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Zinc in PDB 3p10: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol

Enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol

All present enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol:
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 FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol, PDB code: 3p10 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) 19.91 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.540, 67.550, 60.070, 90.00, 95.99, 90.00
R / Rfree (%) 15.9 / 19.2

Other elements in 3p10:

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Cytidine and FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol 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 FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol (pdb code 3p10). 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 FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol, PDB code: 3p10:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3p10

Go back to Zinc Binding Sites List in 3p10
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 FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol


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 FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn164

b:12.1
occ:0.75
 OD2 A:ASP10 1.9 10.1 1.0
O B:HOH173 2.0 16.3 1.0
ND1 A:HIS44 2.0 9.9 1.0
NE2 A:HIS12 2.1 12.4 1.0
CG A:ASP10 2.8 12.5 1.0
OD1 A:ASP10 2.9 13.0 1.0
CE1 A:HIS44 3.0 14.2 1.0
CD2 A:HIS12 3.0 14.5 1.0
CE1 A:HIS12 3.1 16.5 1.0
CG A:HIS44 3.1 9.7 1.0
CB A:HIS44 3.5 9.4 1.0
O B:HOH385 3.7 32.5 1.0
O B:HOH188 3.9 26.9 1.0
NE2 A:HIS44 4.1 10.0 1.0
ND1 A:HIS12 4.2 13.9 1.0
CG A:HIS12 4.2 13.6 1.0
CB A:ASP10 4.2 9.3 1.0
CD2 A:HIS44 4.2 10.1 1.0
NZ B:LYS134 4.2 21.2 1.0
O A:HOH168 4.5 8.8 1.0
CA A:VAL41 4.5 8.6 1.0
O A:ASP40 4.7 8.6 1.0
CA A:HIS44 5.0 7.7 1.0
C A:ASP40 5.0 8.3 1.0
N A:VAL41 5.0 8.7 1.0

Zinc binding site 2 out of 3 in 3p10

Go back to Zinc Binding Sites List in 3p10
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 FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol


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 FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn163

b:27.1
occ:0.75
 OD2 B:ASP10 2.0 22.1 1.0
ND1 B:HIS44 2.0 23.1 1.0
NE2 B:HIS12 2.0 27.3 1.0
O B:HOH228 2.1 31.3 1.0
CG B:ASP10 2.7 22.1 1.0
CE1 B:HIS44 2.9 27.6 1.0
OD1 B:ASP10 2.9 22.9 1.0
CE1 B:HIS12 2.9 31.4 1.0
CG B:HIS44 3.1 23.7 1.0
CD2 B:HIS12 3.1 28.6 1.0
CB B:HIS44 3.5 21.6 1.0
NE2 B:HIS44 4.0 26.3 1.0
ND1 B:HIS12 4.1 28.4 1.0
CB B:ASP10 4.1 17.8 1.0
CD2 B:HIS44 4.1 25.7 1.0
CG B:HIS12 4.2 28.2 1.0
NZ C:LYS134 4.3 33.2 1.0
O B:HOH239 4.4 42.7 1.0
CA B:VAL41 4.6 21.0 1.0
O B:ASP40 4.8 23.7 1.0
O B:VAL11 4.9 22.3 1.0
N B:VAL41 5.0 22.9 1.0
C B:ASP40 5.0 24.0 1.0

Zinc binding site 3 out of 3 in 3p10

Go back to Zinc Binding Sites List in 3p10
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 FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol


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 FOL694, 2- (Thiophen-2-Yl)Phenyl Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn164

b:18.4
occ:0.75
 ND1 C:HIS44 1.9 12.3 1.0
OD2 C:ASP10 1.9 15.4 1.0
NE2 C:HIS12 2.0 20.5 1.0
O C:HOH208 2.0 24.3 1.0
CG C:ASP10 2.8 14.4 1.0
CE1 C:HIS44 2.9 16.1 1.0
OD1 C:ASP10 2.9 16.4 1.0
CG C:HIS44 3.0 13.8 1.0
CD2 C:HIS12 3.0 19.9 1.0
CE1 C:HIS12 3.0 24.3 1.0
CB C:HIS44 3.4 12.4 1.0
NE2 C:HIS44 4.0 16.9 1.0
CD2 C:HIS44 4.1 14.2 1.0
O A:HOH304 4.1 38.2 1.0
ND1 C:HIS12 4.1 22.4 1.0
CG C:HIS12 4.1 17.8 1.0
CB C:ASP10 4.2 11.1 1.0
O C:HOH198 4.3 32.3 1.0
NZ A:LYS134 4.4 22.1 1.0
CA C:VAL41 4.7 12.7 1.0
CA C:HIS44 4.9 11.1 1.0
O C:ASP40 4.9 12.7 1.0
O C:VAL11 5.0 14.0 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 04:42:04 2020

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