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Magnesium in PDB 6a4b: Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang

Enzymatic activity of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang

All present enzymatic activity of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang:
3.1.11.2;

Protein crystallography data

The structure of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang, PDB code: 6a4b 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) 29.23 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.715, 87.317, 432.941, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.3

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang (pdb code 6a4b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang, PDB code: 6a4b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 6a4b

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Magnesium binding site 1 out of 11 in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:75.4
occ:1.00
 OD1 A:ASP14 2.5 67.5 1.0
O3' H:DT17 2.9 77.0 1.0
OP1 H:DT18 3.1 81.2 1.0
OD1 A:ASP123 3.2 65.5 1.0
CG A:ASP14 3.5 63.7 1.0
P H:DT18 3.6 80.1 1.0
OD2 A:ASP123 3.7 60.7 1.0
CG A:ASP123 3.8 63.1 1.0
C4' H:DT17 3.9 78.3 1.0
C3' H:DT17 3.9 79.4 1.0
O A:HIS117 4.0 70.2 1.0
OD2 A:ASP14 4.3 64.2 1.0
CB A:ASP14 4.4 57.8 1.0
N A:LEU15 4.5 58.0 1.0
C5' H:DT18 4.5 62.9 1.0
MG A:MG302 4.5 75.1 1.0
C5' H:DT17 4.5 75.0 1.0
CA A:ASP14 4.6 55.3 1.0
O5' H:DT18 4.6 59.2 1.0
C2' H:DT17 4.7 81.1 1.0
O A:LEU15 4.7 65.1 1.0
OP2 H:DT18 4.8 79.4 1.0

Magnesium binding site 2 out of 11 in 6a4b

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Magnesium binding site 2 out of 11 in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:75.1
occ:1.00
 OE2 A:GLU16 2.3 73.9 1.0
OP1 H:DT18 2.3 81.2 1.0
OD2 A:ASP14 2.4 64.2 1.0
OD2 A:ASP193 2.5 64.5 1.0
CG A:ASP14 3.1 63.7 1.0
OD1 A:ASP14 3.2 67.5 1.0
CD A:GLU16 3.2 73.1 1.0
CG A:ASP193 3.5 62.3 1.0
P H:DT18 3.6 80.1 1.0
OE1 A:GLU16 3.8 74.2 1.0
O5' H:DT18 4.0 59.2 1.0
CB A:ASP193 4.0 59.4 1.0
O A:LEU15 4.0 65.1 1.0
C5' H:DT18 4.1 62.9 1.0
CG A:GLU16 4.2 70.2 1.0
MG A:MG301 4.5 75.4 1.0
OP2 H:DT18 4.5 79.4 1.0
CB A:ASP14 4.6 57.8 1.0
C A:LEU15 4.6 61.9 1.0
CA A:ALA190 4.6 60.7 1.0
OD1 A:ASP193 4.6 61.0 1.0
O3' H:DT17 4.7 77.0 1.0
O A:SER189 4.8 69.1 1.0
O3' H:DT18 4.8 72.8 1.0
N A:LEU15 5.0 58.0 1.0

Magnesium binding site 3 out of 11 in 6a4b

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Magnesium binding site 3 out of 11 in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:69.4
occ:1.00
 OD2 B:ASP193 2.1 59.6 1.0
OD2 B:ASP14 2.4 57.6 1.0
OE2 B:GLU16 2.4 72.0 1.0
OP1 G:DT18 2.6 51.9 1.0
CG B:ASP14 3.0 57.3 1.0
OD1 B:ASP14 3.0 59.4 1.0
CG B:ASP193 3.1 57.9 1.0
CB B:ASP193 3.4 57.2 1.0
CD B:GLU16 3.6 70.4 1.0
P G:DT18 3.9 49.7 1.0
MG G:MG101 3.9 62.4 1.0
OE1 B:GLU16 4.0 79.4 1.0
CA B:HIS188 4.2 77.2 1.0
OD1 B:ASP193 4.2 56.0 1.0
O B:LEU15 4.2 60.9 1.0
CB B:ASP14 4.4 56.5 1.0
C B:HIS188 4.4 74.7 1.0
ND1 B:HIS188 4.5 76.4 1.0
OP2 G:DT18 4.5 50.6 1.0
O5' G:DT18 4.7 54.0 1.0
O B:SER189 4.7 72.5 1.0
CA B:ALA190 4.7 59.4 1.0
CG B:GLU16 4.8 60.8 1.0
N B:SER189 4.8 76.7 1.0
C B:SER189 4.8 66.2 1.0
O B:HIS188 4.9 76.7 1.0
N B:ALA190 4.9 65.3 1.0
CA B:ASP193 4.9 55.4 1.0
C5' G:DT18 4.9 57.6 1.0
N B:HIS188 5.0 82.7 1.0
C B:LEU15 5.0 55.5 1.0
O3' G:DT17 5.0 62.5 1.0

Magnesium binding site 4 out of 11 in 6a4b

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Magnesium binding site 4 out of 11 in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:87.1
occ:1.00
 OD2 C:ASP193 2.2 80.2 1.0
OP1 I:DT18 2.2 70.5 1.0
OE2 C:GLU16 2.3 84.6 1.0
OD2 C:ASP14 3.1 59.9 1.0
OD1 C:ASP14 3.2 61.7 1.0
CG C:ASP193 3.3 74.4 1.0
CD C:GLU16 3.4 83.8 1.0
P I:DT18 3.4 64.5 1.0
CG C:ASP14 3.5 60.6 1.0
CB C:ASP193 3.9 72.6 1.0
OE1 C:GLU16 3.9 87.6 1.0
O5' I:DT18 4.0 64.2 1.0
OP2 I:DT18 4.1 65.5 1.0
O C:LEU15 4.4 72.2 1.0
OD1 C:ASP193 4.4 73.3 1.0
MG I:MG101 4.4 66.5 1.0
C5' I:DT18 4.4 69.2 1.0
CE1 C:HIS188 4.6 0.6 1.0
CG C:GLU16 4.6 74.7 1.0
O3' I:DT17 4.7 71.8 1.0
O C:SER189 4.9 79.3 1.0
CB C:ASP14 5.0 60.4 1.0

Magnesium binding site 5 out of 11 in 6a4b

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Magnesium binding site 5 out of 11 in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:75.1
occ:1.00
 OP1 J:DT18 2.6 78.1 1.0
OD2 D:ASP14 2.7 70.4 1.0
O3' J:DT17 2.8 74.2 1.0
P J:DT18 3.3 75.6 1.0
O D:LEU15 3.4 77.2 1.0
CG D:ASP14 3.4 69.8 1.0
OD1 D:ASP123 3.5 82.3 1.0
OD2 D:ASP123 3.6 81.3 1.0
C5' J:DT18 3.7 83.1 1.0
N D:LEU15 3.8 76.0 1.0
OD1 D:ASP14 3.8 73.2 1.0
CG D:ASP123 4.0 81.7 1.0
O D:HOH404 4.0 52.7 1.0
O5' J:DT18 4.0 83.5 1.0
C3' J:DT17 4.1 77.7 1.0
C D:LEU15 4.3 75.8 1.0
CB D:ASP14 4.4 66.4 1.0
CA D:ASP14 4.4 67.1 1.0
C4' J:DT17 4.5 79.6 1.0
OE2 D:GLU16 4.5 92.5 1.0
OP2 J:DT18 4.6 75.7 1.0
C D:ASP14 4.6 71.3 1.0
CA D:LEU15 4.6 75.0 1.0
C2' J:DT17 4.6 79.9 1.0
CD2 D:TYR122 5.0 74.2 1.0

Magnesium binding site 6 out of 11 in 6a4b

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Magnesium binding site 6 out of 11 in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:75.1
occ:1.00
 OD1 E:ASP14 2.3 80.3 1.0
O3' K:DT17 2.4 71.4 1.0
OP1 K:DT18 2.5 67.9 1.0
P K:DT18 3.0 67.2 1.0
OD1 E:ASP123 3.5 80.9 1.0
CG E:ASP14 3.5 77.2 1.0
O5' K:DT18 3.6 70.7 1.0
OD2 E:ASP123 3.7 81.3 1.0
C3' K:DT17 3.7 71.7 1.0
O E:LEU15 3.8 77.6 1.0
CG E:ASP123 4.0 80.7 1.0
MG E:MG302 4.0 83.8 1.0
C4' K:DT17 4.0 69.9 1.0
OD2 E:ASP14 4.1 79.6 1.0
N E:LEU15 4.3 71.6 1.0
C2' K:DT17 4.4 71.4 1.0
OP2 K:DT18 4.4 60.6 1.0
CB E:ASP14 4.6 71.4 1.0
C5' K:DT17 4.7 67.7 1.0
O E:HIS117 4.7 69.0 1.0
CD2 E:TYR122 4.7 74.6 1.0
CA E:ASP14 4.8 69.9 1.0
C E:LEU15 4.8 73.2 1.0
C5' K:DT18 4.8 73.8 1.0
CE2 E:TYR122 4.9 74.8 1.0

Magnesium binding site 7 out of 11 in 6a4b

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Magnesium binding site 7 out of 11 in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:83.8
occ:1.00
 OE2 E:GLU16 2.0 87.1 1.0
OP1 K:DT18 2.1 67.9 1.0
OD2 E:ASP193 2.2 92.7 1.0
OD2 E:ASP14 2.8 79.6 1.0
CD E:GLU16 3.1 85.3 1.0
CG E:ASP193 3.4 85.0 1.0
P K:DT18 3.4 67.2 1.0
CG E:ASP14 3.5 77.2 1.0
OD1 E:ASP14 3.5 80.3 1.0
OE1 E:GLU16 3.6 88.1 1.0
O5' K:DT18 3.7 70.7 1.0
CB E:ASP193 3.9 76.9 1.0
MG E:MG301 4.0 75.1 1.0
OP2 K:DT18 4.1 60.6 1.0
CG E:GLU16 4.3 78.6 1.0
OD1 E:ASP193 4.4 84.3 1.0
O E:LEU15 4.4 77.6 1.0
CA E:HIS188 4.6 0.4 1.0
C E:HIS188 4.6 0.1 1.0
O3' K:DT17 4.6 71.4 1.0
O E:HIS188 4.6 0.8 1.0
O E:SER189 4.7 81.1 1.0
C E:SER189 4.9 83.0 1.0
C5' K:DT18 5.0 73.8 1.0
CB E:ASP14 5.0 71.4 1.0

