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Magnesium in PDB 5ywt: Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang

Enzymatic activity of Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang

All present enzymatic activity of Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang:
3.1.11.2;

Protein crystallography data

The structure of Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang, PDB code: 5ywt 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) 28.79 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.170, 80.350, 85.220, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 21.9

Other elements in 5ywt:

The structure of Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang also contains other interesting chemical elements:

Cobalt (Co) 3 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 5ywt

Go back to Magnesium Binding Sites List in 5ywt
Magnesium binding site 1 out of 4 in the Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang


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 Duplex Dna with 3' Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:9.9
occ:1.00
 OE1 A:GLU20 1.9 13.7 1.0
OD2 A:ASP18 2.1 13.8 1.0
OD2 A:ASP200 2.2 17.8 1.0
OP1 C:DT9 2.2 15.6 1.0
CD A:GLU20 2.8 13.0 1.0
CG A:ASP18 2.9 12.0 1.0
OD1 A:ASP18 3.0 13.9 1.0
HA A:HIS195 3.1 20.5 1.0
HB2 A:ASP200 3.1 17.0 1.0
CG A:ASP200 3.2 15.4 1.0
OE2 A:GLU20 3.2 12.2 1.0
CB A:ASP200 3.5 13.4 1.0
MG A:MG304 3.5 15.5 1.0
P C:DT9 3.6 16.6 1.0
HB3 A:ASP200 3.7 17.0 1.0
O A:LEU19 3.7 13.0 1.0
HA A:ALA197 3.8 11.5 1.0
O A:THR196 3.9 13.8 1.0
CA A:HIS195 4.0 17.1 1.0
HG2 A:GLU20 4.1 11.7 1.0
CG A:GLU20 4.1 11.5 1.0
H A:HIS195 4.2 20.7 1.0
O A:HOH595 4.2 14.0 1.0
C A:HIS195 4.3 17.3 1.0
CB A:ASP18 4.3 10.2 1.0
OD1 A:ASP200 4.3 13.7 1.0
O5' C:DT9 4.3 15.8 1.0
C A:THR196 4.3 14.1 1.0
O A:HOH440 4.3 13.4 1.0
OP2 C:DT9 4.4 18.1 1.0
HB3 A:ASP18 4.5 10.8 1.0
C A:LEU19 4.5 11.7 1.0
N A:THR196 4.5 16.9 1.0
N A:HIS195 4.5 17.3 1.0
HA A:GLU20 4.6 10.7 1.0
C5' C:DT9 4.6 15.0 1.0
O3' C:DT8 4.6 16.7 1.0
CA A:ALA197 4.6 11.4 1.0
HG3 A:GLU20 4.7 11.7 1.0
N A:ALA197 4.7 12.2 1.0
HB2 A:ASP18 4.7 10.8 1.0
H A:THR196 4.7 22.7 1.0
H A:LEU19 4.8 11.4 1.0
H A:ASP200 4.8 13.8 1.0
O A:HIS195 4.8 16.4 1.0
N A:LEU19 4.9 10.6 1.0
N A:GLU20 5.0 11.7 1.0
CA A:ASP200 5.0 12.5 1.0
HB3 A:HIS195 5.0 23.5 1.0

Magnesium binding site 2 out of 4 in 5ywt

Go back to Magnesium Binding Sites List in 5ywt
Magnesium binding site 2 out of 4 in the Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang


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 Duplex Dna with 3' Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:15.5
occ:1.00
 OD1 A:ASP18 2.1 13.9 1.0
O A:HOH435 2.2 11.2 1.0
O A:HOH440 2.3 13.4 1.0
O A:HOH595 2.4 14.0 1.0
OP1 C:DT9 2.5 15.6 1.0
O3' C:DT8 2.5 16.7 1.0
P C:DT9 3.1 16.6 1.0
CG A:ASP18 3.3 12.0 1.0
MG A:MG301 3.5 9.9 1.0
C3' C:DT8 3.8 17.4 1.0
O A:HOH490 3.9 9.6 1.0
OD2 A:ASP18 3.9 13.8 1.0
C4' C:DT8 4.0 17.1 1.0
H A:LEU19 4.0 11.4 1.0
OD2 A:ASP130 4.0 13.6 1.0
O A:LEU19 4.1 13.0 1.0
OP2 C:DT9 4.1 18.1 1.0
OD1 A:ASP130 4.2 13.7 1.0
O5' C:DT9 4.2 15.8 1.0
HA A:ASP18 4.2 11.7 1.0
O A:HOH581 4.3 10.9 1.0
O C:HOH408 4.3 16.4 1.0
C5' C:DT9 4.3 15.0 1.0
O A:HIS124 4.4 12.7 1.0
C5' C:DT8 4.4 17.7 1.0
HB3 A:HIS124 4.5 11.4 1.0
CB A:ASP18 4.5 10.2 1.0
CG A:ASP130 4.5 12.7 1.0
HB3 A:ASP200 4.6 17.0 1.0
OD2 A:ASP200 4.6 17.8 1.0
HB2 A:ASP18 4.6 10.8 1.0
N A:LEU19 4.7 10.6 1.0
C2' C:DT8 4.7 17.1 1.0
CA A:ASP18 4.8 10.6 1.0
HD2 A:TYR129 4.9 14.9 1.0
H A:HIS124 5.0 11.4 1.0

Magnesium binding site 3 out of 4 in 5ywt

Go back to Magnesium Binding Sites List in 5ywt
Magnesium binding site 3 out of 4 in the Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang


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 Duplex Dna with 3' Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:11.0
occ:1.00
 OE1 B:GLU20 1.9 14.4 1.0
OD2 B:ASP200 2.0 17.0 1.0
OP1 D:DT6 2.2 17.0 1.0
OD2 B:ASP18 2.2 14.9 1.0
CG B:ASP18 2.9 13.4 1.0
OD1 B:ASP18 2.9 15.4 1.0
CD B:GLU20 2.9 13.6 1.0
CG B:ASP200 3.0 15.3 1.0
HA B:HIS195 3.1 20.8 1.0
HB2 B:ASP200 3.1 14.8 1.0
OE2 B:GLU20 3.3 13.9 1.0
CB B:ASP200 3.5 12.9 1.0
MG B:MG303 3.5 15.7 1.0
HB3 B:ASP200 3.6 14.8 1.0
P D:DT6 3.6 18.2 1.0
O B:LEU19 3.8 12.6 1.0
HA B:ALA197 3.9 9.4 1.0
CA B:HIS195 4.0 16.3 1.0
O B:THR196 4.0 13.5 1.0
OD1 B:ASP200 4.2 15.2 1.0
HG2 B:GLU20 4.2 14.5 1.0
O B:HOH551 4.2 15.2 1.0
CG B:GLU20 4.2 12.6 1.0
H B:HIS195 4.2 19.8 1.0
O B:HOH446 4.2 12.2 1.0
C B:HIS195 4.3 17.4 1.0
CB B:ASP18 4.3 11.1 1.0
O5' D:DT6 4.3 15.2 1.0
C B:THR196 4.4 12.7 1.0
OP2 D:DT6 4.4 19.5 1.0
C5' D:DT6 4.5 14.1 1.0
HB3 B:ASP18 4.5 11.9 1.0
N B:THR196 4.5 16.9 1.0
O3' D:DC5 4.6 15.7 1.0
N B:HIS195 4.6 15.9 1.0
C B:LEU19 4.6 11.2 1.0
HA B:GLU20 4.7 12.7 1.0
HG3 B:GLU20 4.7 14.5 1.0
H B:THR196 4.7 21.4 1.0
CA B:ALA197 4.7 10.9 1.0
HB2 B:ASP18 4.7 11.9 1.0
N B:ALA197 4.8 11.4 1.0
H B:ASP200 4.8 11.7 1.0
O B:HIS195 4.8 18.5 1.0
H B:LEU19 4.9 9.7 1.0
ND1 B:HIS195 4.9 23.2 1.0
CA B:ASP200 4.9 11.6 1.0
HB3 B:HIS195 5.0 23.4 1.0

Magnesium binding site 4 out of 4 in 5ywt

Go back to Magnesium Binding Sites List in 5ywt
Magnesium binding site 4 out of 4 in the Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang


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 Duplex Dna with 3' Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:15.7
occ:1.00
 OD1 B:ASP18 2.1 15.4 1.0
O B:HOH446 2.2 12.2 1.0
O B:HOH431 2.2 11.5 1.0
O B:HOH551 2.4 15.2 1.0
OP1 D:DT6 2.5 17.0 1.0
O3' D:DC5 2.6 15.7 1.0
P D:DT6 3.1 18.2 1.0
CG B:ASP18 3.3 13.4 1.0
MG B:MG301 3.5 11.0 1.0
C3' D:DC5 3.8 16.0 1.0
OD2 B:ASP18 3.9 14.9 1.0
C4' D:DC5 3.9 17.0 1.0
O B:HOH447 4.0 10.2 1.0
OD2 B:ASP130 4.0 13.7 1.0
H B:LEU19 4.0 9.7 1.0
OD1 B:ASP130 4.1 15.3 1.0
O B:LEU19 4.1 12.6 1.0
OP2 D:DT6 4.2 19.5 1.0
HA B:ASP18 4.2 10.6 1.0
O D:HOH408 4.2 17.7 1.0
O5' D:DT6 4.3 15.2 1.0
O B:HOH540 4.3 11.7 1.0
C5' D:DT6 4.4 14.1 1.0
C5' D:DC5 4.4 17.6 1.0
O B:HIS124 4.4 12.9 1.0
OD2 B:ASP200 4.4 17.0 1.0
HB3 B:HIS124 4.4 10.9 1.0
CB B:ASP18 4.4 11.1 1.0
CG B:ASP130 4.5 14.4 1.0
HB3 B:ASP200 4.5 14.8 1.0
HB2 B:ASP18 4.5 11.9 1.0
C2' D:DC5 4.7 16.5 1.0
N B:LEU19 4.7 10.7 1.0
CA B:ASP18 4.8 10.6 1.0
HD2 B:TYR129 4.8 13.0 1.0
H B:HIS124 5.0 10.5 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: Mon Sep 30 11:37:02 2024

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