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Magnesium in PDB 2o4g: Structure of TREX1 in Complex with A Nucleotide

Enzymatic activity of Structure of TREX1 in Complex with A Nucleotide

All present enzymatic activity of Structure of TREX1 in Complex with A Nucleotide:
3.1.11.2;

Protein crystallography data

The structure of Structure of TREX1 in Complex with A Nucleotide, PDB code: 2o4g was solved by M.Brucet, M.J.Macias, I.Fita, A.Celada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.183, 81.459, 93.127, 90.00, 103.22, 90.00
R / Rfree (%) 20.3 / 25.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of TREX1 in Complex with A Nucleotide (pdb code 2o4g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of TREX1 in Complex with A Nucleotide, PDB code: 2o4g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 2o4g

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Magnesium binding site 1 out of 8 in the Structure of TREX1 in Complex with A Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of TREX1 in Complex with A Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg800

b:29.8
occ:1.00
 O3P A:TMP1000 1.7 26.5 0.5
OD2 A:ASP18 2.3 24.0 1.0
OD2 A:ASP200 2.4 24.3 1.0
OE2 A:GLU20 2.5 27.2 1.0
MG A:MG801 2.7 17.9 1.0
P A:TMP1000 2.8 28.0 0.5
OD1 A:ASP18 2.9 24.7 1.0
O2P A:TMP1000 3.0 27.2 0.5
CG A:ASP18 3.0 22.6 1.0
O A:HOH1042 3.4 19.2 1.0
CD A:GLU20 3.4 25.3 1.0
CG A:ASP200 3.5 23.3 1.0
O A:LEU19 3.5 22.3 1.0
O A:HOH1041 3.6 16.9 1.0
OE1 A:GLU20 3.6 24.8 1.0
O1P A:TMP1000 3.7 28.0 0.5
O A:HOH1037 3.9 23.0 1.0
CB A:ASP200 3.9 21.5 1.0
O A:HOH1052 4.0 16.5 1.0
O5' A:TMP1000 4.1 27.0 0.5
C5' A:TMP1000 4.4 26.4 0.5
C A:LEU19 4.5 22.6 1.0
CA A:HIS195 4.5 26.7 1.0
CB A:ASP18 4.5 22.0 1.0
OD1 A:ASP200 4.6 21.0 1.0
ND1 A:HIS195 4.7 28.7 1.0
O A:HOH1039 4.7 17.5 1.0
CG A:GLU20 4.8 24.0 1.0
O A:THR196 4.8 25.0 1.0
N A:LEU19 4.9 22.2 1.0

Magnesium binding site 2 out of 8 in 2o4g

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Magnesium binding site 2 out of 8 in the Structure of TREX1 in Complex with A Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of TREX1 in Complex with A Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:17.9
occ:1.00
 O A:HOH1052 1.9 16.5 1.0
O A:HOH1041 2.0 16.9 1.0
OD1 A:ASP18 2.1 24.7 1.0
O A:HOH1039 2.1 17.5 1.0
O3P A:TMP1000 2.2 26.5 0.5
O A:HOH1042 2.3 19.2 1.0
MG A:MG800 2.7 29.8 1.0
CG A:ASP18 3.2 22.6 1.0
OD2 A:ASP18 3.6 24.0 1.0
P A:TMP1000 3.6 28.0 0.5
O1P A:TMP1000 3.9 28.0 0.5
OD2 A:ASP130 3.9 26.0 1.0
O A:LEU19 4.0 22.3 1.0
O A:HOH1037 4.0 23.0 1.0
OD1 A:ASP130 4.1 25.0 1.0
O5' A:TMP1000 4.2 27.0 0.5
O A:HIS124 4.3 22.2 1.0
O A:HOH1007 4.3 11.1 1.0
O A:HOH1053 4.4 26.6 1.0
CB A:ASP18 4.4 22.0 1.0
CG A:ASP130 4.5 24.5 1.0
OD2 A:ASP200 4.6 24.3 1.0
O2P A:TMP1000 4.6 27.2 0.5
C5' A:TMP1000 4.7 26.4 0.5
N A:LEU19 4.7 22.2 1.0
CA A:ASP18 4.9 22.2 1.0
OE2 A:GLU20 4.9 27.2 1.0

Magnesium binding site 3 out of 8 in 2o4g

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Magnesium binding site 3 out of 8 in the Structure of TREX1 in Complex with A Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of TREX1 in Complex with A Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg800

b:19.8
occ:1.00
 OE2 B:GLU20 1.8 25.5 1.0
OD2 B:ASP18 2.0 24.6 1.0
OD2 B:ASP200 2.1 24.2 1.0
O3P B:TMP1000 2.2 47.9 1.0
CD B:GLU20 2.9 24.2 1.0
O2P B:TMP1000 2.9 50.0 1.0
CG B:ASP18 3.0 24.8 1.0
P B:TMP1000 3.1 50.7 1.0
CG B:ASP200 3.1 23.5 1.0
OE1 B:GLU20 3.3 22.8 1.0
OD1 B:ASP18 3.4 27.3 1.0
MG B:MG801 3.5 13.8 1.0
CB B:ASP200 3.5 22.8 1.0
O B:LEU19 3.6 22.7 1.0
CA B:HIS195 3.9 26.4 1.0
O B:THR196 4.0 24.3 1.0
O B:HOH1037 4.0 17.5 1.0
O1P B:TMP1000 4.1 49.8 1.0
CG B:GLU20 4.2 23.3 1.0
O B:HOH1001 4.2 11.4 1.0
OD1 B:ASP200 4.3 23.4 1.0
O5' B:TMP1000 4.3 48.3 1.0
C B:HIS195 4.3 25.7 1.0
C B:THR196 4.3 24.5 1.0
CB B:ASP18 4.4 23.6 1.0
C B:LEU19 4.4 22.6 1.0
N B:THR196 4.5 25.4 1.0
N B:HIS195 4.5 26.4 1.0
C5' B:TMP1000 4.5 47.0 1.0
CA B:ALA197 4.6 24.3 1.0
N B:ALA197 4.6 24.4 1.0
O B:HOH1045 4.7 28.4 1.0
O B:HOH1044 4.8 30.4 1.0
CB B:HIS195 4.9 26.6 1.0
N B:LEU19 4.9 22.9 1.0
O B:HIS195 4.9 25.9 1.0
ND1 B:HIS195 5.0 28.9 1.0
N B:GLU20 5.0 21.9 1.0

Magnesium binding site 4 out of 8 in 2o4g

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Magnesium binding site 4 out of 8 in the Structure of TREX1 in Complex with A Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of TREX1 in Complex with A Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:13.8
occ:1.00
 OD1 B:ASP18 1.9 27.3 1.0
O B:HOH1043 2.0 12.9 1.0
O B:HOH1037 2.1 17.5 1.0
O B:HOH1044 2.1 30.4 1.0
O B:HOH1001 2.1 11.4 1.0
O3P B:TMP1000 2.4 47.9 1.0
CG B:ASP18 3.0 24.8 1.0
OD2 B:ASP18 3.4 24.6 1.0
MG B:MG800 3.5 19.8 1.0
P B:TMP1000 3.7 50.7 1.0
OD1 B:ASP130 3.9 31.3 1.0
O B:HOH1021 4.0 17.1 1.0
OD2 B:ASP130 4.0 28.6 1.0
O B:LEU19 4.1 22.7 1.0
O1P B:TMP1000 4.2 49.8 1.0
O B:HIS124 4.2 23.1 1.0
O B:HOH1008 4.2 18.2 1.0
CB B:ASP18 4.3 23.6 1.0
O5' B:TMP1000 4.3 48.3 1.0
O B:HOH1045 4.4 28.4 1.0
CG B:ASP130 4.4 25.7 1.0
C5' B:TMP1000 4.5 47.0 1.0
OD2 B:ASP200 4.6 24.2 1.0
N B:LEU19 4.6 22.9 1.0
CA B:ASP18 4.7 23.0 1.0
O2P B:TMP1000 4.8 50.0 1.0

