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Zinc in PDB 3qhd: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to Cytidine, FOL795 and FOL955

Enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to Cytidine, FOL795 and FOL955

All present enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to Cytidine, FOL795 and FOL955:
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 Bound to Cytidine, FOL795 and FOL955, PDB code: 3qhd 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) 19.95 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.820, 67.950, 60.220, 90.00, 96.30, 90.00
R / Rfree (%) 15.7 / 18.6

Other elements in 3qhd:

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to Cytidine, FOL795 and FOL955 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 Bound to Cytidine, FOL795 and FOL955 (pdb code 3qhd). 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 Bound to Cytidine, FOL795 and FOL955, PDB code: 3qhd:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3qhd

Go back to Zinc Binding Sites List in 3qhd
Zinc binding site 1 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to Cytidine, FOL795 and FOL955


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 Bound to Cytidine, FOL795 and FOL955 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn163

b:13.4
occ:1.00
 OD2 A:ASP10 1.9 9.3 1.0
NFE A:MSR166 2.1 16.4 1.0
NE2 A:HIS12 2.1 11.5 1.0
ND1 A:HIS44 2.1 9.1 1.0
CG A:ASP10 2.8 12.0 1.0
OD1 A:ASP10 3.0 13.8 1.0
CE1 A:HIS44 3.0 12.0 1.0
C2 A:MSR166 3.0 18.1 1.0
CE1 A:HIS12 3.0 14.2 1.0
CD2 A:HIS12 3.0 13.4 1.0
C5 A:MSR166 3.0 19.4 1.0
CG A:HIS44 3.1 9.4 1.0
CB A:HIS44 3.4 10.1 1.0
O B:HOH169 3.6 21.4 1.0
N3 A:MSR166 4.1 19.1 1.0
ND1 A:HIS12 4.1 13.2 1.0
NE2 A:HIS44 4.2 9.7 1.0
CG A:HIS12 4.2 12.2 1.0
CB A:ASP10 4.2 10.0 1.0
C4 A:MSR166 4.2 18.1 1.0
CD2 A:HIS44 4.2 9.9 1.0
NZ B:LYS134 4.4 23.9 1.0
CL A:CL164 4.5 18.4 1.0
CA A:VAL41 4.5 8.4 1.0
O A:ASP40 4.7 7.7 1.0
C A:ASP40 4.9 8.1 1.0
N A:VAL41 4.9 8.7 1.0
CA A:HIS44 4.9 9.0 1.0
C A:ALA39 5.0 9.5 1.0

Zinc binding site 2 out of 3 in 3qhd

Go back to Zinc Binding Sites List in 3qhd
Zinc binding site 2 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to Cytidine, FOL795 and FOL955


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 Bound to Cytidine, FOL795 and FOL955 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn164

b:28.8
occ:1.00
 NE2 B:HIS12 1.9 22.6 1.0
OD2 B:ASP10 2.0 19.2 1.0
ND1 B:HIS44 2.0 27.9 1.0
O C:HOH168 2.3 16.9 1.0
CG B:ASP10 2.8 22.6 1.0
CE1 B:HIS12 2.8 29.6 1.0
OD1 B:ASP10 2.9 24.1 1.0
CE1 B:HIS44 2.9 33.0 1.0
CD2 B:HIS12 3.0 26.7 1.0
CG B:HIS44 3.1 27.4 1.0
CB B:HIS44 3.5 24.3 1.0
ND1 B:HIS12 3.9 29.0 1.0
NE2 B:HIS44 4.1 32.6 1.0
CG B:HIS12 4.1 25.4 1.0
CD2 B:HIS44 4.2 30.6 1.0
CB B:ASP10 4.2 18.3 1.0
NZ C:LYS134 4.4 33.0 1.0
O B:HOH166 4.4 16.7 1.0
CA B:VAL41 4.5 23.7 1.0
O B:ASP40 4.9 26.2 1.0
N B:VAL41 5.0 26.0 1.0
CA B:HIS44 5.0 24.0 1.0
O B:VAL11 5.0 21.6 1.0

Zinc binding site 3 out of 3 in 3qhd

Go back to Zinc Binding Sites List in 3qhd
Zinc binding site 3 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei Bound to Cytidine, FOL795 and FOL955


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 Bound to Cytidine, FOL795 and FOL955 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn163

b:16.6
occ:1.00
 OD2 C:ASP10 2.0 13.8 1.0
O A:HOH364 2.0 10.8 1.0
NE2 C:HIS12 2.0 14.7 1.0
ND1 C:HIS44 2.1 12.9 1.0
CG C:ASP10 2.8 14.6 1.0
CD2 C:HIS12 3.0 15.0 1.0
OD1 C:ASP10 3.0 14.6 1.0
CE1 C:HIS12 3.0 19.8 1.0
CE1 C:HIS44 3.0 15.1 1.0
CG C:HIS44 3.1 14.1 1.0
CB C:HIS44 3.4 12.6 1.0
O A:HOH177 4.1 22.8 1.0
ND1 C:HIS12 4.1 18.7 1.0
CG C:HIS12 4.1 14.4 1.0
NE2 C:HIS44 4.1 15.6 1.0
CD2 C:HIS44 4.2 13.6 1.0
CB C:ASP10 4.2 12.5 1.0
O A:HOH365 4.4 31.9 1.0
NZ A:LYS134 4.4 21.9 1.0
O C:HOH176 4.4 24.4 1.0
CA C:VAL41 4.7 12.9 1.0
CA C:HIS44 4.9 11.5 1.0
O C:ASP40 4.9 14.4 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 12:07:03 2024

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