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Zinc in PDB 3t80: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine

Enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine

All present enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine, PDB code: 3t80 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), B.L.Staker, T.E.Edwards, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 200.013, 147.657, 56.919, 90.00, 106.38, 90.00
R / Rfree (%) 21.1 / 24.5

Other elements in 3t80:

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine (pdb code 3t80). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine, PDB code: 3t80:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3t80

Go back to Zinc Binding Sites List in 3t80
Zinc binding site 1 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:80.1
occ:1.00
 OD2 A:ASP8 2.1 42.6 1.0
ND1 A:HIS42 2.7 51.0 1.0
NE2 A:HIS10 2.7 50.7 1.0
CG A:ASP8 2.8 41.1 1.0
OD1 A:ASP8 2.8 44.1 1.0
CE1 A:HIS10 2.9 52.0 1.0
MG A:MG302 3.3 57.6 1.0
CE1 A:HIS42 3.4 51.7 1.0
O A:HOH189 3.8 65.8 1.0
CG A:HIS42 3.8 47.2 1.0
CD2 A:HIS10 3.8 48.1 1.0
ND1 A:HIS10 4.1 52.3 1.0
CB A:HIS42 4.2 43.3 1.0
O A:HOH188 4.2 59.9 1.0
CB A:ASP8 4.2 39.3 1.0
O C:HOH177 4.3 78.6 1.0
CD1 A:ILE57 4.4 60.1 1.0
O A:VAL9 4.6 45.5 1.0
CG A:HIS10 4.6 47.4 1.0
NE2 A:HIS42 4.6 51.1 1.0
CD2 A:HIS42 4.8 49.7 1.0

Zinc binding site 2 out of 6 in 3t80

Go back to Zinc Binding Sites List in 3t80
Zinc binding site 2 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:86.3
occ:1.00
 OD2 B:ASP8 2.3 45.6 1.0
OD1 B:ASP8 2.6 48.8 1.0
ND1 B:HIS42 2.7 55.5 1.0
CG B:ASP8 2.8 43.9 1.0
NE2 B:HIS10 2.9 55.2 1.0
MG A:MG160 3.3 66.1 1.0
O B:HOH175 3.3 65.7 1.0
CE1 B:HIS42 3.4 56.8 1.0
CE1 B:HIS10 3.5 55.2 1.0
CG B:HIS42 3.6 52.2 1.0
CD2 B:HIS10 3.8 52.3 1.0
CB B:HIS42 4.0 47.7 1.0
CB B:ASP8 4.2 42.5 1.0
NE2 B:HIS42 4.5 56.0 1.0
ND1 B:HIS10 4.5 55.7 1.0
O B:VAL9 4.6 47.9 1.0
CD2 B:HIS42 4.6 53.0 1.0
CG B:HIS10 4.7 52.0 1.0
OE2 A:GLU135 4.8 66.7 1.0

Zinc binding site 3 out of 6 in 3t80

Go back to Zinc Binding Sites List in 3t80
Zinc binding site 3 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


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 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:81.2
occ:1.00
 OD2 C:ASP8 2.2 46.0 1.0
NE2 C:HIS10 2.4 55.4 1.0
ND1 C:HIS42 2.4 53.5 1.0
CG C:ASP8 2.9 44.4 1.0
OD1 C:ASP8 2.9 46.9 1.0
CE1 C:HIS10 3.1 57.2 1.0
CE1 C:HIS42 3.1 56.6 1.0
CG C:HIS42 3.4 47.7 1.0
CD2 C:HIS10 3.4 53.8 1.0
MG C:MG302 3.5 58.4 1.0
CB C:HIS42 3.8 43.3 1.0
O B:HOH183 4.1 69.2 1.0
ND1 C:HIS10 4.2 58.0 1.0
NE2 C:HIS42 4.2 56.1 1.0
CB C:ASP8 4.3 43.9 1.0
CD2 C:HIS42 4.4 51.8 1.0
CG C:HIS10 4.4 55.5 1.0
CD1 C:ILE57 4.6 65.3 1.0
O C:VAL9 4.7 48.2 1.0
OE1 B:GLU135 4.8 72.2 1.0
O B:HOH179 4.9 55.7 1.0

