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

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

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine:
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 Cytidine, PDB code: 3ieq 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) 19.42 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.270, 67.700, 60.340, 90.00, 96.38, 90.00
R / Rfree (%) 17.2 / 22.5

Other elements in 3ieq:

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 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 with Cytidine (pdb code 3ieq). 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 Cytidine, PDB code: 3ieq:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3ieq

Go back to Zinc Binding Sites List in 3ieq
Zinc binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine


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

b:30.2
occ:1.00
 ND1 A:HIS44 2.1 15.1 1.0
OD2 A:ASP10 2.1 18.4 1.0
NE2 A:HIS12 2.1 20.0 1.0
O A:HOH223 2.5 30.6 1.0
CG A:ASP10 2.9 16.7 1.0
OD1 A:ASP10 2.9 17.5 1.0
CE1 A:HIS12 3.0 19.5 1.0
CG A:HIS44 3.1 13.7 1.0
CE1 A:HIS44 3.1 15.2 1.0
CD2 A:HIS12 3.2 18.5 1.0
CB A:HIS44 3.4 11.7 1.0
O A:HOH261 3.5 26.9 1.0
ND1 A:HIS12 4.2 20.1 1.0
NE2 A:HIS44 4.2 15.7 1.0
CD2 A:HIS44 4.2 13.8 1.0
CG A:HIS12 4.3 19.4 1.0
CB A:ASP10 4.3 15.8 1.0
O A:HOH201 4.5 10.8 1.0
CA A:VAL41 4.8 11.7 1.0
CA A:HIS44 4.9 11.9 1.0
O A:ASP40 4.9 11.9 1.0
O A:VAL11 4.9 16.4 1.0
O A:HOH200 5.0 18.8 1.0

Zinc binding site 2 out of 3 in 3ieq

Go back to Zinc Binding Sites List in 3ieq
Zinc binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine


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 Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn164

b:74.1
occ:1.00
 NE2 B:HIS12 1.9 30.8 1.0
OD2 B:ASP10 2.3 21.6 1.0
ND1 B:HIS44 2.4 24.7 1.0
CD2 B:HIS12 2.8 29.4 1.0
O C:HOH224 2.8 46.8 1.0
CE1 B:HIS12 3.0 29.3 1.0
OD1 B:ASP10 3.0 17.3 1.0
CG B:ASP10 3.0 20.1 1.0
CE1 B:HIS44 3.1 26.5 1.0
CG B:HIS44 3.6 22.8 1.0
CG B:HIS12 3.9 27.0 1.0
ND1 B:HIS12 4.0 28.2 1.0
CB B:HIS44 4.1 19.9 1.0
NZ C:LYS134 4.3 30.9 1.0
NE2 B:HIS44 4.3 26.2 1.0
CB B:ASP10 4.5 18.5 1.0
O B:VAL11 4.5 22.2 1.0
CD2 B:HIS44 4.6 25.3 1.0
CA B:VAL41 5.0 23.0 1.0
CA B:ALA39 5.0 30.2 1.0

Zinc binding site 3 out of 3 in 3ieq

Go back to Zinc Binding Sites List in 3ieq
Zinc binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine


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

b:53.9
occ:1.00
 NE2 C:HIS12 2.1 23.5 1.0
OD2 C:ASP10 2.1 20.2 1.0
ND1 C:HIS44 2.3 19.5 1.0
O C:HOH225 2.6 34.4 1.0
CG C:ASP10 2.8 16.6 1.0
CE1 C:HIS12 2.8 25.2 1.0
OD1 C:ASP10 2.9 14.5 1.0
CD2 C:HIS12 3.1 23.2 1.0
CE1 C:HIS44 3.2 20.7 1.0
CG C:HIS44 3.3 17.8 1.0
CB C:HIS44 3.6 15.0 1.0
ND1 C:HIS12 4.0 24.8 1.0
CG C:HIS12 4.2 22.4 1.0
CB C:ASP10 4.3 15.6 1.0
NE2 C:HIS44 4.3 21.6 1.0
CD2 C:HIS44 4.4 19.6 1.0
O C:VAL11 4.9 18.2 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.
ISSN: ISSN 1345-711X
PubMed: 21359640
DOI: 10.1007/S10969-011-9102-6
Page generated: Sat Oct 26 07:01:53 2024

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