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Zinc in PDB 3q8h: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with Cytidine Derivative EBSI01028

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with Cytidine Derivative EBSI01028

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with Cytidine Derivative EBSI01028:
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 Cytidine Derivative EBSI01028, PDB code: 3q8h 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) 19.90 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.690, 67.760, 60.020, 90.00, 96.02, 90.00
R / Rfree (%) 15.5 / 18.4

Other elements in 3q8h:

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with Cytidine Derivative EBSI01028 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 Cytidine Derivative EBSI01028 (pdb code 3q8h). 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 Cytidine Derivative EBSI01028, PDB code: 3q8h:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3q8h

Go back to Zinc Binding Sites List in 3q8h
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 Cytidine Derivative EBSI01028


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 Cytidine Derivative EBSI01028 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn163

b:15.9
occ:1.00
 OD2 A:ASP10 2.0 11.9 1.0
ND1 A:HIS44 2.1 12.3 1.0
NE2 A:HIS12 2.1 13.9 1.0
O B:HOH166 2.4 5.0 1.0
CG A:ASP10 2.8 12.7 1.0
OD1 A:ASP10 3.0 14.2 1.0
CD2 A:HIS12 3.0 14.4 1.0
CE1 A:HIS44 3.0 14.6 1.0
CG A:HIS44 3.1 12.2 1.0
CE1 A:HIS12 3.1 20.0 1.0
O A:HOH288 3.2 20.1 1.0
CB A:HIS44 3.4 9.9 1.0
N35 A:AO9165 4.0 44.3 1.0
O B:HOH304 4.1 29.9 1.0
NE2 A:HIS44 4.1 13.2 1.0
CG A:HIS12 4.2 15.1 1.0
ND1 A:HIS12 4.2 18.4 1.0
CD2 A:HIS44 4.2 12.7 1.0
CB A:ASP10 4.2 10.4 1.0
NZ B:LYS134 4.4 20.5 1.0
C36 A:AO9165 4.6 43.8 1.0
CA A:VAL41 4.7 11.8 1.0
O A:ASP40 4.8 11.5 1.0
CA A:HIS44 4.9 9.4 1.0
C A:ALA39 5.0 15.3 1.0
CA A:ALA39 5.0 16.9 1.0

Zinc binding site 2 out of 3 in 3q8h

Go back to Zinc Binding Sites List in 3q8h
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 Cytidine Derivative EBSI01028


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 Cytidine Derivative EBSI01028 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn163

b:24.3
occ:1.00
 NE2 B:HIS12 1.9 20.7 1.0
ND1 B:HIS44 2.0 20.8 1.0
OD2 B:ASP10 2.0 15.0 1.0
O B:HOH291 2.2 5.9 1.0
CE1 B:HIS12 2.8 28.2 1.0
CG B:ASP10 2.8 16.7 1.0
CE1 B:HIS44 2.9 26.6 1.0
OD1 B:ASP10 2.9 17.3 1.0
CD2 B:HIS12 3.0 24.5 1.0
CG B:HIS44 3.0 20.6 1.0
CB B:HIS44 3.4 19.4 1.0
ND1 B:HIS12 3.9 28.1 1.0
NE2 B:HIS44 4.0 27.1 1.0
CG B:HIS12 4.1 25.1 1.0
N35 B:AO9165 4.1 41.1 0.5
CD2 B:HIS44 4.1 23.6 1.0
CB B:ASP10 4.2 14.5 1.0
NZ C:LYS134 4.4 27.5 1.0
CA B:VAL41 4.6 20.0 1.0
C36 B:AO9165 4.8 40.9 0.5
O B:ASP40 4.8 23.1 1.0
CB B:HIS36 4.8 42.6 1.0
O B:HIS36 4.9 41.5 0.5
CA B:ALA39 4.9 31.1 1.0
CA B:HIS44 5.0 19.4 1.0
C B:ALA39 5.0 28.5 1.0

Zinc binding site 3 out of 3 in 3q8h

Go back to Zinc Binding Sites List in 3q8h
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 Cytidine Derivative EBSI01028


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 Cytidine Derivative EBSI01028 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn163

b:19.4
occ:1.00
 NE2 C:HIS12 2.0 18.4 1.0
ND1 C:HIS44 2.0 13.6 1.0
OD2 C:ASP10 2.1 14.2 1.0
O A:HOH195 2.1 5.2 1.0
CG C:ASP10 2.8 15.7 1.0
OD1 C:ASP10 2.9 17.4 1.0
CE1 C:HIS12 3.0 23.4 1.0
CE1 C:HIS44 3.0 17.1 1.0
CD2 C:HIS12 3.0 17.7 1.0
CG C:HIS44 3.0 14.0 1.0
O C:HOH224 3.4 17.5 1.0
CB C:HIS44 3.4 13.5 1.0
N35 A:AO9164 4.0 57.7 1.0
ND1 C:HIS12 4.1 21.1 1.0
NE2 C:HIS44 4.1 17.2 1.0
CG C:HIS12 4.1 17.6 1.0
CD2 C:HIS44 4.2 15.3 1.0
CB C:ASP10 4.2 12.2 1.0
O A:HOH208 4.3 31.1 1.0
NZ A:LYS134 4.4 22.1 1.0
CA C:VAL41 4.6 14.3 1.0
C36 A:AO9164 4.8 57.5 1.0
O C:ASP40 4.9 13.8 1.0
CA C:HIS44 4.9 11.6 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. 23 6860 2013.
ISSN: ISSN 0960-894X
PubMed: 24157367
DOI: 10.1016/J.BMCL.2013.09.101
Page generated: Sat Oct 26 11:56:17 2024

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