Atomistry » Magnesium » PDB 3t2c-3taq » 3t80
Atomistry »
  Magnesium »
    PDB 3t2c-3taq »
      3t80 »

Magnesium 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:

Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 1 out of 8 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 Magnesium with other atoms in the Mg 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:Mg302

b:57.6
occ:1.00
OD1 A:ASP8 2.3 44.1 1.0
O A:HOH188 2.5 59.9 1.0
O C:HOH177 2.6 78.6 1.0
OG1 C:THR132 2.6 47.6 1.0
ZN A:ZN301 3.3 80.1 1.0
CG A:ASP8 3.3 41.1 1.0
OD2 A:ASP8 3.9 42.6 1.0
CB C:THR132 3.9 45.8 1.0
CB A:ASP8 4.3 39.3 1.0
O C:THR133 4.4 43.8 1.0
CD1 A:ILE57 4.4 60.1 1.0
O5' C:CTN401 4.4 60.4 1.0
CA A:ASP8 4.5 39.3 1.0
N C:THR133 4.7 46.1 1.0
CG2 C:THR133 4.7 48.3 1.0
N A:VAL9 4.7 41.0 1.0
O A:PHE7 4.7 41.9 1.0
CA C:THR132 4.8 44.8 1.0
CG2 C:THR132 4.8 44.4 1.0
O A:VAL9 4.9 45.5 1.0

Magnesium binding site 2 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 2 out of 8 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 Magnesium with other atoms in the Mg 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
A:Mg160

b:66.1
occ:1.00
OD1 B:ASP8 3.0 48.8 1.0
ZN B:ZN301 3.3 86.3 1.0
OE2 A:GLU135 3.3 66.7 1.0
OG1 A:THR132 3.9 45.4 1.0
O A:THR133 4.1 43.1 1.0
CD A:GLU135 4.1 62.4 1.0
O B:VAL9 4.2 47.9 1.0
CG B:ASP8 4.2 43.9 1.0
O5' A:CTN401 4.4 42.5 1.0
CE1 B:HIS10 4.4 55.2 1.0
OD2 B:ASP8 4.6 45.6 1.0
CG A:GLU135 4.7 57.4 1.0
OG1 A:THR133 4.8 43.2 1.0
NE2 B:HIS10 4.8 55.2 1.0
OE1 A:GLU135 4.9 71.0 1.0
O B:HOH175 5.0 65.7 1.0

Magnesium binding site 3 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 3 out of 8 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 Magnesium with other atoms in the Mg 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
B:Mg160

b:39.2
occ:1.00
OE2 B:GLU149 1.6 57.9 1.0
OE2 A:GLU149 2.0 55.0 1.0
OE1 C:GLU149 2.2 51.1 1.0
OE2 C:GLU149 2.2 59.6 1.0
CD C:GLU149 2.4 51.5 1.0
CD A:GLU149 2.5 47.2 1.0
OE1 A:GLU149 2.5 49.3 1.0
CD B:GLU149 2.5 52.2 1.0
OE1 B:GLU149 2.9 59.6 1.0
CG C:GLU149 3.8 50.4 1.0
CG A:GLU149 3.9 45.0 1.0
CG B:GLU149 3.9 51.5 1.0
NE2 A:HIS5 4.4 43.2 1.0
NE2 C:HIS5 4.5 44.1 1.0
NE2 B:HIS5 4.7 41.4 1.0
CE1 A:HIS5 4.7 44.9 1.0
CE1 B:HIS5 4.9 44.1 1.0
CB C:GLU149 4.9 46.1 1.0
CB A:GLU149 5.0 41.6 1.0

Magnesium binding site 4 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 4 out of 8 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 Magnesium with other atoms in the Mg 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
C:Mg302

b:58.4
occ:1.00
O B:HOH179 2.3 55.7 1.0
OD1 C:ASP8 2.3 46.9 1.0
O B:HOH183 2.4 69.2 1.0
OG1 B:THR132 2.7 48.0 1.0
CG C:ASP8 3.3 44.4 1.0
ZN C:ZN301 3.5 81.2 1.0
O5' B:CTN401 3.9 60.6 1.0
CB B:THR132 3.9 45.0 1.0
OD2 C:ASP8 4.0 46.0 1.0
CB C:ASP8 4.3 43.9 1.0
CD1 C:ILE57 4.4 65.3 1.0
O C:PHE7 4.6 50.0 1.0
O B:THR133 4.6 46.5 1.0
CA C:ASP8 4.6 44.0 1.0
CA B:THR132 4.7 43.6 1.0
N C:VAL9 4.9 44.5 1.0
N B:THR133 4.9 44.2 1.0
C5' B:CTN401 4.9 55.2 1.0
CG2 B:THR132 4.9 43.1 1.0

