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Zinc in PDB 3f0g: Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp

Enzymatic activity of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp

All present enzymatic activity of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp:
4.6.1.12;

Protein crystallography data

The structure of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp, PDB code: 3f0g 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 / 2.08
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.662, 69.760, 116.671, 90.00, 130.04, 90.00
R / Rfree (%) 21.3 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp (pdb code 3f0g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp, PDB code: 3f0g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3f0g

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Zinc binding site 1 out of 6 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp


Mono view


Stereo pair view

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

b:24.4
occ:1.00
 OD2 A:ASP10 2.0 14.5 1.0
O B:HOH197 2.0 17.8 1.0
NE2 A:HIS12 2.1 16.9 1.0
ND1 A:HIS44 2.1 13.1 1.0
CG A:ASP10 2.8 14.8 1.0
OD1 A:ASP10 3.0 16.3 1.0
CE1 A:HIS12 3.0 17.3 1.0
CE1 A:HIS44 3.1 13.5 1.0
CG A:HIS44 3.1 12.1 1.0
CD2 A:HIS12 3.1 16.9 1.0
CB A:HIS44 3.4 11.7 1.0
O A:HOH358 3.6 40.6 1.0
ND1 A:HIS12 4.1 17.9 1.0
NZ B:LYS134 4.2 21.1 1.0
NE2 A:HIS44 4.2 12.4 1.0
CG A:HIS12 4.2 17.5 1.0
CB A:ASP10 4.2 14.5 1.0
CD2 A:HIS44 4.2 12.1 1.0
O A:HOH505 4.5 36.9 1.0
O A:HOH425 4.5 22.5 1.0
CA A:VAL41 4.7 13.0 1.0
O A:ASP40 4.8 13.0 1.0
CA A:HIS44 4.9 11.6 1.0
C A:ALA39 5.0 13.9 1.0

Zinc binding site 2 out of 6 in 3f0g

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Zinc binding site 2 out of 6 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn164

b:39.5
occ:1.00
 OD2 B:ASP10 1.9 18.9 1.0
NE2 B:HIS12 2.1 22.4 1.0
ND1 B:HIS44 2.2 16.9 1.0
CG B:ASP10 2.7 18.4 1.0
OD1 B:ASP10 2.9 19.4 1.0
CD2 B:HIS12 3.0 22.1 1.0
CE1 B:HIS44 3.1 16.3 1.0
CE1 B:HIS12 3.1 23.0 1.0
CG B:HIS44 3.2 15.7 1.0
CB B:HIS44 3.5 14.3 1.0
CB B:ASP10 4.1 17.7 1.0
NZ C:LYS134 4.2 22.1 1.0
CG B:HIS12 4.2 22.4 1.0
ND1 B:HIS12 4.2 22.9 1.0
NE2 B:HIS44 4.2 17.0 1.0
CD2 B:HIS44 4.3 16.8 1.0
CA B:VAL41 4.8 16.3 1.0
O B:ASP40 4.9 17.2 1.0
CA B:HIS44 5.0 14.0 1.0
OG B:SER37 5.0 28.2 1.0

Zinc binding site 3 out of 6 in 3f0g

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Zinc binding site 3 out of 6 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn164

b:38.1
occ:1.00
 OD2 C:ASP10 2.0 18.9 1.0
ND1 C:HIS44 2.0 18.0 1.0
O C:HOH424 2.1 31.7 1.0
NE2 C:HIS12 2.1 23.3 1.0
CG C:ASP10 2.7 17.4 1.0
OD1 C:ASP10 2.9 17.5 1.0
CE1 C:HIS44 3.0 17.8 1.0
CD2 C:HIS12 3.0 22.4 1.0
CG C:HIS44 3.0 16.9 1.0
CE1 C:HIS12 3.1 23.0 1.0
CB C:HIS44 3.4 15.9 1.0
NE2 C:HIS44 4.1 18.5 1.0
CB C:ASP10 4.2 17.0 1.0
CD2 C:HIS44 4.2 17.8 1.0
CG C:HIS12 4.2 22.3 1.0
ND1 C:HIS12 4.2 22.9 1.0
NZ A:LYS134 4.6 23.0 1.0
CA C:VAL41 4.8 18.2 1.0
O C:ASP40 4.8 19.5 1.0
CA C:HIS44 4.9 15.6 1.0
O C:HOH476 5.0 24.1 1.0

