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Copper in PDB 1w77: 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana

Enzymatic activity of 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana

All present enzymatic activity of 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana:
2.7.7.60;

Protein crystallography data

The structure of 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana, PDB code: 1w77 was solved by M.Gabrielsen, J.Kaiser, F.Rohdich, W.Eisenreich, A.Bacher, C.S.Bond, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.95 / 2.00
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 74.496, 74.496, 223.026, 90.00, 90.00, 120.00
R / Rfree (%) 23.2 / 34.9

Other elements in 1w77:

The structure of 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana also contains other interesting chemical elements:

Cadmium (Cd) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana (pdb code 1w77). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana, PDB code: 1w77:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 1w77

Go back to Copper Binding Sites List in 1w77
Copper binding site 1 out of 4 in the 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1001

b:22.4
occ:0.50
 OE2 A:GLU167 2.4 32.4 1.0
CD A:GLU167 3.3 75.0 1.0
OE1 A:GLU167 3.5 68.8 1.0
O A:GLN166 4.6 47.0 1.0
CG A:GLU167 4.7 45.3 1.0
NH2 A:ARG149 4.8 66.8 1.0

Copper binding site 2 out of 4 in 1w77

Go back to Copper Binding Sites List in 1w77
Copper binding site 2 out of 4 in the 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1002

b:41.3
occ:1.00
 OE1 A:GLU138 1.4 34.0 1.0
OE1 A:GLU141 1.9 38.0 1.0
CD A:GLU138 2.1 63.3 1.0
OE2 A:GLU138 2.2 60.5 1.0
CD A:GLU141 2.8 50.9 1.0
OE2 A:GLU141 2.9 48.2 1.0
CG A:GLU138 3.6 48.5 1.0
O A:HOH2037 4.0 55.0 1.0
CG A:GLU141 4.2 36.7 1.0
CB A:GLU138 4.4 54.9 1.0
CB A:GLU141 4.8 44.5 1.0

Copper binding site 3 out of 4 in 1w77

Go back to Copper Binding Sites List in 1w77
Copper binding site 3 out of 4 in the 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1003

b:59.7
occ:0.33
 O A:HOH2162 4.3 58.8 1.0
O A:HOH2090 4.3 68.5 1.0

Copper binding site 4 out of 4 in 1w77

Go back to Copper Binding Sites List in 1w77
Copper binding site 4 out of 4 in the 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of 2C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase (Ispd) From Arabidopsis Thaliana within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1004

b:98.4
occ:1.00
 OD2 A:ASP290 2.3 45.8 1.0
OD1 A:ASP290 2.7 64.3 1.0
CG A:ASP290 2.9 67.8 1.0
OG1 A:THR286 3.2 63.1 1.0
O A:HOH2161 4.2 60.0 1.0
O A:LYS284 4.2 65.4 1.0
OG1 A:THR287 4.3 55.4 1.0
CB A:ASP290 4.5 48.7 1.0
CB A:THR286 4.6 82.8 1.0
N A:THR287 4.8 74.3 1.0
CB A:THR287 4.9 74.0 1.0
N A:THR286 4.9 77.0 1.0

Reference:

M.Gabrielsen, J.Kaiser, F.Rohdich, W.Eisenreich, R.Laupitz, A.Bacher, C.S.Bond, W.N.Hunter. The Crystal Structure of A Plant 2C-Methyl-D- Erythritol 4-Phosphate Cytidylyltransferase Exhibits A Distinct Quaternary Structure Compared to Bacterial Homologues and A Possible Role in Feedback Regulation For Cytidine Monophosphate. Febs J. V. 273 1065 2006.
ISSN: ISSN 1742-464X
PubMed: 16478479
DOI: 10.1111/J.1742-4658.2006.05133.X
Page generated: Sun Dec 13 11:02:43 2020

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