Atomistry » Zinc » PDB 3t5w-3te7 » 3t80
Atomistry »
  Zinc »
    PDB 3t5w-3te7 »
      3t80 »

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: Wed Dec 16 04:51:39 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy