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Zinc in PDB 3f0d: High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei

Enzymatic activity of High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei

All present enzymatic activity of High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei:
4.6.1.12;

Protein crystallography data

The structure of High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei, PDB code: 3f0d 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) 50.00 / 1.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.887, 69.042, 116.581, 90.00, 130.15, 90.00
R / Rfree (%) 18.5 / 20.9

Zinc Binding Sites:

The binding sites of Zinc atom in the High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei (pdb code 3f0d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei, PDB code: 3f0d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3f0d

Go back to Zinc Binding Sites List in 3f0d
Zinc binding site 1 out of 6 in the High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn163

b:17.5
occ:1.00
 OD2 A:ASP10 1.9 15.7 1.0
NE2 A:HIS12 2.0 16.9 1.0
ND1 A:HIS44 2.0 15.2 1.0
O A:HOH216 2.0 19.7 1.0
CG A:ASP10 2.8 14.6 1.0
CE1 A:HIS12 2.9 17.6 1.0
OD1 A:ASP10 3.0 15.9 1.0
CE1 A:HIS44 3.0 14.7 1.0
CD2 A:HIS12 3.0 16.1 1.0
CG A:HIS44 3.0 13.3 1.0
CB A:HIS44 3.4 12.5 1.0
O A:HOH415 3.8 29.1 1.0
ND1 A:HIS12 4.1 17.7 1.0
CG A:HIS12 4.1 16.3 1.0
NE2 A:HIS44 4.1 14.5 1.0
CB A:ASP10 4.2 12.6 1.0
CD2 A:HIS44 4.2 14.2 1.0
O A:HOH503 4.4 14.4 1.0
NZ B:LYS134 4.5 21.8 1.0
CA A:VAL41 4.6 12.0 0.5
CA A:VAL41 4.7 11.9 0.5
CG1 A:VAL41 4.8 18.0 0.5
O A:ASP40 4.9 12.7 1.0
CA A:HIS44 4.9 12.1 1.0
O A:VAL11 5.0 14.8 1.0

Zinc binding site 2 out of 6 in 3f0d

Go back to Zinc Binding Sites List in 3f0d
Zinc binding site 2 out of 6 in the High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn163

b:28.2
occ:1.00
 OD2 B:ASP10 1.8 20.9 1.0
ND1 B:HIS44 1.9 20.4 1.0
O B:HOH169 2.0 30.4 1.0
NE2 B:HIS12 2.1 28.4 1.0
CG B:ASP10 2.7 19.2 1.0
CE1 B:HIS44 2.8 23.1 1.0
CG B:HIS44 2.9 17.7 1.0
OD1 B:ASP10 3.0 19.9 1.0
CE1 B:HIS12 3.1 29.5 1.0
CD2 B:HIS12 3.1 26.2 1.0
CB B:HIS44 3.4 16.9 1.0
NE2 B:HIS44 3.9 23.1 1.0
CD2 B:HIS44 4.0 19.7 1.0
CB B:ASP10 4.0 15.7 1.0
ND1 B:HIS12 4.2 28.4 1.0
CG B:HIS12 4.2 22.9 1.0
NZ C:LYS134 4.5 31.2 1.0
CA B:VAL41 4.7 16.9 1.0
O B:ASP40 4.7 17.8 1.0
CA B:HIS44 4.9 14.9 1.0
CG1 B:VAL41 4.9 22.3 1.0
CA B:ALA39 4.9 23.3 1.0
C B:ALA39 4.9 21.6 1.0
O B:VAL11 5.0 17.7 1.0
OG B:SER37 5.0 35.0 1.0
C B:ASP40 5.0 16.8 1.0

Zinc binding site 3 out of 6 in 3f0d

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Zinc binding site 3 out of 6 in the High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn163

b:27.4
occ:1.00
 OD2 C:ASP10 1.8 19.6 1.0
O C:HOH502 1.9 30.0 1.0
ND1 C:HIS44 2.0 21.2 1.0
NE2 C:HIS12 2.1 25.6 1.0
CG C:ASP10 2.7 17.8 1.0
OD1 C:ASP10 2.9 20.1 1.0
CE1 C:HIS44 2.9 23.5 1.0
CE1 C:HIS12 3.0 24.6 1.0
CG C:HIS44 3.1 17.7 1.0
CD2 C:HIS12 3.1 21.9 1.0
CB C:HIS44 3.5 16.4 1.0
CB C:ASP10 4.1 16.1 1.0
NE2 C:HIS44 4.1 23.1 1.0
ND1 C:HIS12 4.2 25.2 1.0
CD2 C:HIS44 4.2 21.0 1.0
CG C:HIS12 4.2 20.8 1.0
O C:HOH177 4.3 26.7 1.0
CA C:VAL41 4.7 16.1 0.5
CA C:VAL41 4.7 15.6 0.5
NZ A:LYS134 4.7 30.7 1.0
CG1 C:VAL41 4.9 18.3 0.5
O C:ASP40 4.9 17.3 1.0
CA C:HIS44 5.0 14.8 1.0

