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Magnesium in PDB 5ywv: Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna

Enzymatic activity of Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna

All present enzymatic activity of Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna:
3.1.11.2;

Protein crystallography data

The structure of Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna, PDB code: 5ywv was solved by Y.Y.Hsiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.31 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.192, 80.713, 85.247, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 22

Other elements in 5ywv:

The structure of Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna (pdb code 5ywv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna, PDB code: 5ywv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5ywv

Go back to Magnesium Binding Sites List in 5ywv
Magnesium binding site 1 out of 4 in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna


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 TREX1 in Complex with A Inosine Contained Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:38.4
occ:1.00
 OD2 A:ASP200 2.3 29.6 1.0
OE1 A:GLU20 2.4 29.0 1.0
OP1 C:DG7 2.6 26.5 1.0
OD2 A:ASP18 2.7 31.8 1.0
CG A:ASP200 3.1 26.4 1.0
OD1 A:ASP18 3.3 19.3 1.0
CB A:ASP200 3.3 20.6 1.0
CG A:ASP18 3.4 25.4 1.0
CD A:GLU20 3.4 28.4 1.0
OE2 A:GLU20 3.6 26.1 1.0
H1 C:HOH210 3.8 27.3 1.0
CA A:HIS195 3.8 33.8 1.0
MG A:MG304 3.8 28.8 1.0
O A:THR196 3.9 28.9 1.0
P C:DG7 4.0 26.2 1.0
N A:HIS195 4.1 32.1 1.0
O C:HOH210 4.1 22.8 1.0
ND1 A:HIS195 4.2 42.5 1.0
OD1 A:ASP200 4.3 25.7 1.0
O A:HOH415 4.3 40.2 1.0
C A:HIS195 4.4 31.5 1.0
O A:LEU19 4.5 26.1 1.0
C A:THR196 4.5 26.7 1.0
N A:THR196 4.6 30.0 1.0
O A:HOH438 4.7 25.4 1.0
OP2 C:DG7 4.7 25.1 1.0
O5' C:DG7 4.7 20.0 1.0
CG A:GLU20 4.7 22.0 1.0
CA A:ASP200 4.8 21.9 1.0
CB A:ASP18 4.8 20.2 1.0
CB A:HIS195 4.9 39.2 1.0
O C:HOH204 4.9 25.6 1.0
CG A:HIS195 4.9 42.8 1.0
O3' C:DI6 5.0 24.9 1.0
C5' C:DG7 5.0 21.2 1.0
O A:HOH472 5.0 17.6 1.0

Magnesium binding site 2 out of 4 in 5ywv

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Magnesium binding site 2 out of 4 in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna


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 TREX1 in Complex with A Inosine Contained Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:28.8
occ:1.00
 O A:HOH418 2.2 16.4 1.0
O A:HOH438 2.2 25.4 1.0
O C:HOH210 2.2 22.8 1.0
OD1 A:ASP18 2.6 19.3 1.0
OP1 C:DG7 2.7 26.5 1.0
O3' C:DI6 2.7 24.9 1.0
H1 A:HOH418 2.8 19.7 1.0
H1 A:HOH438 2.8 30.4 1.0
H1 C:HOH210 2.8 27.3 1.0
P C:DG7 3.3 26.2 1.0
CG A:ASP18 3.8 25.4 1.0
MG A:MG301 3.8 38.4 1.0
C3' C:DI6 3.9 24.1 1.0
O A:HOH442 4.0 14.4 1.0
C4' C:DI6 4.0 23.6 1.0
OD1 A:ASP130 4.1 26.9 1.0
O C:HOH204 4.2 25.6 1.0
OD2 A:ASP130 4.2 22.2 1.0
O A:HOH472 4.2 17.6 1.0
O A:LEU19 4.3 26.1 1.0
OP2 C:DG7 4.3 25.1 1.0
C5' C:DG7 4.3 21.2 1.0
O5' C:DG7 4.4 20.0 1.0
OD2 A:ASP18 4.4 31.8 1.0
C5' C:DI6 4.4 21.9 1.0
O A:HIS124 4.4 22.0 1.0
CG A:ASP130 4.6 24.7 1.0
C2' C:DI6 4.7 26.3 1.0
N A:LEU19 4.8 23.8 1.0
CB A:ASP18 4.9 20.2 1.0
CA A:ASP18 5.0 18.6 1.0

Magnesium binding site 3 out of 4 in 5ywv

Go back to Magnesium Binding Sites List in 5ywv
Magnesium binding site 3 out of 4 in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna


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 TREX1 in Complex with A Inosine Contained Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:46.3
occ:1.00
 OE1 B:GLU20 2.4 32.1 1.0
OP1 D:DG7 2.5 30.4 1.0
OD2 B:ASP200 2.6 29.9 1.0
OD2 B:ASP18 3.0 29.4 1.0
CD B:GLU20 3.3 29.8 1.0
CG B:ASP200 3.4 27.6 1.0
OE2 B:GLU20 3.4 28.0 1.0
OD1 B:ASP18 3.4 27.0 1.0
CA B:HIS195 3.5 31.1 1.0
H1 D:HOH204 3.5 37.6 1.0
CB B:ASP200 3.6 21.8 1.0
CG B:ASP18 3.6 27.6 1.0
ND1 B:HIS195 3.9 40.2 1.0
P D:DG7 3.9 31.6 1.0
O B:THR196 4.0 20.9 1.0
O D:HOH204 4.0 31.3 1.0
MG B:MG306 4.0 36.7 1.0
N B:HIS195 4.0 32.7 1.0
C B:HIS195 4.2 28.2 1.0
O B:LEU19 4.3 26.4 1.0
O B:HOH416 4.4 32.6 1.0
OD1 B:ASP200 4.4 28.4 1.0
CB B:HIS195 4.4 34.8 1.0
CG B:HIS195 4.5 40.4 1.0
C B:THR196 4.6 19.8 1.0
OP2 D:DG7 4.6 30.4 1.0
O5' D:DG7 4.6 27.3 1.0
N B:THR196 4.6 24.8 1.0
CG B:GLU20 4.6 25.7 1.0
CE1 B:HIS195 4.7 38.2 1.0
O B:HIS195 4.8 29.8 1.0
H1 B:HOH418 4.9 29.7 1.0
C5' D:DG7 5.0 21.1 1.0
O D:HOH202 5.0 25.1 1.0
O3' D:DI6 5.0 22.5 1.0

Magnesium binding site 4 out of 4 in 5ywv

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Magnesium binding site 4 out of 4 in the Crystal Structure of TREX1 in Complex with A Inosine Contained Ssdna


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 TREX1 in Complex with A Inosine Contained Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:36.7
occ:1.00
 O B:HOH437 2.2 22.4 1.0
O B:HOH418 2.2 24.8 1.0
O D:HOH204 2.2 31.3 1.0
OD1 B:ASP18 2.6 27.0 1.0
OP1 D:DG7 2.7 30.4 1.0
O3' D:DI6 2.7 22.5 1.0
H1 B:HOH437 2.8 26.9 1.0
H1 B:HOH418 2.8 29.7 1.0
H1 D:HOH204 2.8 37.6 1.0
P D:DG7 3.3 31.6 1.0
CG B:ASP18 3.9 27.6 1.0
OD2 B:ASP130 3.9 28.7 1.0
OD1 B:ASP130 3.9 30.7 1.0
C3' D:DI6 3.9 23.9 1.0
O B:HOH419 3.9 15.5 1.0
MG B:MG301 4.0 46.3 1.0
C4' D:DI6 4.0 24.9 1.0
O B:LEU19 4.1 26.4 1.0
O5' D:DG7 4.4 27.3 1.0
CG B:ASP130 4.4 27.5 1.0
C5' D:DG7 4.4 21.1 1.0
C5' D:DI6 4.4 22.1 1.0
OP2 D:DG7 4.4 30.4 1.0
O B:HIS124 4.4 18.9 1.0
O D:HOH202 4.5 25.1 1.0
OD2 B:ASP18 4.5 29.4 1.0
O B:HOH452 4.5 25.6 1.0
N B:LEU19 4.7 19.8 1.0
C2' D:DI6 4.8 25.1 1.0
CB B:ASP18 4.9 22.3 1.0
CA B:ASP18 4.9 20.5 1.0

Reference:

K.W.Huang, T.C.Liu, R.Y.Liang, L.Y.Chu, H.L.Cheng, J.W.Chu, Y.Y.Hsiao. Structural Basis For Overhang Excision and Terminal Unwinding of Dna Duplexes By TREX1 Plos Biol. V. 16 05653 2018.
ISSN: ESSN 1545-7885
PubMed: 29734329
DOI: 10.1371/JOURNAL.PBIO.2005653
Page generated: Wed Aug 13 01:12:37 2025

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