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Zinc in PDB 3ke1: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with A Fragment- Nucleoside Fusion D000161829

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with A Fragment- Nucleoside Fusion D000161829

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with A Fragment- Nucleoside Fusion D000161829:
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 A Fragment- Nucleoside Fusion D000161829, PDB code: 3ke1 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) 28.22 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.083, 66.964, 59.166, 90.00, 95.42, 90.00
R / Rfree (%) 18.4 / 22.1

Other elements in 3ke1:

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with A Fragment- Nucleoside Fusion D000161829 also contains other interesting chemical elements:

Potassium (K) 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 in Complex with A Fragment- Nucleoside Fusion D000161829 (pdb code 3ke1). 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 in Complex with A Fragment- Nucleoside Fusion D000161829, PDB code: 3ke1:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3ke1

Go back to Zinc Binding Sites List in 3ke1
Zinc binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with A Fragment- Nucleoside Fusion D000161829


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 in Complex with A Fragment- Nucleoside Fusion D000161829 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn163

b:24.7
occ:1.00
 OD2 A:ASP10 1.9 24.3 1.0
ND1 A:HIS44 2.0 21.5 1.0
NE2 A:HIS12 2.0 25.5 1.0
N10 A:829164 2.1 37.8 1.0
CG A:ASP10 2.8 25.0 1.0
CD2 A:HIS12 2.9 23.8 1.0
C11 A:829164 2.9 39.7 1.0
CE1 A:HIS44 2.9 23.0 1.0
OD1 A:ASP10 3.0 31.5 1.0
CG A:HIS44 3.0 23.0 1.0
CE1 A:HIS12 3.1 25.7 1.0
C09 A:829164 3.1 39.6 1.0
CB A:HIS44 3.4 19.8 1.0
NE2 A:HIS44 4.1 23.7 1.0
CG A:HIS12 4.1 22.2 1.0
ND1 A:HIS12 4.1 25.1 1.0
CD2 A:HIS44 4.1 24.0 1.0
CB A:ASP10 4.2 22.0 1.0
C12 A:829164 4.3 41.1 1.0
C08 A:829164 4.4 40.3 1.0
O A:HOH182 4.5 34.8 1.0
CA A:VAL41 4.7 20.5 1.0
O A:ASP40 4.8 20.5 1.0
O A:VAL11 4.9 20.3 1.0
CA A:HIS44 4.9 20.2 1.0
C13 A:829164 4.9 40.7 1.0

Zinc binding site 2 out of 3 in 3ke1

Go back to Zinc Binding Sites List in 3ke1
Zinc binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with A Fragment- Nucleoside Fusion D000161829


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 in Complex with A Fragment- Nucleoside Fusion D000161829 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn163

b:32.4
occ:1.00
 ND1 B:HIS44 1.9 27.1 1.0
NE2 B:HIS12 2.1 31.5 1.0
OD2 B:ASP10 2.1 28.2 1.0
N10 B:829164 2.2 51.6 1.0
CG B:ASP10 2.8 23.5 1.0
OD1 B:ASP10 2.8 23.3 1.0
CE1 B:HIS44 2.8 28.3 1.0
CD2 B:HIS12 2.9 30.6 1.0
C09 B:829164 2.9 51.9 1.0
CG B:HIS44 3.0 23.6 1.0
CE1 B:HIS12 3.2 31.0 1.0
C11 B:829164 3.2 51.0 1.0
CB B:HIS44 3.4 20.6 1.0
NE2 B:HIS44 4.0 28.3 1.0
CD2 B:HIS44 4.1 25.9 1.0
CG B:HIS12 4.1 27.6 1.0
ND1 B:HIS12 4.2 31.0 1.0
CB B:ASP10 4.2 21.5 1.0
C08 B:829164 4.3 50.9 1.0
C12 B:829164 4.5 50.6 1.0
NZ C:LYS134 4.6 35.7 1.0
CA B:VAL41 4.6 21.1 1.0
O B:ASP40 4.7 21.5 1.0
O B:VAL11 4.8 23.3 1.0
C13 B:829164 4.9 49.7 1.0
C B:ASP40 4.9 22.5 1.0
CA B:HIS44 4.9 20.6 1.0
N B:VAL41 5.0 21.5 1.0

Zinc binding site 3 out of 3 in 3ke1

Go back to Zinc Binding Sites List in 3ke1
Zinc binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with A Fragment- Nucleoside Fusion D000161829


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 in Complex with A Fragment- Nucleoside Fusion D000161829 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn163

b:32.9
occ:1.00
 OD2 C:ASP10 1.9 24.4 1.0
NE2 C:HIS12 2.0 30.5 1.0
ND1 C:HIS44 2.1 25.1 1.0
N10 C:829164 2.3 48.7 1.0
CG C:ASP10 2.7 22.0 1.0
OD1 C:ASP10 2.9 28.8 1.0
C11 C:829164 3.0 48.8 1.0
CE1 C:HIS12 3.0 30.5 1.0
CD2 C:HIS12 3.0 27.8 1.0
CE1 C:HIS44 3.0 25.6 1.0
CG C:HIS44 3.1 23.2 1.0
C09 C:829164 3.4 49.9 1.0
CB C:HIS44 3.4 20.3 1.0
ND1 C:HIS12 4.1 28.4 1.0
CG C:HIS12 4.1 25.3 1.0
NE2 C:HIS44 4.1 28.0 1.0
CB C:ASP10 4.2 20.1 1.0
CD2 C:HIS44 4.2 24.2 1.0
C12 C:829164 4.3 49.5 1.0
C08 C:829164 4.6 50.3 1.0
CA C:VAL41 4.7 21.0 1.0
O C:VAL11 4.8 21.0 1.0
O C:ASP40 4.9 19.9 1.0
CA C:HIS44 4.9 20.2 1.0

Reference:

Z.Zhang, S.Jakkaraju, J.Blain, K.Gogol, L.Zhao, R.C.Hartley, C.A.Karlsson, B.L.Staker, T.E.Edwards, L.J.Stewart, P.J.Myler, M.Clare, D.W.Begley, J.R.Horn, T.J.Hagen. Cytidine Derivatives As Ispf Inhibitors of Burkolderia Pseudomallei. Bioorg.Med.Chem.Lett. V. 8 53851 2013.
ISSN: ISSN 0960-894X
PubMed: 24157367
DOI: 10.1016/J.BMCL.2013.09.101
Page generated: Wed Dec 16 04:29:53 2020

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