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Zinc in PDB 3p0z: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol

Enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol

All present enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol, PDB code: 3p0z 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) 19.83 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.550, 67.630, 59.770, 90.00, 95.99, 90.00
R / Rfree (%) 15.2 / 19.1

Other elements in 3p0z:

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol (pdb code 3p0z). 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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol, PDB code: 3p0z:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3p0z

Go back to Zinc Binding Sites List in 3p0z
Zinc binding site 1 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn164

b:18.7
occ:1.00
 NFE A:MSR170 1.9 29.8 1.0
OD2 A:ASP10 2.0 14.9 1.0
ND1 A:HIS44 2.0 15.2 1.0
NE2 A:HIS12 2.1 15.6 1.0
CG A:ASP10 2.8 16.5 1.0
C2 A:MSR170 2.9 32.1 1.0
C5 A:MSR170 2.9 33.0 1.0
CE1 A:HIS44 3.0 17.5 1.0
OD1 A:ASP10 3.0 16.4 1.0
CD2 A:HIS12 3.0 15.4 1.0
CG A:HIS44 3.0 15.8 1.0
CE1 A:HIS12 3.1 20.9 1.0
CB A:HIS44 3.4 13.3 1.0
N3 A:MSR170 3.9 36.4 1.0
C4 A:MSR170 4.0 32.9 1.0
NE2 A:HIS44 4.1 15.1 1.0
CD2 A:HIS44 4.2 16.2 1.0
CG A:HIS12 4.2 15.8 1.0
ND1 A:HIS12 4.2 19.9 1.0
CB A:ASP10 4.2 12.8 1.0
NZ B:LYS134 4.3 30.7 1.0
O A:HOH176 4.4 6.2 1.0
CA A:VAL41 4.5 12.3 1.0
O A:ASP40 4.7 12.4 1.0
CA A:HIS44 4.9 12.8 1.0
C A:ASP40 4.9 13.5 1.0
N A:VAL41 5.0 13.3 1.0
C A:ALA39 5.0 16.6 1.0

Zinc binding site 2 out of 3 in 3p0z

Go back to Zinc Binding Sites List in 3p0z
Zinc binding site 2 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn163

b:34.0
occ:1.00
 NE2 B:HIS12 1.9 24.8 1.0
ND1 B:HIS44 1.9 26.0 1.0
OD2 B:ASP10 2.1 23.7 1.0
O B:HOH176 2.5 20.3 1.0
CE1 B:HIS12 2.7 36.3 1.0
CG B:ASP10 2.8 23.8 1.0
CE1 B:HIS44 2.8 33.8 1.0
OD1 B:ASP10 2.9 20.8 1.0
CD2 B:HIS12 3.0 29.9 1.0
CG B:HIS44 3.0 26.5 1.0
CB B:HIS44 3.5 25.0 1.0
ND1 B:HIS12 3.9 32.9 1.0
NE2 B:HIS44 4.0 31.2 1.0
CG B:HIS12 4.0 29.2 1.0
CD2 B:HIS44 4.1 32.2 1.0
NZ C:LYS134 4.2 38.1 1.0
CB B:ASP10 4.2 20.7 1.0
CA B:VAL41 4.6 24.3 1.0
O B:ASP40 4.7 26.1 1.0
O B:HOH200 4.8 27.6 1.0
O B:VAL11 4.9 27.6 1.0
CA B:HIS44 5.0 25.0 1.0

Zinc binding site 3 out of 3 in 3p0z

Go back to Zinc Binding Sites List in 3p0z
Zinc binding site 3 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL955, 4- (1H-Imidazol)-1-Yl)Phenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn164

b:25.7
occ:1.00
 NE2 C:HIS12 1.9 29.5 1.0
OD2 C:ASP10 2.0 21.2 1.0
ND1 C:HIS44 2.1 16.9 1.0
O A:HOH177 2.1 14.9 1.0
CG C:ASP10 2.8 18.4 1.0
CD2 C:HIS12 2.9 25.9 1.0
CE1 C:HIS12 2.9 29.4 1.0
CE1 C:HIS44 3.0 20.9 1.0
OD1 C:ASP10 3.0 19.4 1.0
CG C:HIS44 3.1 18.4 1.0
CB C:HIS44 3.4 18.2 1.0
ND1 C:HIS12 4.0 30.8 1.0
CG C:HIS12 4.1 23.8 1.0
NE2 C:HIS44 4.1 23.5 1.0
CD2 C:HIS44 4.2 21.6 1.0
CB C:ASP10 4.2 16.9 1.0
NZ A:LYS134 4.3 35.7 1.0
CA C:VAL41 4.6 20.0 1.0
O C:ASP40 4.8 20.1 1.0
CA C:HIS44 4.9 17.6 1.0
N C:VAL41 5.0 21.2 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: Sat Oct 26 11:14:36 2024

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