Magnesium in PDB 5yws: Crystal Structure of TREX1 in Complex with A Y Structured Dna

Enzymatic activity of Crystal Structure of TREX1 in Complex with A Y Structured Dna

All present enzymatic activity of Crystal Structure of TREX1 in Complex with A Y Structured Dna:
3.1.11.2;

Protein crystallography data

The structure of Crystal Structure of TREX1 in Complex with A Y Structured Dna, PDB code: 5yws 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) 29.33 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.532, 96.604, 101.112, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of TREX1 in Complex with A Y Structured Dna (pdb code 5yws). 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 Y Structured Dna, PDB code: 5yws:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5yws

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Magnesium binding site 1 out of 4 in the Crystal Structure of TREX1 in Complex with A Y Structured Dna


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 Y Structured Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:26.8
occ:1.00
 OD2 A:ASP200 2.1 31.6 1.0
OP1 C:DC22 2.3 25.9 1.0
OE1 A:GLU20 2.3 27.4 1.0
OD2 A:ASP18 2.4 26.0 1.0
HA A:HIS195 2.9 41.9 1.0
HB2 A:ASP200 3.1 27.2 1.0
CD A:GLU20 3.1 26.0 1.0
CG A:ASP200 3.2 27.5 1.0
CG A:ASP18 3.2 25.5 1.0
OD1 A:ASP18 3.3 26.9 1.0
OE2 A:GLU20 3.3 26.0 1.0
CB A:ASP200 3.5 24.3 1.0
MG A:MG302 3.6 31.2 1.0
HB3 A:ASP200 3.6 27.2 1.0
P C:DC22 3.7 26.7 1.0
O A:LEU19 3.8 22.4 1.0
CA A:HIS195 3.8 31.7 1.0
H5'' C:DC22 4.0 29.3 1.0
HA A:ALA197 4.1 24.8 1.0
H A:HIS195 4.1 39.9 1.0
O A:HOH526 4.2 25.2 1.0
ND1 A:HIS195 4.2 36.0 1.0
C A:HIS195 4.2 30.3 1.0
OD1 A:ASP200 4.3 27.2 1.0
O A:THR196 4.3 25.0 1.0
O5' C:DC22 4.4 26.4 1.0
OP2 C:DC22 4.4 27.5 1.0
N A:HIS195 4.5 30.7 1.0
CG A:GLU20 4.5 23.7 1.0
HG2 A:GLU20 4.6 29.7 1.0
C A:THR196 4.6 24.9 1.0
N A:THR196 4.6 29.1 1.0
CB A:ASP18 4.6 23.3 1.0
C A:LEU19 4.6 22.7 1.0
C5' C:DC22 4.7 25.4 1.0
O A:HOH417 4.7 23.5 1.0
HB3 A:HIS195 4.7 46.0 1.0
CB A:HIS195 4.7 33.9 1.0
HA A:GLU20 4.7 25.7 1.0
O3' C:DT21 4.7 22.1 1.0
O A:HIS195 4.8 30.1 1.0
HB3 A:ASP18 4.8 28.4 1.0
H A:LEU19 4.8 27.0 1.0
H A:ASP200 4.8 20.7 1.0
H A:THR196 4.8 37.1 1.0
CG A:HIS195 4.9 35.6 1.0
CA A:ALA197 4.9 23.0 1.0
N A:ALA197 5.0 23.2 1.0
CA A:ASP200 5.0 22.5 1.0

Magnesium binding site 2 out of 4 in 5yws

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Magnesium binding site 2 out of 4 in the Crystal Structure of TREX1 in Complex with A Y Structured Dna


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 Y Structured Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:31.2
occ:1.00
 OD1 A:ASP18 2.2 26.9 1.0
O A:HOH465 2.2 25.8 1.0
OP1 C:DC22 2.3 25.9 1.0
O A:HOH526 2.4 25.2 1.0
O A:HOH417 2.4 23.5 1.0
O3' C:DT21 2.6 22.1 1.0
P C:DC22 3.0 26.7 1.0
CG A:ASP18 3.3 25.5 1.0
H4' C:DT21 3.5 27.1 1.0
MG A:MG301 3.6 26.8 1.0
C3' C:DT21 3.8 23.4 1.0
H5'' C:DT21 3.8 24.9 1.0
H A:LEU19 3.9 27.0 1.0
OD2 A:ASP18 3.9 26.0 1.0
H5'' C:DC22 4.0 29.3 1.0
OP2 C:DC22 4.0 27.5 1.0
H5' C:DC22 4.0 29.3 1.0
O A:HOH436 4.0 21.4 1.0
C4' C:DT21 4.0 23.8 1.0
O A:LEU19 4.0 22.4 1.0
O5' C:DC22 4.1 26.4 1.0
OD2 A:ASP130 4.2 28.2 1.0
C5' C:DC22 4.3 25.4 1.0
O C:HOH217 4.3 24.5 1.0
OD1 A:ASP130 4.3 28.6 1.0
HA A:ASP18 4.3 24.4 1.0
H3' C:DT21 4.4 26.5 1.0
O A:HOH513 4.4 22.9 1.0
C5' C:DT21 4.4 22.9 1.0
O A:HIS124 4.5 22.0 1.0
H2'' C:DT21 4.5 28.1 1.0
CB A:ASP18 4.5 23.3 1.0
HB3 A:HIS124 4.6 25.2 1.0
N A:LEU19 4.6 22.7 1.0
HB2 A:ASP18 4.7 28.4 1.0
CG A:ASP130 4.7 27.7 1.0
HB3 A:ASP200 4.7 27.2 1.0
OD2 A:ASP200 4.7 31.6 1.0
C2' C:DT21 4.8 24.3 1.0
CA A:ASP18 4.9 21.5 1.0