Zinc binding site 4 out of 6 in 3f0g

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Zinc binding site 4 out of 6 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn164

b:26.2
occ:1.00
 OD2 D:ASP10 2.0 13.9 1.0
O E:HOH180 2.0 19.7 1.0
NE2 D:HIS12 2.0 16.8 1.0
ND1 D:HIS44 2.1 14.2 1.0
CG D:ASP10 2.8 14.8 1.0
CE1 D:HIS12 3.0 16.6 1.0
OD1 D:ASP10 3.0 15.0 1.0
CE1 D:HIS44 3.1 14.6 1.0
CD2 D:HIS12 3.1 16.7 1.0
CG D:HIS44 3.1 13.3 1.0
CB D:HIS44 3.4 12.5 1.0
O E:HOH196 3.9 41.9 1.0
ND1 D:HIS12 4.1 16.6 1.0
NE2 D:HIS44 4.2 15.4 1.0
CG D:HIS12 4.2 17.0 1.0
CB D:ASP10 4.2 14.9 1.0
CD2 D:HIS44 4.2 14.5 1.0
NZ E:LYS134 4.2 22.1 1.0
O D:HOH165 4.3 14.7 1.0
CA D:VAL41 4.6 12.7 1.0
O D:ASP40 4.8 13.7 1.0
CA D:HIS44 5.0 12.4 1.0

Zinc binding site 5 out of 6 in 3f0g

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Zinc binding site 5 out of 6 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn164

b:44.9
occ:1.00
 ND1 E:HIS44 2.0 17.6 1.0
OD2 E:ASP10 2.1 20.3 1.0
O F:HOH427 2.2 22.3 1.0
NE2 E:HIS12 2.2 18.6 1.0
CG E:ASP10 2.8 19.3 1.0
CE1 E:HIS44 2.9 17.3 1.0
OD1 E:ASP10 2.9 19.7 1.0
CD2 E:HIS12 3.0 19.2 1.0
CG E:HIS44 3.0 16.6 1.0
CE1 E:HIS12 3.3 18.9 1.0
CB E:HIS44 3.5 15.5 1.0
O F:HOH508 3.5 30.2 1.0
NE2 E:HIS44 4.0 17.8 1.0
CD2 E:HIS44 4.1 17.8 1.0
CB E:ASP10 4.2 18.6 1.0
NZ F:LYS134 4.2 25.2 1.0
CG E:HIS12 4.3 19.0 1.0
ND1 E:HIS12 4.4 19.0 1.0
CA E:ALA39 4.7 18.8 1.0
O E:ASP40 4.7 16.6 1.0
CA E:VAL41 4.7 16.9 1.0
O E:HOH167 4.7 9.8 1.0
C E:ALA39 4.8 18.3 1.0
C E:ASP40 4.9 17.0 1.0
N E:VAL41 5.0 16.9 1.0

Zinc binding site 6 out of 6 in 3f0g

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Zinc binding site 6 out of 6 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase with Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn164

b:39.4
occ:1.00
 O D:HOH170 2.1 39.9 1.0
ND1 F:HIS44 2.1 21.6 1.0
NE2 F:HIS12 2.1 25.1 1.0
OD2 F:ASP10 2.3 22.7 1.0
OD1 F:ASP10 2.8 20.7 1.0
CG F:ASP10 2.9 21.0 1.0
CG F:HIS44 3.0 20.8 1.0
CE1 F:HIS44 3.1 21.5 1.0
CD2 F:HIS12 3.1 24.8 1.0
CE1 F:HIS12 3.1 25.3 1.0
CB F:HIS44 3.3 20.2 1.0
NE2 F:HIS44 4.2 22.3 1.0
CD2 F:HIS44 4.2 21.2 1.0
ND1 F:HIS12 4.2 25.2 1.0
CG F:HIS12 4.2 25.1 1.0
NZ D:LYS134 4.3 24.6 1.0
CB F:ASP10 4.3 20.2 1.0
CA F:VAL41 4.8 23.5 1.0
CA F:HIS44 4.9 20.1 1.0
O F:ASP40 4.9 24.8 1.0
O F:HOH491 4.9 26.8 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 13:00:57 2024

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