Atomistry » Zinc » PDB 3q87-3qmb » 3qhd
Atomistry »
  Zinc »
    PDB 3q87-3qmb »
      3qhd »

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

Last articles

Mg in 1KK3
Mg in 1KK2
Mg in 1KJY
Mg in 1KK1
Mg in 1KJJ
Mg in 1KJQ
Mg in 1KJI
Mg in 1KJ9
Mg in 1KJ8
Mg in 1KIZ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy