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

Go back to Magnesium Binding Sites List in 6a4b
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

Go back to Magnesium Binding Sites List in 6a4b
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

Go back to Magnesium Binding Sites List in 6a4b
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

Go back to Magnesium Binding Sites List in 6a4b
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

Go back to Magnesium Binding Sites List in 6a4b
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

Go back to Magnesium Binding Sites List in 6a4b
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

Go back to Magnesium Binding Sites List in 6a4b
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

Go back to Magnesium Binding Sites List in 6a4b
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

Go back to Magnesium Binding Sites List in 6a4b
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

Go back to Magnesium Binding Sites List in 6a4b
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 Dec 14 22:19:16 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy