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Magnesium in PDB 7uyz: Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg

Enzymatic activity of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg

All present enzymatic activity of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg:
2.7.7.86;

Protein crystallography data

The structure of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg, PDB code: 7uyz was solved by S.Wu, S.B.Gabelli, J.Sohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.85 / 2.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.341, 98.515, 142.695, 90, 90, 90
R / Rfree (%) 21.4 / 25.1

Other elements in 7uyz:

The structure of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg (pdb code 7uyz). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg, PDB code: 7uyz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7uyz

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Magnesium binding site 1 out of 4 in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:40.6
occ:1.00
 O A:HOH725 2.1 38.8 1.0
O2G A:GTP605 2.1 39.4 1.0
OE1 A:GLU211 2.2 47.6 1.0
OD2 A:ASP213 2.2 44.5 1.0
O1B A:GTP605 2.2 38.2 1.0
O1A A:GTP605 2.3 41.6 1.0
CG A:ASP213 3.1 41.8 1.0
CD A:GLU211 3.2 45.0 1.0
PB A:GTP605 3.2 41.1 1.0
O3A A:GTP605 3.3 43.9 1.0
PA A:GTP605 3.3 43.1 1.0
PG A:GTP605 3.3 39.7 1.0
OD1 A:ASP213 3.5 42.1 1.0
O3B A:GTP605 3.5 41.2 1.0
OE2 A:GLU211 3.6 47.6 1.0
MG A:MG602 3.8 43.0 1.0
OG A:SER199 4.0 44.6 1.0
O A:HOH721 4.1 30.7 1.0
O1G A:GTP605 4.2 38.7 1.0
N A:SER199 4.3 37.6 1.0
O2A A:GTP605 4.3 42.4 1.0
N2 A:G604 4.4 68.0 1.0
CG A:GLU211 4.4 44.4 1.0
O3G A:GTP605 4.4 39.7 1.0
CB A:SER199 4.5 40.8 1.0
O A:GLU211 4.5 38.5 1.0
O5' A:GTP605 4.5 48.8 1.0
CB A:ASP213 4.5 40.8 1.0
O2B A:GTP605 4.6 44.0 1.0
CB A:GLU211 4.6 42.3 1.0
C A:GLU211 4.7 39.8 1.0
CA A:GLY198 4.8 36.5 1.0
N A:ASP213 4.9 39.8 1.0

Magnesium binding site 2 out of 4 in 7uyz

Go back to Magnesium Binding Sites List in 7uyz
Magnesium binding site 2 out of 4 in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:43.0
occ:1.00
 OE2 A:GLU211 2.0 47.6 1.0
OD2 A:ASP307 2.0 46.8 1.0
O1A A:GTP605 2.0 41.6 1.0
OD1 A:ASP213 2.4 42.1 1.0
PA A:GTP605 3.1 43.1 1.0
CD A:GLU211 3.1 45.0 1.0
CG A:ASP307 3.3 43.1 1.0
O5' A:GTP605 3.4 48.8 1.0
CG A:ASP213 3.5 41.8 1.0
OE1 A:GLU211 3.5 47.6 1.0
O2A A:GTP605 3.7 42.4 1.0
MG A:MG601 3.8 40.6 1.0
N2 A:G604 3.8 68.0 1.0
OD2 A:ASP213 3.9 44.5 1.0
O3' A:GTP605 4.0 59.6 1.0
OD1 A:ASP307 4.1 44.9 1.0
CB A:ASP307 4.1 42.3 1.0
CG A:GLU211 4.4 44.4 1.0
O3A A:GTP605 4.5 43.9 1.0
C2 A:G604 4.5 72.1 1.0
O2G A:GTP605 4.7 39.4 1.0
N3 A:G604 4.7 73.0 1.0
CB A:ASP213 4.8 40.8 1.0
C5' A:GTP605 4.8 52.3 1.0
C3' A:GTP605 4.9 58.7 1.0

Magnesium binding site 3 out of 4 in 7uyz

Go back to Magnesium Binding Sites List in 7uyz
Magnesium binding site 3 out of 4 in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:39.5
occ:1.00
 O1B C:GTP605 2.1 38.8 1.0
O2G C:GTP605 2.1 38.7 1.0
O C:HOH721 2.1 37.0 1.0
O1A C:GTP605 2.1 40.5 1.0
OE1 C:GLU211 2.2 49.7 1.0
OD2 C:ASP213 2.2 47.9 1.0
PB C:GTP605 3.1 38.8 1.0
CD C:GLU211 3.2 47.2 1.0
CG C:ASP213 3.2 46.6 1.0
PA C:GTP605 3.2 42.1 1.0
O3A C:GTP605 3.3 42.4 1.0
PG C:GTP605 3.3 38.0 1.0
OD1 C:ASP213 3.5 49.2 1.0
O3B C:GTP605 3.5 37.2 1.0
OE2 C:GLU211 3.6 49.2 1.0
MG C:MG602 3.8 42.7 1.0
O C:HOH703 4.1 31.9 1.0
O2A C:GTP605 4.1 42.4 1.0
OG C:SER199 4.1 44.9 1.0
O1G C:GTP605 4.1 38.0 1.0
N2 C:G604 4.2 63.5 1.0
N C:SER199 4.2 38.0 1.0
CG C:GLU211 4.4 46.7 1.0
O5' C:GTP605 4.4 44.3 1.0
O3G C:GTP605 4.5 37.5 1.0
O2B C:GTP605 4.5 42.2 1.0
O C:GLU211 4.5 43.1 1.0
CB C:SER199 4.5 41.5 1.0
CB C:ASP213 4.5 46.5 1.0
CB C:GLU211 4.6 45.3 1.0
CA C:GLY198 4.7 37.3 1.0
C C:GLU211 4.7 44.7 1.0
C C:GLY198 4.9 37.4 1.0
N C:ASP213 4.9 45.2 1.0

Magnesium binding site 4 out of 4 in 7uyz

Go back to Magnesium Binding Sites List in 7uyz
Magnesium binding site 4 out of 4 in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:42.7
occ:1.00
 OD2 C:ASP307 1.9 51.0 1.0
OD1 C:ASP213 2.0 49.2 1.0
OE2 C:GLU211 2.0 49.2 1.0
O1A C:GTP605 2.4 40.5 1.0
CD C:GLU211 3.1 47.2 1.0
CG C:ASP307 3.1 48.9 1.0
CG C:ASP213 3.1 46.6 1.0
PA C:GTP605 3.2 42.1 1.0
OE1 C:GLU211 3.5 49.7 1.0
O5' C:GTP605 3.6 44.3 1.0
OD2 C:ASP213 3.6 47.9 1.0
O2A C:GTP605 3.7 42.4 1.0
MG C:MG601 3.8 39.5 1.0
CB C:ASP307 3.9 49.1 1.0
N2 C:G604 4.0 63.5 1.0
OD1 C:ASP307 4.0 50.8 1.0
O3' C:GTP605 4.3 49.4 1.0
CB C:ASP213 4.4 46.5 1.0
CG C:GLU211 4.4 46.7 1.0
O3A C:GTP605 4.7 42.4 1.0
C2 C:G604 4.8 63.8 1.0
O2G C:GTP605 4.9 38.7 1.0
O C:PHE212 4.9 45.1 1.0
N3 C:G604 5.0 65.4 1.0

Reference:

S.Wu, S.B.Gabelli, J.S.Sohn. Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Pppg(2 ,5 )Pg To Be Published.
Page generated: Thu Oct 3 10:17:55 2024

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