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Cobalt in PDB 1t0a: Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis, PDB code: 1t0a was solved by S.Ni, H.Robinson, G.C.Marsing, D.E.Bussiere, M.A.Kennedy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.80 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 117.088, 117.088, 108.937, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.3

Other elements in 1t0a:

The structure of Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis (pdb code 1t0a). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis, PDB code: 1t0a:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in 1t0a

Go back to Cobalt Binding Sites List in 1t0a
Cobalt binding site 1 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co662

b:35.6
occ:1.00
 OD1 A:ASP10 2.3 12.6 1.0
OG1 B:THR134 2.4 14.9 1.0
O B:HOH803 2.4 17.2 1.0
O A:HOH1841 2.5 16.8 1.0
O A:HOH1842 2.6 16.0 1.0
O A:HOH2015 2.7 21.1 1.0
CG A:ASP10 3.3 13.3 1.0
CB B:THR134 3.6 13.0 1.0
O B:HOH782 3.7 20.0 1.0
ZN A:ZN661 3.9 14.8 1.0
OD2 A:ASP10 3.9 12.5 1.0
O B:HOH845 4.0 28.1 1.0
CB A:ASP10 4.2 10.9 1.0
O A:HOH1852 4.3 17.5 1.0
CA A:ASP10 4.4 10.2 1.0
O B:THR135 4.4 13.6 1.0
CA B:THR134 4.5 13.5 1.0
CG2 B:THR134 4.5 13.6 1.0
O A:PHE9 4.5 12.2 1.0
O A:HOH1861 4.6 23.1 1.0
CD1 A:ILE59 4.6 19.2 1.0
N A:VAL11 4.7 12.2 1.0
O A:HOH1986 4.8 22.8 1.0
O A:VAL11 4.9 12.3 1.0
N B:THR135 4.9 14.0 1.0
NE2 A:HIS12 5.0 11.6 1.0

Cobalt binding site 2 out of 3 in 1t0a

Go back to Cobalt Binding Sites List in 1t0a
Cobalt binding site 2 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co761

b:32.2
occ:1.00
 O C:HOH893 2.4 15.8 1.0
OD1 B:ASP10 2.4 11.5 1.0
OG1 C:THR134 2.4 13.4 1.0
O B:HOH771 2.4 13.7 1.0
O C:HOH916 2.7 19.1 1.0
CG B:ASP10 3.3 8.6 1.0
CB C:THR134 3.6 12.2 1.0
OD2 B:ASP10 3.9 2.1 1.0
ZN B:ZN760 3.9 13.2 1.0
O C:HOH879 3.9 17.2 1.0
O C:HOH949 4.1 30.3 1.0
O B:HOH764 4.2 14.6 1.0
CB B:ASP10 4.2 10.4 1.0
O C:THR135 4.4 14.0 1.0
CA B:ASP10 4.4 9.9 1.0
O B:PHE9 4.5 11.2 1.0
CA C:THR134 4.5 11.8 1.0
CD1 B:ILE59 4.5 17.8 1.0
CG2 C:THR134 4.6 14.9 1.0
O B:HOH857 4.6 23.0 1.0
O B:HOH932 4.6 21.2 1.0
OD2 B:ASP48 4.9 14.2 1.0
N B:VAL11 4.9 10.0 1.0
N C:THR135 5.0 13.0 1.0
CG1 B:ILE59 5.0 16.2 1.0
NE2 B:HIS12 5.0 13.4 1.0

Cobalt binding site 3 out of 3 in 1t0a

Go back to Cobalt Binding Sites List in 1t0a
Cobalt binding site 3 out of 3 in the Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co861

b:30.5
occ:1.00
 OD1 C:ASP10 2.2 10.6 1.0
OG1 A:THR134 2.4 13.0 1.0
O C:HOH862 2.5 12.4 1.0
O A:HOH1858 2.5 14.1 1.0
O A:HOH1856 2.6 16.7 1.0
CG C:ASP10 3.2 11.3 1.0
CB A:THR134 3.6 12.9 1.0
ZN C:ZN860 3.8 13.0 1.0
OD2 C:ASP10 3.9 11.4 1.0
O A:HOH1844 3.9 16.9 1.0
CB C:ASP10 4.1 10.6 1.0
O A:HOH1885 4.1 23.4 1.0
O C:HOH864 4.3 15.4 1.0
CA C:ASP10 4.4 8.9 1.0
O A:THR135 4.4 13.7 1.0
CD1 C:ILE59 4.5 16.5 1.0
O C:HOH868 4.5 16.3 1.0
O C:PHE9 4.5 11.1 1.0
CA A:THR134 4.5 12.9 1.0
CG2 A:THR134 4.6 13.7 1.0
O C:HOH970 4.7 18.3 1.0
N C:VAL11 4.8 10.4 1.0
NE2 C:HIS12 4.9 13.6 1.0
N A:THR135 4.9 13.5 1.0
O C:VAL11 5.0 11.7 1.0

Reference:

S.Ni, H.Robinson, G.C.Marsing, D.E.Bussiere, M.A.Kennedy. Structure of 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase From Shewanella Oneidensis at 1.6 A: Identification of Farnesyl Pyrophosphate Trapped in A Hydrophobic Cavity. Acta Crystallogr.,Sect.D V. 60 1949 2004.
ISSN: ISSN 0907-4449
PubMed: 15502301
DOI: 10.1107/S0907444904021791
Page generated: Tue Jul 30 14:38:06 2024

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