Atomistry » Cobalt » PDB 1rrk-1vlx » 1t0a
Atomistry »
  Cobalt »
    PDB 1rrk-1vlx »
      1t0a »

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: Sun Dec 13 10:36:10 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy