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Zinc in PDB 3jvh: Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 8395

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 8395

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 8395:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 8395, PDB code: 3jvh 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) 19.50 / 1.69
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.120, 67.650, 60.000, 90.00, 96.32, 90.00
R / Rfree (%) 16.7 / 19.5

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 with Fol Fragment 8395 (pdb code 3jvh). 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 with Fol Fragment 8395, PDB code: 3jvh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3jvh

Go back to Zinc Binding Sites List in 3jvh
Zinc binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 8395


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 with Fol Fragment 8395 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn163

b:15.0
occ:1.00
 OD2 A:ASP10 2.0 7.8 1.0
N10 A:HHV164 2.0 18.4 0.8
NE2 A:HIS12 2.0 10.3 1.0
ND1 A:HIS44 2.1 6.0 1.0
C11 A:HHV164 2.8 22.0 0.8
CG A:ASP10 2.8 9.3 1.0
CD2 A:HIS12 3.0 10.2 1.0
OD1 A:ASP10 3.0 10.9 1.0
CE1 A:HIS44 3.0 8.8 1.0
C09 A:HHV164 3.0 22.1 0.8
CE1 A:HIS12 3.0 12.1 1.0
CG A:HIS44 3.1 8.0 1.0
CB A:HIS44 3.4 6.8 1.0
C12 A:HHV164 4.1 22.5 0.8
ND1 A:HIS12 4.1 9.5 1.0
NE2 A:HIS44 4.1 7.3 1.0
CG A:HIS12 4.1 9.7 1.0
CD2 A:HIS44 4.2 8.0 1.0
CB A:ASP10 4.2 7.2 1.0
C08 A:HHV164 4.3 23.8 0.8
O A:HOH229 4.4 7.3 1.0
NZ B:LYS134 4.5 21.8 1.0
CA A:VAL41 4.5 6.9 1.0
O A:ASP40 4.7 7.3 1.0
C13 A:HHV164 4.7 23.7 0.8
CA A:HIS44 4.9 6.8 1.0
C A:ASP40 4.9 6.6 1.0
N A:VAL41 5.0 6.7 1.0
C A:ALA39 5.0 8.2 1.0

Zinc binding site 2 out of 3 in 3jvh

Go back to Zinc Binding Sites List in 3jvh
Zinc binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 8395


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 with Fol Fragment 8395 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn163

b:25.7
occ:1.00
 ND1 B:HIS44 2.0 7.4 1.0
NE2 B:HIS12 2.0 11.3 1.0
OD2 B:ASP10 2.0 7.0 1.0
N10 B:HHV164 2.1 23.1 0.5
CG B:ASP10 2.8 8.8 1.0
OD1 B:ASP10 2.9 9.4 1.0
CE1 B:HIS44 2.9 8.8 1.0
C09 B:HHV164 2.9 24.0 0.5
CE1 B:HIS12 2.9 13.9 1.0
CD2 B:HIS12 3.0 13.4 1.0
C11 B:HHV164 3.0 23.4 0.5
CG B:HIS44 3.1 7.1 1.0
CB B:HIS44 3.4 6.3 1.0
O B:HOH221 3.7 26.9 1.0
ND1 B:HIS12 4.1 12.7 1.0
NE2 B:HIS44 4.1 8.8 1.0
CG B:HIS12 4.1 12.1 1.0
CD2 B:HIS44 4.1 8.1 1.0
CB B:ASP10 4.2 7.9 1.0
O B:HOH320 4.2 15.2 1.0
C08 B:HHV164 4.3 24.2 0.5
C12 B:HHV164 4.3 23.8 0.5
CA B:VAL41 4.5 8.1 1.0
NZ C:LYS134 4.6 19.7 1.0
O B:ASP40 4.7 9.0 1.0
C13 B:HHV164 4.8 24.0 0.5
N B:VAL41 4.9 9.0 1.0
C B:ASP40 4.9 9.6 1.0
CA B:HIS44 5.0 6.5 1.0
O B:VAL11 5.0 10.0 1.0

Zinc binding site 3 out of 3 in 3jvh

Go back to Zinc Binding Sites List in 3jvh
Zinc binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Fol Fragment 8395


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 with Fol Fragment 8395 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn163

b:18.9
occ:1.00
 OD2 C:ASP10 1.9 10.4 1.0
NE2 C:HIS12 2.0 14.1 1.0
ND1 C:HIS44 2.0 7.4 1.0
N10 C:HHV164 2.0 29.1 1.0
CG C:ASP10 2.8 9.8 1.0
C11 C:HHV164 2.8 30.1 1.0
CD2 C:HIS12 2.9 12.7 1.0
CE1 C:HIS12 3.0 17.9 1.0
CE1 C:HIS44 3.0 11.0 1.0
OD1 C:ASP10 3.0 10.5 1.0
C09 C:HHV164 3.0 31.1 1.0
CG C:HIS44 3.0 9.0 1.0
CB C:HIS44 3.4 8.6 1.0
O A:HOH224 3.7 23.9 1.0
ND1 C:HIS12 4.1 16.5 1.0
CG C:HIS12 4.1 12.7 1.0
NE2 C:HIS44 4.1 10.4 1.0
CD2 C:HIS44 4.2 9.9 1.0
C12 C:HHV164 4.2 31.2 1.0
CB C:ASP10 4.2 8.4 1.0
C08 C:HHV164 4.3 31.9 1.0
O C:HOH226 4.4 21.4 1.0
CA C:VAL41 4.6 8.7 1.0
NZ A:LYS134 4.6 21.3 1.0
C13 C:HHV164 4.8 31.4 1.0
O C:ASP40 4.8 10.0 1.0
CA C:HIS44 4.9 7.8 1.0
N C:VAL41 5.0 9.4 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 07:32:20 2024

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