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Zinc 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:

Cobalt (Co) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 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 Shewanella Oneidensis, PDB code: 1t0a:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 1t0a

Go back to Zinc Binding Sites List in 1t0a
Zinc 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 Zinc with other atoms in the Zn 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:Zn661

b:14.8
occ:1.00
 O A:HOH2015 1.9 21.1 1.0
OD2 A:ASP10 2.0 12.5 1.0
NE2 A:HIS12 2.0 11.6 1.0
ND1 A:HIS44 2.0 14.2 1.0
O A:HOH1861 2.6 23.1 1.0
CG A:ASP10 2.8 13.3 1.0
CD2 A:HIS12 3.0 15.2 1.0
CE1 A:HIS12 3.0 17.7 1.0
CE1 A:HIS44 3.0 14.7 1.0
OD1 A:ASP10 3.0 12.6 1.0
CG A:HIS44 3.1 11.8 1.0
CB A:HIS44 3.4 11.6 1.0
CO A:CO662 3.9 35.6 1.0
ND1 A:HIS12 4.1 15.9 1.0
CG A:HIS12 4.1 13.8 1.0
NE2 A:HIS44 4.1 13.9 1.0
CD2 A:HIS44 4.2 12.6 1.0
CB A:ASP10 4.2 10.9 1.0
CD1 A:ILE59 4.5 19.2 1.0
O A:HOH1841 4.5 16.8 1.0
CA A:VAL41 4.7 11.6 1.0
O A:VAL11 4.8 12.3 1.0
O B:HOH845 4.9 28.1 1.0
O A:HOH1842 4.9 16.0 1.0
CA A:HIS44 5.0 11.6 1.0
O A:HOH1899 5.0 29.9 1.0

Zinc binding site 2 out of 3 in 1t0a

Go back to Zinc Binding Sites List in 1t0a
Zinc 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 Zinc with other atoms in the Zn 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:Zn760

b:13.2
occ:1.00
 OD2 B:ASP10 1.7 2.1 1.0
NE2 B:HIS12 2.0 13.4 1.0
ND1 B:HIS44 2.1 12.9 1.0
O B:HOH932 2.6 21.2 1.0
CG B:ASP10 2.7 8.6 1.0
CD2 B:HIS12 3.0 14.5 1.0
CE1 B:HIS12 3.0 18.2 1.0
OD1 B:ASP10 3.0 11.5 1.0
CE1 B:HIS44 3.0 15.2 1.0
CG B:HIS44 3.1 10.3 1.0
CB B:HIS44 3.4 9.5 1.0
CO B:CO761 3.9 32.2 1.0
ND1 B:HIS12 4.1 16.9 1.0
CG B:HIS12 4.1 13.1 1.0
NE2 B:HIS44 4.2 13.5 1.0
CB B:ASP10 4.2 10.4 1.0
CD2 B:HIS44 4.2 10.2 1.0
O C:HOH916 4.5 19.1 1.0
CD1 B:ILE59 4.6 17.8 1.0
CA B:VAL41 4.7 11.3 1.0
O B:VAL11 4.8 11.7 1.0
O B:HOH771 4.9 13.7 1.0
O B:HOH812 4.9 26.1 1.0
O C:HOH949 4.9 30.3 1.0
CA B:HIS44 5.0 10.2 1.0

Zinc binding site 3 out of 3 in 1t0a

Go back to Zinc Binding Sites List in 1t0a
Zinc 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 Zinc with other atoms in the Zn 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:Zn860

b:13.0
occ:1.00
 OD2 C:ASP10 2.0 11.4 1.0
ND1 C:HIS44 2.0 11.9 1.0
NE2 C:HIS12 2.0 13.6 1.0
O C:HOH868 2.7 16.3 1.0
CG C:ASP10 2.8 11.3 1.0
CE1 C:HIS44 3.0 13.4 1.0
CD2 C:HIS12 3.0 14.9 1.0
OD1 C:ASP10 3.0 10.6 1.0
CE1 C:HIS12 3.0 15.7 1.0
CG C:HIS44 3.1 10.3 1.0
CB C:HIS44 3.4 9.7 1.0
CO C:CO861 3.8 30.5 1.0
NE2 C:HIS44 4.1 11.1 1.0
ND1 C:HIS12 4.1 14.6 1.0
CG C:HIS12 4.1 12.3 1.0
CD2 C:HIS44 4.2 12.1 1.0
CB C:ASP10 4.2 10.6 1.0
CD1 C:ILE59 4.4 16.5 1.0
O A:HOH1856 4.5 16.7 1.0
CA C:VAL41 4.7 10.3 1.0
O A:HOH1885 4.8 23.4 1.0
O C:VAL11 4.8 11.7 1.0
O C:HOH862 4.8 12.4 1.0
CA C:HIS44 4.9 10.2 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: Mon Jan 25 16:13:38 2021

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