Magnesium binding site 5 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 5 out of 8 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 Magnesium with other atoms in the Mg 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
D:Mg302

b:50.2
occ:1.00
OD1 D:ASP8 2.4 46.5 1.0
O D:HOH173 2.4 67.2 1.0
O D:HOH180 2.6 56.7 1.0
OG1 F:THR132 2.7 51.0 1.0
O F:HOH179 3.3 52.7 1.0
CG D:ASP8 3.4 41.8 1.0
ZN D:ZN301 3.7 72.8 1.0
OD2 D:ASP8 4.0 43.0 1.0
CB F:THR132 4.0 47.8 1.0
O5' F:CTN401 4.1 49.9 1.0
O F:THR133 4.4 47.1 1.0
CB D:ASP8 4.5 40.8 1.0
O D:VAL9 4.7 42.9 1.0
OE2 F:GLU135 4.7 60.0 1.0
N F:THR133 4.7 45.4 1.0
CA D:ASP8 4.8 41.0 1.0
N D:VAL9 4.8 39.1 1.0
CA F:THR132 4.8 46.2 1.0
CG2 F:THR132 5.0 46.5 1.0
NE2 D:HIS10 5.0 51.2 1.0
O D:PHE7 5.0 41.9 1.0

Magnesium binding site 6 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 6 out of 8 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 Magnesium with other atoms in the Mg 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
D:Mg160

b:45.1
occ:1.00
OE2 F:GLU149 1.9 61.0 1.0
OE1 E:GLU149 2.2 56.1 1.0
OE1 D:GLU149 2.2 51.5 1.0
CD F:GLU149 2.4 56.0 1.0
OE1 F:GLU149 2.4 56.0 1.0
OE2 E:GLU149 2.6 57.7 1.0
CD E:GLU149 2.6 54.4 1.0
CD D:GLU149 2.7 52.4 1.0
OE2 D:GLU149 2.8 56.7 1.0
CG F:GLU149 3.8 54.0 1.0
CG E:GLU149 4.0 53.0 1.0
CG D:GLU149 4.0 49.1 1.0
NE2 F:HIS5 4.6 49.6 1.0
NE2 E:HIS5 4.7 49.6 1.0
NE2 D:HIS5 4.7 49.9 1.0
CE1 F:HIS5 4.8 51.9 1.0
CB F:GLU149 5.0 49.3 1.0

Magnesium binding site 7 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 7 out of 8 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 Magnesium with other atoms in the Mg binding site number 7 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:Mg302

b:50.9
occ:1.00
OD1 E:ASP8 2.4 58.6 1.0
O E:HOH163 2.7 59.3 1.0
OG1 D:THR132 2.9 51.4 1.0
ZN E:ZN301 3.2 71.0 1.0
CG E:ASP8 3.5 56.7 1.0
OD2 E:ASP8 4.0 58.4 1.0
O5' D:CTN401 4.1 44.1 1.0
CB D:THR132 4.2 50.0 1.0
OE2 D:GLU135 4.2 71.8 1.0
O D:THR133 4.3 54.5 1.0
CB E:ASP8 4.6 54.5 1.0
CD1 E:ILE57 4.7 76.4 1.0
O E:VAL9 4.7 56.1 1.0
N E:VAL9 4.8 52.4 1.0
CA E:ASP8 4.9 52.5 1.0
N D:THR133 4.9 50.1 1.0
CE1 E:HIS10 5.0 66.2 1.0
CA D:THR132 5.0 48.9 1.0

Magnesium binding site 8 out of 8 in 3t80

Go back to Magnesium Binding Sites List in 3t80
Magnesium binding site 8 out of 8 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 Magnesium with other atoms in the Mg binding site number 8 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:Mg302

b:63.0
occ:1.00
OD1 F:ASP8 1.9 59.2 1.0
OG1 E:THR132 2.9 55.1 1.0
CG F:ASP8 3.1 55.0 1.0
ZN F:ZN301 3.3 0.4 1.0
OD2 F:ASP8 3.9 56.6 1.0
CB E:THR132 4.0 55.1 1.0
CA F:ASP8 4.1 52.0 1.0
O E:THR133 4.1 51.6 1.0
CB F:ASP8 4.1 51.6 1.0
N F:VAL9 4.1 53.4 1.0
O F:HOH164 4.4 58.5 1.0
O F:PHE7 4.4 53.0 1.0
O F:VAL9 4.4 61.2 1.0
OE2 E:GLU135 4.5 61.9 1.0
C F:ASP8 4.7 52.1 1.0
CG2 E:THR132 4.8 54.5 1.0
N E:THR133 4.9 55.8 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: Mon Dec 14 08:53:44 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy