Atomistry » Zinc » PDB 3q7f-3qln » 3q8h
Atomistry »
  Zinc »
    PDB 3q7f-3qln »
      3q8h »

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: Wed Dec 16 04:44:49 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy