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Magnesium in PDB 7v0r: Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Ppcpg(2 , 5 )Pa

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

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

Protein crystallography data

The structure of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Ppcpg(2 , 5 )Pa, PDB code: 7v0r 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) 29.61 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.112, 98.446, 142.598, 90, 90, 90
R / Rfree (%) 21.1 / 25

Other elements in 7v0r:

The structure of Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Ppcpg(2 , 5 )Pa 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 -Ppcpg(2 , 5 )Pa (pdb code 7v0r). 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 -Ppcpg(2 , 5 )Pa, PDB code: 7v0r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7v0r

Go back to Magnesium Binding Sites List in 7v0r
Magnesium binding site 1 out of 4 in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Ppcpg(2 , 5 )Pa


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 -Ppcpg(2 , 5 )Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:57.9
occ:1.00
 O9 A:OKX601 1.7 57.7 1.0
O5 A:OKX601 2.0 56.6 1.0
OE1 A:GLU211 2.1 62.0 1.0
O4 A:OKX601 2.2 62.7 1.0
O A:HOH713 2.2 51.0 1.0
OD2 A:ASP213 2.3 59.0 1.0
P3 A:OKX601 3.0 61.1 1.0
P2 A:OKX601 3.1 66.4 1.0
MG A:MG603 3.1 72.8 1.0
CG A:ASP213 3.3 52.2 1.0
O7 A:OKX601 3.3 62.8 1.0
CD A:GLU211 3.4 58.1 1.0
P1 A:OKX601 3.4 72.2 1.0
OD1 A:ASP213 3.5 60.1 1.0
C8 A:OKX601 3.8 70.2 1.0
O10 A:OKX601 4.0 61.0 1.0
O8 A:OKX601 4.0 58.1 1.0
OE2 A:GLU211 4.0 68.0 1.0
O3 A:OKX601 4.1 67.3 1.0
O A:HOH711 4.2 37.6 1.0
N A:SER199 4.2 38.3 1.0
OG A:SER199 4.3 44.1 1.0
CB A:SER199 4.4 40.8 1.0
O6 A:OKX601 4.5 67.6 1.0
CG A:GLU211 4.5 55.0 1.0
CB A:ASP213 4.6 49.2 1.0
O2 A:OKX601 4.6 83.6 1.0
CB A:GLU211 4.7 51.1 1.0
O A:GLU211 4.7 43.7 1.0
CA A:GLY198 4.8 37.1 1.0
C A:GLU211 5.0 44.7 1.0
CA A:SER199 5.0 38.7 1.0

Magnesium binding site 2 out of 4 in 7v0r

Go back to Magnesium Binding Sites List in 7v0r
Magnesium binding site 2 out of 4 in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Ppcpg(2 , 5 )Pa


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 -Ppcpg(2 , 5 )Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:72.8
occ:1.00
 OE2 A:GLU211 2.1 68.0 1.0
OD1 A:ASP213 2.1 60.1 1.0
O18 A:OKX601 2.3 110.1 1.0
O4 A:OKX601 2.3 62.7 1.0
OE1 A:GLU211 2.5 62.0 1.0
CD A:GLU211 2.6 58.1 1.0
OD2 A:ASP307 2.7 60.5 1.0
CG A:ASP213 3.0 52.2 1.0
O17 A:OKX601 3.1 104.8 1.0
MG A:MG602 3.1 57.9 1.0
OD2 A:ASP213 3.3 59.0 1.0
P1 A:OKX601 3.3 72.2 1.0
C20 A:OKX601 3.4 121.8 1.0
C19 A:OKX601 3.5 119.7 1.0
O3 A:OKX601 3.7 67.3 1.0
CG A:ASP307 3.9 52.8 1.0
O2 A:OKX601 3.9 83.6 1.0
O9 A:OKX601 4.0 57.7 1.0
CG A:GLU211 4.1 55.0 1.0
CB A:ASP213 4.4 49.2 1.0
C12 A:OKX601 4.5 125.5 1.0
CB A:ASP307 4.5 50.9 1.0
O5 A:OKX601 4.6 56.6 1.0
OD1 A:ASP307 4.8 55.4 1.0
O A:HOH713 4.8 51.0 1.0
C8 A:OKX601 4.9 70.2 1.0

