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Zinc in PDB 3k2x: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- 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 in Complex with 5'-Iodo- Cytosine, PDB code: 3k2x 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) 27.18 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.475, 67.673, 60.025, 90.00, 96.13, 90.00
R / Rfree (%) 17 / 20.4

Other elements in 3k2x:

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- Cytosine also contains other interesting chemical elements:

Potassium (K) 1 atom
Iodine (I) 4 atoms
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 in Complex with 5'-Iodo- Cytosine (pdb code 3k2x). 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 in Complex with 5'-Iodo- Cytosine, PDB code: 3k2x:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3k2x

Go back to Zinc Binding Sites List in 3k2x
Zinc binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- 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 in Complex with 5'-Iodo- Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn163

b:16.5
occ:1.00
 OD2 A:ASP10 1.9 15.8 1.0
O A:HOH221 2.0 22.3 1.0
NE2 A:HIS12 2.0 17.8 1.0
ND1 A:HIS44 2.1 14.1 1.0
CG A:ASP10 2.9 15.6 1.0
CE1 A:HIS12 3.0 20.3 1.0
CE1 A:HIS44 3.0 16.8 1.0
CD2 A:HIS12 3.0 15.2 1.0
CG A:HIS44 3.1 15.9 1.0
OD1 A:ASP10 3.1 15.1 1.0
O B:HOH239 3.4 29.8 1.0
CB A:HIS44 3.4 12.7 1.0
O A:HOH222 3.8 44.4 1.0
ND1 A:HIS12 4.1 17.5 1.0
NE2 A:HIS44 4.1 16.2 1.0
CG A:HIS12 4.2 15.7 1.0
CD2 A:HIS44 4.2 14.5 1.0
CB A:ASP10 4.3 13.2 1.0
NZ B:LYS134 4.3 26.1 1.0
CA A:VAL41 4.6 12.8 1.0
O A:HOH215 4.6 28.7 1.0
O A:ASP40 4.7 12.9 1.0
CA A:HIS44 5.0 12.6 1.0
C A:ASP40 5.0 13.0 1.0

Zinc binding site 2 out of 3 in 3k2x

Go back to Zinc Binding Sites List in 3k2x
Zinc binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- 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 in Complex with 5'-Iodo- Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn163

b:22.2
occ:1.00
 OD2 B:ASP10 2.0 15.7 1.0
ND1 B:HIS44 2.0 15.0 1.0
NE2 B:HIS12 2.0 19.5 1.0
O C:HOH223 2.1 25.1 1.0
CG B:ASP10 2.8 15.0 1.0
CE1 B:HIS44 2.9 19.2 1.0
OD1 B:ASP10 3.0 13.9 1.0
CE1 B:HIS12 3.0 21.2 1.0
CD2 B:HIS12 3.0 19.2 1.0
CG B:HIS44 3.1 14.3 1.0
CB B:HIS44 3.5 13.8 1.0
O C:HOH224 3.9 38.8 1.0
NE2 B:HIS44 4.1 18.1 1.0
ND1 B:HIS12 4.1 19.8 1.0
CG B:HIS12 4.2 17.1 1.0
CD2 B:HIS44 4.2 16.8 1.0
CB B:ASP10 4.3 13.1 1.0
NZ C:LYS134 4.3 25.4 1.0
CA B:VAL41 4.6 14.0 1.0
O B:ASP40 4.7 13.3 1.0
N B:VAL41 4.9 13.9 1.0
C B:ASP40 5.0 14.5 1.0
O B:VAL11 5.0 14.4 1.0
CA B:HIS44 5.0 13.7 1.0

Zinc binding site 3 out of 3 in 3k2x

Go back to Zinc Binding Sites List in 3k2x
Zinc binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei in Complex with 5'-Iodo- 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 in Complex with 5'-Iodo- Cytosine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn163

b:21.8
occ:1.00
 NE2 C:HIS12 2.0 22.6 1.0
OD2 C:ASP10 2.0 15.9 1.0
ND1 C:HIS44 2.0 14.7 1.0
O A:HOH230 2.1 21.6 1.0
CG C:ASP10 2.8 15.9 1.0
CD2 C:HIS12 2.9 18.4 1.0
OD1 C:ASP10 3.0 15.0 1.0
CE1 C:HIS12 3.0 22.4 1.0
CE1 C:HIS44 3.0 17.7 1.0
CG C:HIS44 3.1 15.5 1.0
CB C:HIS44 3.4 12.7 1.0
CG C:HIS12 4.1 17.6 1.0
ND1 C:HIS12 4.1 21.2 1.0
NE2 C:HIS44 4.1 19.6 1.0
CD2 C:HIS44 4.2 16.2 1.0
CB C:ASP10 4.2 13.1 1.0
NZ A:LYS134 4.4 25.5 1.0
CA C:VAL41 4.7 13.9 1.0
O C:VAL11 4.8 14.0 1.0
O C:ASP40 4.9 12.4 1.0
CA C:HIS44 4.9 12.7 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 Aug 20 10:47:59 2025

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