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Zinc in PDB 3f0e: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei

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

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei, PDB code: 3f0e 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) 50.00 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 116.765, 68.456, 60.882, 90.00, 96.71, 90.00
R / Rfree (%) 20.5 / 24.6

Other elements in 3f0e:

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

Magnesium (Mg) 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 (pdb code 3f0e). 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, PDB code: 3f0e:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3f0e

Go back to Zinc Binding Sites List in 3f0e
Zinc binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei


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

b:18.4
occ:1.00
 O A:HOH167 1.9 20.4 1.0
OD2 A:ASP10 1.9 16.1 1.0
NE2 A:HIS12 2.1 15.9 1.0
ND1 A:HIS44 2.1 13.1 1.0
CG A:ASP10 2.8 15.4 1.0
CD2 A:HIS12 3.0 16.0 1.0
OD1 A:ASP10 3.0 15.6 1.0
CG A:HIS44 3.1 11.3 1.0
CE1 A:HIS12 3.1 16.9 1.0
CE1 A:HIS44 3.1 13.0 1.0
CB A:HIS44 3.3 10.4 1.0
O A:HOH247 3.7 28.9 1.0
ND1 A:HIS12 4.1 16.8 1.0
CG A:HIS12 4.2 16.5 1.0
CB A:ASP10 4.2 14.8 1.0
CD2 A:HIS44 4.2 11.4 1.0
NE2 A:HIS44 4.2 12.3 1.0
CA A:VAL41 4.6 10.8 1.0
O A:HOH196 4.7 33.8 1.0
O A:ASP40 4.8 11.5 1.0
CA A:HIS44 4.9 10.2 1.0
O A:VAL11 5.0 16.4 1.0

Zinc binding site 2 out of 3 in 3f0e

Go back to Zinc Binding Sites List in 3f0e
Zinc binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei


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

b:61.5
occ:1.00
 NE2 B:HIS12 2.1 30.6 1.0
OD2 B:ASP10 2.2 26.2 1.0
ND1 B:HIS44 2.3 23.8 1.0
O B:HOH183 2.3 43.6 1.0
CG B:ASP10 2.9 24.8 1.0
CD2 B:HIS12 2.9 30.2 1.0
OD1 B:ASP10 2.9 23.3 1.0
CE1 B:HIS44 3.0 24.2 1.0
CE1 B:HIS12 3.2 31.3 1.0
CG B:HIS44 3.3 22.8 1.0
CB B:HIS44 3.7 21.9 1.0
NE2 B:HIS44 4.1 24.3 1.0
CG B:HIS12 4.1 29.2 1.0
CD2 B:HIS44 4.2 23.9 1.0
ND1 B:HIS12 4.2 30.2 1.0
CB B:ASP10 4.3 23.9 1.0
NZ C:LYS134 4.3 29.9 1.0
O B:VAL11 4.7 26.6 1.0
CA B:VAL41 4.8 25.6 1.0
O B:ASP40 4.8 26.7 1.0
CA B:ALA39 4.9 30.6 1.0
C B:ALA39 4.9 29.9 1.0
N B:VAL41 5.0 26.2 1.0
C B:ASP40 5.0 26.8 1.0

Zinc binding site 3 out of 3 in 3f0e

Go back to Zinc Binding Sites List in 3f0e
Zinc binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei


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

b:39.0
occ:1.00
 NE2 C:HIS12 2.0 23.7 1.0
OD2 C:ASP10 2.1 20.6 1.0
ND1 C:HIS44 2.1 17.4 1.0
O C:HOH216 2.4 34.4 1.0
CG C:ASP10 2.8 19.0 1.0
OD1 C:ASP10 2.9 19.8 1.0
CE1 C:HIS12 2.9 23.3 1.0
CD2 C:HIS12 3.0 23.0 1.0
CG C:HIS44 3.1 16.7 1.0
CE1 C:HIS44 3.1 17.9 1.0
CB C:HIS44 3.4 15.8 1.0
ND1 C:HIS12 4.1 23.7 1.0
CG C:HIS12 4.1 22.6 1.0
CB C:ASP10 4.2 18.3 1.0
NE2 C:HIS44 4.2 19.4 1.0
CD2 C:HIS44 4.2 17.1 1.0
NZ A:LYS134 4.6 24.9 1.0
CA C:VAL41 4.8 19.0 1.0
CA C:HIS44 4.9 15.8 1.0
O C:VAL11 5.0 20.2 1.0
O C:ASP40 5.0 19.8 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: Thu Oct 24 13:00:02 2024

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