Fragment 717, Imidazo[2,1-B][1,3]Thiazol-6-Ylmethanol, PDB code: 3mbm:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3mbm

Go back to Zinc Binding Sites List in 3mbm
Zinc binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytosine and 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 Cytosine and Fol Fragment 717, Imidazo[2,1-B][1,3]Thiazol-6-Ylmethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn163

b:21.9
occ:1.00
N2 A:717165 2.0 24.0 1.0
OD2 A:ASP10 2.0 3.2 1.0
NE2 A:HIS12 2.0 2.0 1.0
ND1 A:HIS44 2.0 2.0 1.0
CG A:ASP10 2.9 4.0 1.0
CE1 A:HIS12 3.0 2.0 1.0
C3 A:717165 3.0 26.5 1.0
CE1 A:HIS44 3.0 3.3 1.0
CD2 A:HIS12 3.0 3.5 1.0
C1 A:717165 3.0 29.1 1.0
CG A:HIS44 3.1 2.6 1.0
OD1 A:ASP10 3.1 2.0 1.0
CB A:HIS44 3.4 2.0 1.0
C9 A:717165 3.5 31.1 1.0
S8 A:717165 3.8 25.5 1.0
ND1 A:HIS12 4.1 2.0 1.0
NE2 A:HIS44 4.1 2.0 1.0
CG A:HIS12 4.1 2.0 1.0
N4 A:717165 4.2 28.0 1.0
CD2 A:HIS44 4.2 2.0 1.0
C5 A:717165 4.2 27.1 1.0
NZ B:LYS134 4.2 5.9 1.0
CB A:ASP10 4.3 2.0 1.0
O A:HOH168 4.5 2.0 1.0
O10 A:717165 4.5 32.2 1.0
CA A:VAL41 4.6 2.0 1.0
O A:ASP40 4.8 2.0 1.0
CA A:HIS44 5.0 2.0 1.0

Zinc binding site 2 out of 3 in 3mbm

Go back to Zinc Binding Sites List in 3mbm
Zinc binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytosine and 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 Cytosine and Fol Fragment 717, Imidazo[2,1-B][1,3]Thiazol-6-Ylmethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn163

b:30.0
occ:0.75
NE2 B:HIS12 1.8 2.0 1.0
N2 B:717165 2.0 45.4 0.8
OD2 B:ASP10 2.0 2.0 1.0
ND1 B:HIS44 2.0 2.0 1.0
CE1 B:HIS12 2.7 7.2 1.0
CG B:ASP10 2.7 5.1 1.0
OD1 B:ASP10 2.7 6.0 1.0
CD2 B:HIS12 2.9 6.9 1.0
CE1 B:HIS44 2.9 2.0 1.0
C1 B:717165 2.9 45.9 0.8
CG B:HIS44 3.1 2.0 1.0
C3 B:717165 3.1 47.4 0.8
C9 B:717165 3.3 46.8 0.8
CB B:HIS44 3.6 2.0 1.0
ND1 B:HIS12 3.9 5.8 1.0
CG B:HIS12 4.0 3.8 1.0
S8 B:717165 4.0 49.9 0.8
NE2 B:HIS44 4.1 2.0 1.0
C5 B:717165 4.2 47.3 0.8
CD2 B:HIS44 4.2 2.0 1.0
CB B:ASP10 4.2 3.3 1.0
N4 B:717165 4.2 47.4 0.8
NZ C:LYS134 4.4 11.9 1.0
O10 B:717165 4.5 46.5 0.8
CA B:VAL41 4.6 2.0 1.0
O B:ASP40 4.8 2.0 1.0
O B:VAL11 4.9 3.7 1.0
N B:VAL41 5.0 2.0 1.0

Zinc binding site 3 out of 3 in 3mbm

Go back to Zinc Binding Sites List in 3mbm
Zinc binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytosine and 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 Cytosine and Fol Fragment 717, Imidazo[2,1-B][1,3]Thiazol-6-Ylmethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn164

b:24.8
occ:1.00
OD2 C:ASP10 1.9 2.0 1.0
N2 C:717163 1.9 29.8 0.8
NE2 C:HIS12 2.0 2.0 1.0
ND1 C:HIS44 2.1 2.0 1.0
CG C:ASP10 2.8 3.4 1.0
CD2 C:HIS12 2.9 2.0 1.0
C1 C:717163 2.9 34.1 0.8
OD1 C:ASP10 3.0 2.5 1.0
CE1 C:HIS12 3.0 3.1 1.0
CE1 C:HIS44 3.0 3.0 1.0
C3 C:717163 3.1 35.5 0.8
CG C:HIS44 3.1 2.4 1.0
C9 C:717163 3.4 33.5 0.8
CB C:HIS44 3.4 2.0 1.0
S8 C:717163 4.0 35.6 0.8
CG C:HIS12 4.1 2.0 1.0
ND1 C:HIS12 4.1 2.0 1.0
C5 C:717163 4.1 35.2 0.8
NE2 C:HIS44 4.2 2.0 1.0
N4 C:717163 4.2 34.2 0.8
CB C:ASP10 4.2 2.3 1.0
CD2 C:HIS44 4.2 2.0 1.0
NZ A:LYS134 4.4 2.0 1.0
O10 C:717163 4.5 31.8 0.8
CA C:VAL41 4.7 2.0 1.0
O C:ASP40 4.9 2.0 1.0
CA C:HIS44 5.0 2.0 1.0
O C:VAL11 5.0 2.0 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: Wed Dec 16 04:34:46 2020

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