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

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

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytosine:
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 Cytosine, PDB code: 3ike 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) 28.31 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.659, 68.064, 60.156, 90.00, 96.29, 90.00
R / Rfree (%) 18.5 / 23.4

Other elements in 3ike:

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

Zinc binding site 1 out of 3 in 3ike

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


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 Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:16.8
occ:1.00
 NE2 A:HIS12 2.0 19.3 1.0
ND1 A:HIS44 2.0 18.2 1.0
OD2 A:ASP10 2.1 18.5 1.0
O B:HOH212 2.2 19.1 1.0
CE1 A:HIS12 2.8 23.0 1.0
CG A:ASP10 2.9 17.1 1.0
CE1 A:HIS44 3.0 18.5 1.0
OD1 A:ASP10 3.0 13.3 1.0
CG A:HIS44 3.1 16.2 1.0
CD2 A:HIS12 3.1 20.6 1.0
CB A:HIS44 3.4 13.5 1.0
O B:HOH181 3.5 29.3 1.0
NZ B:LYS134 3.9 31.3 1.0
ND1 A:HIS12 4.0 19.6 1.0
NE2 A:HIS44 4.1 15.0 1.0
CG A:HIS12 4.2 20.1 1.0
CD2 A:HIS44 4.2 15.1 1.0
O A:HOH241 4.3 47.8 1.0
O A:HOH220 4.3 8.1 1.0
CB A:ASP10 4.4 15.9 1.0
CA A:VAL41 4.7 11.8 1.0
O A:ASP40 4.8 14.7 1.0
O A:VAL11 4.9 19.9 1.0
O A:HOH219 4.9 17.0 1.0
CA A:HIS44 4.9 13.4 1.0

Zinc binding site 2 out of 3 in 3ike

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


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 Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:34.9
occ:1.00
 NE2 B:HIS12 1.8 24.4 1.0
ND1 B:HIS44 2.0 28.1 1.0
OD2 B:ASP10 2.2 27.1 1.0
O C:HOH186 2.4 27.0 1.0
CE1 B:HIS12 2.8 27.1 1.0
CE1 B:HIS44 2.9 29.8 1.0
CD2 B:HIS12 2.9 29.7 1.0
CG B:ASP10 3.0 25.3 1.0
OD1 B:ASP10 3.0 24.0 1.0
CG B:HIS44 3.1 26.6 1.0
CB B:HIS44 3.6 24.0 1.0
ND1 B:HIS12 3.9 27.3 1.0
CG B:HIS12 4.0 28.7 1.0
NE2 B:HIS44 4.0 29.2 1.0
NZ C:LYS134 4.1 40.0 1.0
CD2 B:HIS44 4.2 27.6 1.0
CB B:ASP10 4.4 23.8 1.0
CA B:VAL41 4.6 27.5 1.0
O B:VAL11 4.8 28.0 1.0
O B:ASP40 4.8 28.9 1.0
N B:VAL41 4.8 28.8 1.0
C B:ASP40 4.9 29.9 1.0

Zinc binding site 3 out of 3 in 3ike

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


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 Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:23.2
occ:1.00
 NE2 C:HIS12 1.9 28.3 1.0
ND1 C:HIS44 2.0 16.1 1.0
OD2 C:ASP10 2.0 18.3 1.0
O C:HOH226 2.2 24.6 1.0
CG C:ASP10 2.8 17.1 1.0
CE1 C:HIS12 2.9 26.9 1.0
CD2 C:HIS12 2.9 25.9 1.0
CE1 C:HIS44 3.0 15.5 1.0
OD1 C:ASP10 3.0 17.1 1.0
CG C:HIS44 3.0 13.9 1.0
CB C:HIS44 3.3 13.9 1.0
O A:HOH227 3.7 43.9 1.0
ND1 C:HIS12 4.0 26.4 1.0
NE2 C:HIS44 4.1 16.9 1.0
CG C:HIS12 4.1 24.4 1.0
CD2 C:HIS44 4.1 15.5 1.0
CB C:ASP10 4.3 14.5 1.0
O C:HOH228 4.3 33.4 1.0
CA C:VAL41 4.7 18.6 1.0
O C:ASP40 4.8 20.2 1.0
CA C:HIS44 4.9 14.2 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.
PubMed: 21359640
DOI: 10.1007/S10969-011-9102-6
Page generated: Wed Dec 16 04:26:30 2020

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