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Zinc in PDB 3k14: Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate

Enzymatic activity of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate

All present enzymatic activity of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate:
4.6.1.12;

Protein crystallography data

The structure of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate, PDB code: 3k14 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) 26.95 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.117, 67.914, 60.363, 90.00, 96.39, 90.00
R / Rfree (%) 17.7 / 19.8

Other elements in 3k14:

The structure of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate 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 Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate (pdb code 3k14). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate, PDB code: 3k14:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3k14

Go back to Zinc Binding Sites List in 3k14
Zinc binding site 1 out of 3 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn163

b:9.8
occ:0.75
 OD2 A:ASP10 1.9 13.6 1.0
N1 A:535164 1.9 18.7 0.5
ND1 A:HIS44 2.0 11.5 1.0
NE2 A:HIS12 2.1 15.6 1.0
CG A:ASP10 2.8 14.0 1.0
C2 A:535164 2.9 20.3 0.5
CE1 A:HIS44 3.0 13.6 1.0
C5 A:535164 3.0 20.1 0.5
CD2 A:HIS12 3.0 14.8 1.0
CG A:HIS44 3.0 11.8 1.0
CE1 A:HIS12 3.0 17.0 1.0
OD1 A:ASP10 3.1 15.8 1.0
CB A:HIS44 3.4 10.7 1.0
S8 A:535164 3.7 19.7 0.5
N3 A:535164 4.1 21.3 0.5
NE2 A:HIS44 4.1 12.6 1.0
ND1 A:HIS12 4.1 15.8 1.0
CD2 A:HIS44 4.2 12.5 1.0
CG A:HIS12 4.2 14.4 1.0
CB A:ASP10 4.2 12.5 1.0
C4 A:535164 4.3 20.4 0.5
O A:HOH208 4.5 10.8 1.0
CA A:VAL41 4.6 11.3 1.0
O A:ASP40 4.7 11.1 1.0
CA A:HIS44 4.9 11.0 1.0
N A:VAL41 5.0 10.5 1.0
O A:VAL11 5.0 13.4 1.0
C A:ASP40 5.0 10.2 1.0

Zinc binding site 2 out of 3 in 3k14

Go back to Zinc Binding Sites List in 3k14
Zinc binding site 2 out of 3 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn163

b:15.6
occ:0.75
 OD2 B:ASP10 2.0 17.1 1.0
ND1 B:HIS44 2.0 17.3 1.0
NE2 B:HIS12 2.0 18.1 1.0
N1 B:535164 2.1 31.3 0.8
CG B:ASP10 2.8 16.3 1.0
OD1 B:ASP10 2.9 17.3 1.0
CE1 B:HIS44 3.0 19.8 1.0
CD2 B:HIS12 3.0 18.0 1.0
CE1 B:HIS12 3.1 19.6 1.0
C2 B:535164 3.1 33.0 0.8
CG B:HIS44 3.1 16.0 1.0
C5 B:535164 3.2 32.2 0.8
CB B:HIS44 3.5 15.1 1.0
S8 B:535164 3.7 33.8 0.8
O C:HOH294 3.8 41.4 1.0
NE2 B:HIS44 4.1 19.4 1.0
ND1 B:HIS12 4.1 18.2 1.0
CG B:HIS12 4.1 16.9 1.0
CD2 B:HIS44 4.2 18.3 1.0
CB B:ASP10 4.2 14.7 1.0
N3 B:535164 4.2 33.2 0.8
O B:HOH295 4.3 25.1 1.0
C4 B:535164 4.4 32.9 0.8
CA B:VAL41 4.5 14.5 1.0
NZ C:LYS134 4.6 24.6 1.0
O B:ASP40 4.8 15.1 1.0
O B:VAL11 4.8 14.4 1.0
N B:VAL41 4.9 14.9 1.0
C B:ASP40 4.9 15.6 1.0
CA B:HIS44 5.0 14.6 1.0

Zinc binding site 3 out of 3 in 3k14

Go back to Zinc Binding Sites List in 3k14
Zinc binding site 3 out of 3 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 535, Ethyl 3-Methyl-5,6-Dihydroimidazo[2,1-B][1,3]Thiazole-2-Carboxylate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn163

b:13.5
occ:0.75
 OD2 C:ASP10 1.9 15.5 1.0
NE2 C:HIS12 2.0 18.1 1.0
ND1 C:HIS44 2.0 12.7 1.0
N1 C:535164 2.1 24.9 0.5
CG C:ASP10 2.8 14.7 1.0
CE1 C:HIS44 2.9 14.4 1.0
CE1 C:HIS12 3.0 21.5 1.0
CD2 C:HIS12 3.0 17.4 1.0
CG C:HIS44 3.0 13.8 1.0
OD1 C:ASP10 3.0 15.4 1.0
C2 C:535164 3.1 26.2 0.5
C5 C:535164 3.1 26.0 0.5
CB C:HIS44 3.4 12.3 1.0
S8 C:535164 3.8 25.9 0.5
NE2 C:HIS44 4.1 15.7 1.0
ND1 C:HIS12 4.1 20.1 1.0
CD2 C:HIS44 4.1 13.5 1.0
CG C:HIS12 4.1 15.6 1.0
CB C:ASP10 4.2 13.5 1.0
N3 C:535164 4.2 26.8 0.5
C4 C:535164 4.4 26.6 0.5
O C:HOH234 4.4 23.1 1.0
CA C:VAL41 4.6 13.4 1.0
O C:ASP40 4.8 13.2 1.0
CA C:HIS44 4.9 12.0 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: Sat Oct 26 07:37:07 2024

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