Magnesium binding site 3 out of 4 in 7v0r

Go back to Magnesium Binding Sites List in 7v0r
Magnesium binding site 3 out of 4 in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Ppcpg(2 , 5 )Pa


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 -Ppcpg(2 , 5 )Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:56.8
occ:1.00
 O5 C:OKX601 1.9 60.9 1.0
O9 C:OKX601 2.0 60.9 1.0
O4 C:OKX601 2.1 60.8 1.0
OD2 C:ASP213 2.2 64.3 1.0
O C:HOH708 2.3 51.9 1.0
OE1 C:GLU211 2.4 69.1 1.0
P2 C:OKX601 3.0 67.1 1.0
MG C:MG603 3.1 63.3 1.0
CG C:ASP213 3.2 57.6 1.0
P1 C:OKX601 3.2 67.3 1.0
P3 C:OKX601 3.3 61.2 1.0
O7 C:OKX601 3.4 63.4 1.0
OD1 C:ASP213 3.5 62.5 1.0
CD C:GLU211 3.6 65.9 1.0
C8 C:OKX601 3.7 68.6 1.0
O3 C:OKX601 3.8 66.8 1.0
O10 C:OKX601 4.2 58.5 1.0
N C:SER199 4.2 43.9 1.0
O C:HOH702 4.3 33.5 1.0
O8 C:OKX601 4.3 59.8 1.0
O6 C:OKX601 4.3 66.8 1.0
OG C:SER199 4.4 48.0 1.0
CB C:SER199 4.4 45.8 1.0
CG C:GLU211 4.5 60.9 1.0
OE2 C:GLU211 4.5 74.4 1.0
CB C:GLU211 4.6 56.9 1.0
O C:GLU211 4.6 47.8 1.0
O2 C:OKX601 4.6 75.1 1.0
CB C:ASP213 4.6 56.8 1.0
CA C:GLY198 4.7 42.5 1.0
C C:GLU211 4.8 52.0 1.0
C C:GLY198 4.9 42.8 1.0
CA C:SER199 5.0 44.3 1.0

Magnesium binding site 4 out of 4 in 7v0r

Go back to Magnesium Binding Sites List in 7v0r
Magnesium binding site 4 out of 4 in the Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Ppcpg(2 , 5 )Pa


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 -Ppcpg(2 , 5 )Pa within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:63.3
occ:1.00
 OE1 C:GLU211 1.8 69.1 1.0
OD1 C:ASP213 2.1 62.5 1.0
OE2 C:GLU211 2.2 74.4 1.0
CD C:GLU211 2.3 65.9 1.0
OD2 C:ASP307 2.5 65.1 1.0
O4 C:OKX601 2.6 60.8 1.0
O18 C:OKX601 2.7 91.3 1.0
CG C:ASP213 3.0 57.6 1.0
MG C:MG602 3.1 56.8 1.0
OD2 C:ASP213 3.2 64.3 1.0
P1 C:OKX601 3.6 67.3 1.0
CG C:ASP307 3.7 56.2 1.0
O17 C:OKX601 3.7 91.8 1.0
O3 C:OKX601 3.7 66.8 1.0
CG C:GLU211 3.8 60.9 1.0
C20 C:OKX601 4.0 97.9 1.0
C19 C:OKX601 4.3 94.5 1.0
O2 C:OKX601 4.3 75.1 1.0
O9 C:OKX601 4.4 60.9 1.0
CB C:ASP213 4.4 56.8 1.0
CB C:ASP307 4.4 54.4 1.0
O C:PHE212 4.6 53.1 1.0
OD1 C:ASP307 4.6 59.2 1.0
O5 C:OKX601 4.6 60.9 1.0
CB C:GLU211 4.7 56.9 1.0
O C:HOH708 4.8 51.9 1.0
C C:PHE212 4.8 51.6 1.0
C12 C:OKX601 5.0 101.6 1.0
CA C:ASP213 5.0 55.5 1.0

Reference:

S.Wu, S.B.Gabelli, J.S.Sohn. Structure of Ternary Complex of Cgas with Dsdna and Bound 5 -Ppcpg(2 ,5 )Pa To Be Published.
Page generated: Thu Oct 3 10:18:38 2024

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