Magnesium binding site 3 out of 4 in 5yws

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Magnesium binding site 3 out of 4 in the Crystal Structure of TREX1 in Complex with A Y Structured Dna


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 Y Structured Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:23.1
occ:1.00
 OP1 D:DC22 2.1 23.2 1.0
OD2 B:ASP200 2.1 28.0 1.0
OD2 B:ASP18 2.2 23.7 1.0
OE1 B:GLU20 2.3 22.8 1.0
CG B:ASP18 3.0 22.9 1.0
OD1 B:ASP18 3.1 23.9 1.0
CD B:GLU20 3.1 21.5 1.0
HA B:HIS195 3.1 36.5 1.0
CG B:ASP200 3.2 25.7 1.0
HB2 B:ASP200 3.2 28.9 1.0
OE2 B:GLU20 3.4 21.6 1.0
MG B:MG302 3.5 29.3 1.0
CB B:ASP200 3.6 23.1 1.0
P D:DC22 3.6 23.4 1.0
HB3 B:ASP200 3.6 28.9 1.0
O B:LEU19 3.7 20.9 1.0
H5'' D:DC22 3.8 24.7 1.0
HA B:ALA197 4.0 22.3 1.0
CA B:HIS195 4.0 28.0 1.0
O B:HOH542 4.2 20.8 1.0
O5' D:DC22 4.2 22.3 1.0
O B:THR196 4.3 20.9 1.0
OD1 B:ASP200 4.3 25.1 1.0
HG2 B:GLU20 4.3 20.5 1.0
H B:HIS195 4.3 35.7 1.0
C B:HIS195 4.3 27.5 1.0
CG B:GLU20 4.4 19.3 1.0
OP2 D:DC22 4.4 25.0 1.0
O B:HOH424 4.4 22.3 1.0
CB B:ASP18 4.4 20.4 1.0
C5' D:DC22 4.5 22.0 1.0
O3' D:DT21 4.5 18.2 1.0
C B:THR196 4.5 21.7 1.0
C B:LEU19 4.6 20.3 1.0
N B:THR196 4.6 26.0 1.0
HB3 B:ASP18 4.6 23.6 1.0
N B:HIS195 4.7 27.6 1.0
HA B:GLU20 4.8 22.3 1.0
H B:LEU19 4.8 23.2 1.0
H B:THR196 4.8 31.1 1.0
ND1 B:HIS195 4.8 33.6 1.0
CA B:ALA197 4.8 21.0 1.0
O D:HOH226 4.9 23.2 1.0
HB2 B:ASP18 4.9 23.6 1.0
N B:ALA197 4.9 20.6 1.0
O B:HIS195 4.9 28.7 1.0
H5' D:DC22 4.9 24.7 1.0
HG3 B:GLU20 4.9 20.5 1.0
HB3 B:HIS195 5.0 39.3 1.0
H B:ASP200 5.0 24.3 1.0

Magnesium binding site 4 out of 4 in 5yws

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Magnesium binding site 4 out of 4 in the Crystal Structure of TREX1 in Complex with A Y Structured Dna


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 Y Structured Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:29.3
occ:1.00
 O B:HOH447 2.2 19.7 1.0
OD1 B:ASP18 2.3 23.9 1.0
O B:HOH424 2.4 22.3 1.0
O3' D:DT21 2.4 18.2 1.0
O B:HOH542 2.4 20.8 1.0
OP1 D:DC22 2.5 23.2 1.0
P D:DC22 3.0 23.4 1.0
H4' D:DT21 3.3 27.2 1.0
CG B:ASP18 3.5 22.9 1.0
MG B:MG301 3.5 23.1 1.0
H5'' D:DT21 3.6 28.8 1.0
C3' D:DT21 3.6 21.0 1.0
C4' D:DT21 3.8 22.5 1.0
H5' D:DC22 3.9 24.7 1.0
H5'' D:DC22 4.0 24.7 1.0
OD2 B:ASP18 4.0 23.7 1.0
O B:HOH432 4.0 15.8 1.0
OP2 D:DC22 4.1 25.0 1.0
H B:LEU19 4.1 23.2 1.0
O D:HOH226 4.1 23.2 1.0
O5' D:DC22 4.2 22.3 1.0
O B:HOH540 4.2 24.9 1.0
O B:LEU19 4.2 20.9 1.0
C5' D:DT21 4.2 23.3 1.0
OD1 B:ASP130 4.2 27.9 1.0
OD2 B:ASP130 4.2 24.0 1.0
H3' D:DT21 4.2 24.5 1.0
C5' D:DC22 4.2 22.0 1.0
H2'' D:DT21 4.3 26.4 1.0
HA B:ASP18 4.4 20.2 1.0
O B:HIS124 4.4 18.2 1.0
HB3 B:HIS124 4.4 17.8 1.0
C2' D:DT21 4.6 22.1 1.0
OD2 B:ASP200 4.7 28.0 1.0
CG B:ASP130 4.7 24.7 1.0
HB3 B:ASP200 4.7 28.9 1.0
CB B:ASP18 4.7 20.4 1.0
N B:LEU19 4.8 19.9 1.0
HB2 B:ASP18 4.8 23.6 1.0
H5' D:DT21 4.8 28.8 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: Mon Dec 14 22:15:27 2020

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