Magnesium binding site 8 out of 11 in 6a4b

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Magnesium binding site 8 out of 11 in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:76.6
occ:1.00
 OP1 L:DT18 2.1 68.1 1.0
OD2 F:ASP193 2.4 77.1 1.0
OE2 F:GLU16 2.5 71.4 1.0
OD2 F:ASP14 2.7 60.8 1.0
P L:DT18 3.5 68.8 1.0
CG F:ASP14 3.5 61.6 1.0
CD F:GLU16 3.5 69.3 1.0
CG F:ASP193 3.5 75.5 1.0
OD1 F:ASP14 3.6 64.0 1.0
MG L:MG101 3.7 69.5 1.0
OE1 F:GLU16 3.8 72.1 1.0
O5' L:DT18 3.9 62.9 1.0
CB F:ASP193 4.0 73.5 1.0
C5' L:DT18 4.1 63.7 1.0
OP2 L:DT18 4.4 63.9 1.0
O3' L:DT17 4.5 81.8 1.0
OD1 F:ASP193 4.6 75.8 1.0
O F:LEU15 4.6 70.0 1.0
CG F:GLU16 4.8 63.4 1.0
CB F:ASP14 4.9 62.6 1.0
CA F:ALA190 5.0 66.6 1.0

Magnesium binding site 9 out of 11 in 6a4b

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Magnesium binding site 9 out of 11 in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg101

b:62.4
occ:1.00
 OP1 G:DT18 2.3 51.9 1.0
OD1 B:ASP14 2.4 59.4 1.0
O3' G:DT17 2.4 62.5 1.0
P G:DT18 2.9 49.7 1.0
CG B:ASP14 3.6 57.3 1.0
C3' G:DT17 3.6 63.7 1.0
OD2 B:ASP123 3.8 64.4 1.0
C4' G:DT17 3.9 66.5 1.0
OD1 B:ASP123 3.9 68.5 1.0
MG B:MG301 3.9 69.4 1.0
OP2 G:DT18 4.0 50.6 1.0
O5' G:DT18 4.1 54.0 1.0
C5' G:DT18 4.2 57.6 1.0
OD2 B:ASP14 4.2 57.6 1.0
CG B:ASP123 4.3 65.9 1.0
C5' G:DT17 4.3 65.7 1.0
O B:HIS117 4.4 67.2 1.0
O B:LEU15 4.5 60.9 1.0
C2' G:DT17 4.5 64.9 1.0
CB B:ASP14 4.7 56.5 1.0
N B:LEU15 4.9 52.4 1.0

Magnesium binding site 10 out of 11 in 6a4b

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Magnesium binding site 10 out of 11 in the Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of TREX2 in Complex with A Duplex Dna with 2 Nucleotide 3'- Overhang within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg101

b:66.5
occ:1.00
 OD1 C:ASP14 2.5 61.7 1.0
OP1 I:DT18 2.8 70.5 1.0
O3' I:DT17 2.9 71.8 1.0
OD1 C:ASP123 3.4 73.6 1.0
P I:DT18 3.5 64.5 1.0
CG C:ASP14 3.8 60.6 1.0
OD2 C:ASP123 3.8 62.6 1.0
O C:HIS117 3.9 75.2 1.0
CG C:ASP123 4.0 71.3 1.0
C3' I:DT17 4.0 74.5 1.0
C4' I:DT17 4.1 77.9 1.0
C5' I:DT17 4.4 80.9 1.0
MG C:MG301 4.4 87.1 1.0
OP2 I:DT18 4.5 65.5 1.0
CB C:ASP14 4.5 60.4 1.0
O5' I:DT18 4.6 64.2 1.0
C5' I:DT18 4.6 69.2 1.0
OD2 C:ASP14 4.7 59.9 1.0
N C:LEU15 4.8 60.1 1.0
O C:LEU15 4.8 72.2 1.0
CA C:ASP14 4.8 60.3 1.0
C2' I:DT17 4.9 74.4 1.0

Reference:

H.L.Cheng, C.T.Lin, K.W.Huang, S.Wang, Y.T.Lin, S.I.Toh, Y.Y.Hsiao. Structural Insights Into the Duplex Dna Processing of TREX2 Nucleic Acids Res. V. 46 12166 2018.
ISSN: ESSN 1362-4962
PubMed: 30357414
DOI: 10.1093/NAR/GKY970
Page generated: Mon Sep 30 18:57:45 2024

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