Zinc binding site 4 out of 6 in 3t80

Go back to Zinc Binding Sites List in 3t80
Zinc binding site 4 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:72.8
occ:1.00
 OD2 D:ASP8 1.9 43.0 1.0
NE2 D:HIS10 2.1 51.2 1.0
ND1 D:HIS42 2.3 48.0 1.0
O D:HOH173 2.3 67.2 1.0
CG D:ASP8 2.8 41.8 1.0
CD2 D:HIS10 2.9 49.3 1.0
OD1 D:ASP8 3.0 46.5 1.0
CE1 D:HIS10 3.1 51.1 1.0
CE1 D:HIS42 3.1 48.1 1.0
CG D:HIS42 3.4 45.7 1.0
MG D:MG302 3.7 50.2 1.0
CB D:HIS42 3.8 42.7 1.0
CG D:HIS10 4.1 47.7 1.0
ND1 D:HIS10 4.1 51.4 1.0
CB D:ASP8 4.1 40.8 1.0
NE2 D:HIS42 4.3 45.1 1.0
CD2 D:HIS42 4.4 45.7 1.0
O D:HOH180 4.6 56.7 1.0
O D:VAL9 4.6 42.9 1.0
CA D:VAL39 5.0 40.7 1.0
N D:VAL9 5.0 39.1 1.0

Zinc binding site 5 out of 6 in 3t80

Go back to Zinc Binding Sites List in 3t80
Zinc binding site 5 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:71.0
occ:1.00
 OD2 E:ASP8 2.2 58.4 1.0
ND1 E:HIS42 2.5 64.6 1.0
NE2 E:HIS10 2.7 65.2 1.0
CG E:ASP8 2.8 56.7 1.0
OD1 E:ASP8 2.8 58.6 1.0
CE1 E:HIS10 3.0 66.2 1.0
CE1 E:HIS42 3.1 67.2 1.0
MG E:MG302 3.2 50.9 1.0
CG E:HIS42 3.3 63.7 1.0
CD2 E:HIS10 3.8 63.8 1.0
CB E:HIS42 3.9 60.7 1.0
NE2 E:HIS42 4.1 66.5 1.0
ND1 E:HIS10 4.1 64.4 1.0
CB E:ASP8 4.2 54.5 1.0
CD2 E:HIS42 4.2 65.9 1.0
CD1 E:ILE57 4.3 76.4 1.0
O E:HOH163 4.4 59.3 1.0
CG E:HIS10 4.5 62.3 1.0
OE2 D:GLU135 4.6 71.8 1.0
O E:VAL9 4.7 56.1 1.0

Zinc binding site 6 out of 6 in 3t80

Go back to Zinc Binding Sites List in 3t80
Zinc binding site 6 out of 6 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:0.4
occ:1.00
 NE2 F:HIS10 2.2 62.2 1.0
OD2 F:ASP8 2.3 56.6 1.0
CE1 F:HIS10 2.4 62.6 1.0
OD1 F:ASP8 2.6 59.2 1.0
CG F:ASP8 2.8 55.0 1.0
ND1 F:HIS42 3.3 62.8 1.0
CD2 F:HIS10 3.3 59.9 1.0
MG F:MG302 3.3 63.0 1.0
ND1 F:HIS10 3.5 61.2 1.0
CE1 F:HIS42 3.7 64.0 1.0
O F:HOH164 3.7 58.5 1.0
O F:VAL9 3.8 61.2 1.0
OE2 E:GLU135 3.9 61.9 1.0
CG F:HIS10 4.0 59.0 1.0
CB F:ASP8 4.3 51.6 1.0
CG F:HIS42 4.3 59.2 1.0
N F:VAL9 4.7 53.4 1.0
C F:VAL9 4.7 56.1 1.0
NE2 F:HIS42 4.8 62.4 1.0
CB F:HIS42 4.8 53.6 1.0
CD E:GLU135 5.0 62.1 1.0

Reference:

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), B.L.Staker, T.E.Edwards. Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Salmonella Typhimurium Bound to Cytidine To Be Published.
Page generated: Sat Oct 26 16:21:56 2024

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