Zinc binding site 4 out of 6 in 3f0d

Go back to Zinc Binding Sites List in 3f0d
Zinc binding site 4 out of 6 in the High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn163

b:17.8
occ:1.00
 OD2 D:ASP10 1.9 15.2 1.0
O E:HOH182 2.0 20.1 1.0
NE2 D:HIS12 2.0 16.6 1.0
ND1 D:HIS44 2.0 16.2 1.0
CG D:ASP10 2.7 13.6 1.0
CE1 D:HIS12 2.9 17.3 1.0
OD1 D:ASP10 3.0 15.7 1.0
CE1 D:HIS44 3.0 15.1 1.0
CD2 D:HIS12 3.0 15.9 1.0
CG D:HIS44 3.1 12.7 1.0
CB D:HIS44 3.4 12.7 1.0
O D:HOH215 3.8 26.4 1.0
ND1 D:HIS12 4.1 17.6 1.0
NE2 D:HIS44 4.1 14.8 1.0
CB D:ASP10 4.1 13.6 1.0
CG D:HIS12 4.2 15.1 1.0
CD2 D:HIS44 4.2 13.9 1.0
NZ E:LYS134 4.3 22.9 1.0
O D:HOH164 4.4 13.9 1.0
CA D:VAL41 4.6 11.2 1.0
O D:ASP40 4.8 13.1 1.0
O D:VAL11 4.9 15.4 1.0
CA D:HIS44 5.0 12.0 1.0

Zinc binding site 5 out of 6 in 3f0d

Go back to Zinc Binding Sites List in 3f0d
Zinc binding site 5 out of 6 in the High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn163

b:26.9
occ:1.00
 OD2 E:ASP10 1.8 20.1 1.0
ND1 E:HIS44 1.9 19.3 1.0
O E:HOH505 2.0 28.7 1.0
NE2 E:HIS12 2.1 27.4 1.0
CG E:ASP10 2.7 17.7 1.0
CE1 E:HIS44 2.8 22.3 1.0
OD1 E:ASP10 2.9 22.3 1.0
CG E:HIS44 3.0 18.4 1.0
CD2 E:HIS12 3.0 22.0 1.0
CE1 E:HIS12 3.2 27.4 1.0
CB E:HIS44 3.5 16.6 1.0
NE2 E:HIS44 3.9 23.1 1.0
CD2 E:HIS44 4.1 21.8 1.0
CB E:ASP10 4.1 16.7 1.0
CG E:HIS12 4.2 20.1 1.0
ND1 E:HIS12 4.3 24.1 1.0
NZ F:LYS134 4.4 34.4 1.0
CA E:VAL41 4.7 17.3 0.5
CA E:VAL41 4.7 16.9 0.5
O E:ASP40 4.8 16.6 1.0
O E:HOH167 4.8 20.6 1.0
CG1 E:VAL41 4.9 17.2 0.5
CA E:ALA39 5.0 21.1 1.0
CA E:HIS44 5.0 16.6 1.0

Zinc binding site 6 out of 6 in 3f0d

Go back to Zinc Binding Sites List in 3f0d
Zinc binding site 6 out of 6 in the High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of High Resolution Crystal Structure of 2C-Methyl-D-Erythritol 2,4- Cyclodiphosphatase Synthase From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn163

b:23.5
occ:1.00
 OD2 F:ASP10 1.9 20.6 1.0
O F:HOH164 2.0 26.6 1.0
ND1 F:HIS44 2.0 19.9 1.0
NE2 F:HIS12 2.0 23.3 1.0
CG F:ASP10 2.8 19.2 1.0
CE1 F:HIS44 2.9 21.8 1.0
CE1 F:HIS12 2.9 22.8 1.0
OD1 F:ASP10 3.0 20.4 1.0
CG F:HIS44 3.0 17.1 1.0
CD2 F:HIS12 3.1 20.9 1.0
CB F:HIS44 3.4 16.6 1.0
NE2 F:HIS44 4.0 21.6 1.0
ND1 F:HIS12 4.1 24.5 1.0
CD2 F:HIS44 4.1 21.1 1.0
CB F:ASP10 4.2 17.7 1.0
CG F:HIS12 4.2 18.9 1.0
O F:HOH177 4.4 25.9 1.0
CA F:VAL41 4.7 17.4 1.0
CA F:HIS44 4.9 16.2 1.0
NZ D:LYS134 4.9 34.0 1.0
O F:ASP40 4.9 18.2 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.
ISSN: ISSN 1345-711X
PubMed: 21359640
DOI: 10.1007/S10969-011-9102-6
Page generated: Thu Oct 24 12:59:51 2024

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