Atomistry » Zinc » PDB 3k14-3kek » 3k2x
Atomistry »
  Zinc »
    PDB 3k14-3kek »
      3k2x »

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: Sat Oct 26 07:37:07 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy