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Zinc in PDB 1h47: Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product

Enzymatic activity of Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product

All present enzymatic activity of Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product:
4.6.1.12;

Protein crystallography data

The structure of Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product, PDB code: 1h47 was solved by L.E.Kemp, M.S.Alphey, 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) 87.71 / 2.0
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.082, 117.582, 54.215, 90.00, 90.21, 90.00
R / Rfree (%) 21.4 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product (pdb code 1h47). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product, PDB code: 1h47:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1h47

Go back to Zinc Binding Sites List in 1h47
Zinc binding site 1 out of 6 in the Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1158

b:63.1
occ:1.00
 ND1 A:HIS42 2.0 37.8 1.0
OD2 A:ASP8 2.1 27.5 1.0
NE2 A:HIS10 2.2 30.6 1.0
OD1 A:ASP8 2.8 25.1 1.0
CG A:ASP8 2.8 23.5 1.0
CE1 A:HIS42 2.9 35.6 1.0
CG A:HIS42 3.1 28.1 1.0
CD2 A:HIS10 3.1 32.0 1.0
CE1 A:HIS10 3.2 37.1 1.0
CB A:HIS42 3.5 23.2 1.0
NE2 A:HIS42 4.1 38.6 1.0
CD2 A:HIS42 4.2 34.0 1.0
ND1 A:HIS10 4.3 35.3 1.0
CB A:ASP8 4.3 22.0 1.0
CG A:HIS10 4.3 31.7 1.0
O1P B:C5P1157 4.5 42.3 1.0
CD1 A:ILE57 4.7 40.6 1.0
O A:VAL9 4.7 23.2 1.0
OG A:SER35 4.8 53.2 1.0
O A:ASP38 4.9 25.4 1.0
CA A:VAL39 5.0 24.1 1.0

Zinc binding site 2 out of 6 in 1h47

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Zinc binding site 2 out of 6 in the Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1158

b:69.3
occ:1.00
 OD2 B:ASP8 2.1 36.6 1.0
NE2 B:HIS10 2.3 29.5 1.0
CG B:HIS42 2.8 35.0 1.0
CG B:ASP8 2.9 31.3 1.0
ND1 B:HIS42 2.9 45.0 1.0
OD1 B:ASP8 2.9 31.7 1.0
CD2 B:HIS42 3.1 41.7 1.0
CE1 B:HIS42 3.1 45.8 1.0
NE2 B:HIS42 3.2 43.4 1.0
CD2 B:HIS10 3.2 30.8 1.0
CE1 B:HIS10 3.3 34.3 1.0
CB B:HIS42 3.5 29.7 1.0
CB B:ASP8 4.3 27.1 1.0
ND1 B:HIS10 4.3 32.5 1.0
CG B:HIS10 4.4 30.2 1.0
OG B:SER35 4.8 48.5 1.0
O B:VAL9 4.9 27.1 1.0
O1P C:C5P1157 4.9 46.1 1.0
CA B:HIS42 5.0 28.8 1.0

Zinc binding site 3 out of 6 in 1h47

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Zinc binding site 3 out of 6 in the Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1158

b:56.3
occ:1.00
 OD2 C:ASP8 1.9 24.7 1.0
ND1 C:HIS42 2.3 38.8 1.0
NE2 C:HIS10 2.4 29.8 1.0
CG C:ASP8 2.8 23.0 1.0
OD1 C:ASP8 3.0 23.8 1.0
CG C:HIS42 3.1 28.9 1.0
O C:HOH2031 3.2 48.5 1.0
CD2 C:HIS10 3.2 27.9 1.0
CE1 C:HIS42 3.3 37.8 1.0
CB C:HIS42 3.3 23.8 1.0
CE1 C:HIS10 3.4 31.2 1.0
CB C:ASP8 4.1 23.3 1.0
CD2 C:HIS42 4.3 34.4 1.0
CG C:HIS10 4.4 30.0 1.0
NE2 C:HIS42 4.4 35.3 1.0
ND1 C:HIS10 4.4 32.2 1.0
O C:HOH2007 4.5 45.7 1.0
CA C:VAL39 4.7 27.5 1.0
O C:ASP38 4.8 26.0 1.0
CG1 C:VAL39 4.9 30.7 1.0
O C:VAL9 4.9 24.6 1.0
CA C:HIS42 4.9 22.4 1.0
OG C:SER35 4.9 43.6 1.0
O1P A:C5P1159 5.0 48.4 1.0

Zinc binding site 4 out of 6 in 1h47

Go back to Zinc Binding Sites List in 1h47
Zinc binding site 4 out of 6 in the Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1158

b:58.0
occ:1.00
 OD2 D:ASP8 2.1 25.6 1.0
NE2 D:HIS10 2.1 35.6 1.0
ND1 D:HIS42 2.3 36.6 1.0
OD1 D:ASP8 2.6 27.8 1.0
CG D:ASP8 2.7 23.5 1.0
CD2 D:HIS10 3.1 35.0 1.0
CE1 D:HIS10 3.1 38.5 1.0
CE1 D:HIS42 3.2 38.0 1.0
CG D:HIS42 3.3 30.2 1.0
CB D:HIS42 3.6 24.4 1.0
CB D:ASP8 4.2 23.5 1.0
ND1 D:HIS10 4.2 37.7 1.0
CG D:HIS10 4.2 32.0 1.0
NE2 D:HIS42 4.3 39.0 1.0
CD2 D:HIS42 4.4 36.3 1.0
O1P E:C5P1157 4.5 48.9 1.0
CD1 D:ILE57 4.6 44.1 1.0
O D:VAL9 4.7 24.6 1.0

Zinc binding site 5 out of 6 in 1h47

Go back to Zinc Binding Sites List in 1h47
Zinc binding site 5 out of 6 in the Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1158

b:62.8
occ:1.00
 OD2 E:ASP8 2.0 34.7 1.0
NE2 E:HIS10 2.2 33.8 1.0
CD2 E:HIS42 2.7 30.8 0.4
CG E:HIS42 2.8 30.0 0.4
CG E:ASP8 2.8 31.1 1.0
OD1 E:ASP8 2.9 32.3 1.0
CE1 E:HIS10 3.0 36.3 1.0
NE2 E:HIS42 3.0 30.4 0.4
ND1 E:HIS42 3.1 31.9 0.4
CE1 E:HIS42 3.2 31.1 0.4
CD2 E:HIS10 3.2 34.7 1.0
CB E:HIS42 3.4 28.0 0.4
O E:HOH2003 3.8 48.9 1.0
ND1 E:HIS10 4.1 36.4 1.0
CB E:ASP8 4.3 26.7 1.0
CG E:HIS10 4.3 33.2 1.0
OG E:SER35 4.7 48.9 1.0
O E:VAL9 4.8 28.3 1.0
CA E:HIS42 4.9 28.3 1.0
O1P F:C5P1157 4.9 47.5 1.0
O E:ASP38 4.9 30.8 1.0
CA E:VAL39 5.0 31.7 1.0

Zinc binding site 6 out of 6 in 1h47

Go back to Zinc Binding Sites List in 1h47
Zinc binding site 6 out of 6 in the Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structures of Mecp Synthase in Complex with (I) Cmp and (II) Cmp and Product within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1158

b:69.1
occ:1.00
 OD2 F:ASP8 2.1 28.2 1.0
NE2 F:HIS10 2.2 37.9 1.0
ND1 F:HIS42 2.3 35.5 1.0
O F:HOH2037 2.7 55.6 1.0
CE1 F:HIS10 2.8 41.2 1.0
OD1 F:ASP8 2.8 27.8 1.0
CG F:ASP8 2.8 25.8 1.0
CD2 F:HIS10 3.2 36.7 1.0
CG F:HIS42 3.3 28.4 1.0
CE1 F:HIS42 3.3 32.4 1.0
CB F:HIS42 3.5 24.7 1.0
ND1 F:HIS10 3.9 40.6 1.0
CG F:HIS10 4.1 35.2 1.0
CB F:ASP8 4.2 22.5 1.0
NE2 F:HIS42 4.4 33.8 1.0
CD2 F:HIS42 4.4 30.9 1.0
OG F:SER35 4.6 47.7 1.0
O1P D:C5P1159 4.6 42.5 1.0
O F:VAL9 4.6 25.0 1.0

Reference:

L.E.Kemp, M.S.Alphey, C.S.Bond, M.Ferguson, S.Hecht, A.Bacher, W.Eisenreich, F.Rohdich, W.N.Hunter. The Identification of Isoprenoids That Bind in the Intersubunit Cavity of Escherichia Coli 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase By Complementary Biophysical Methods Acta Crystallogr.,Sect.D V. 61 45 2005.
ISSN: ISSN 0907-4449
PubMed: 15608374
DOI: 10.1107/S0907444904025971
Page generated: Sun Oct 13 01:56:56 2024

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