Magnesium binding site 5 out of 8 in 2o4g

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Magnesium binding site 5 out of 8 in the Structure of TREX1 in Complex with A Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of TREX1 in Complex with A Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg800

b:25.8
occ:1.00
 OD2 C:ASP18 1.8 24.1 1.0
OE2 C:GLU20 1.8 22.2 1.0
OD2 C:ASP200 2.2 22.9 1.0
O3P C:TMP1000 2.5 25.5 0.5
CG C:ASP18 2.8 22.1 1.0
CD C:GLU20 3.0 21.3 1.0
CG C:ASP200 3.1 22.8 1.0
OD1 C:ASP18 3.2 22.4 1.0
CB C:ASP200 3.3 22.2 1.0
O2P C:TMP1000 3.4 26.7 0.5
P C:TMP1000 3.5 28.1 0.5
MG C:MG801 3.6 18.3 1.0
OE1 C:GLU20 3.7 18.7 1.0
O C:LEU19 3.8 22.2 1.0
O C:THR196 3.8 25.2 1.0
CA C:HIS195 4.0 25.9 1.0
CB C:ASP18 4.1 22.5 1.0
C C:THR196 4.2 24.5 1.0
CG C:GLU20 4.2 22.7 1.0
O C:HOH1029 4.2 18.6 1.0
OD1 C:ASP200 4.2 23.7 1.0
CA C:ALA197 4.3 24.1 1.0
C C:HIS195 4.4 25.3 1.0
O1P C:TMP1000 4.4 27.2 0.5
O C:HOH1020 4.4 12.9 1.0
N C:ALA197 4.4 24.2 1.0
C C:LEU19 4.4 22.3 1.0
N C:THR196 4.5 25.2 1.0
N C:HIS195 4.5 26.0 1.0
CA C:ASP200 4.7 22.0 1.0
O5' C:TMP1000 4.8 26.2 0.5
N C:LEU19 4.8 22.8 1.0
O C:HOH1037 4.9 22.8 1.0
CA C:THR196 4.9 24.8 1.0
ND1 C:HIS195 5.0 31.1 1.0
N C:GLU20 5.0 22.1 1.0

Magnesium binding site 6 out of 8 in 2o4g

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Magnesium binding site 6 out of 8 in the Structure of TREX1 in Complex with A Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of TREX1 in Complex with A Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg801

b:18.3
occ:1.00
 O C:HOH1037 2.0 22.8 1.0
OD1 C:ASP18 2.0 22.4 1.0
O C:HOH1017 2.1 14.2 1.0
O C:HOH1020 2.1 12.9 1.0
O3P C:TMP1000 2.3 25.5 0.5
O C:HOH1029 2.3 18.6 1.0
CG C:ASP18 3.1 22.1 1.0
P C:TMP1000 3.5 28.1 0.5
OD2 C:ASP18 3.6 24.1 1.0
MG C:MG800 3.6 25.8 1.0
O1P C:TMP1000 3.8 27.2 0.5
OD2 C:ASP130 3.9 28.1 1.0
O C:LEU19 4.0 22.2 1.0
O C:HOH1009 4.0 13.9 1.0
OD1 C:ASP130 4.1 28.2 1.0
O5' C:TMP1000 4.2 26.2 0.5
O C:HIS124 4.2 22.9 1.0
CB C:ASP18 4.4 22.5 1.0
CG C:ASP130 4.4 25.1 1.0
O C:HOH1013 4.5 20.9 1.0
C5' C:TMP1000 4.6 26.6 0.5
N C:LEU19 4.6 22.8 1.0
OD2 C:ASP200 4.7 22.9 1.0
O2P C:TMP1000 4.7 26.7 0.5
CA C:ASP18 4.8 22.5 1.0
OE2 C:GLU20 4.9 22.2 1.0

Magnesium binding site 7 out of 8 in 2o4g

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Magnesium binding site 7 out of 8 in the Structure of TREX1 in Complex with A Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of TREX1 in Complex with A Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg800

b:26.5
occ:1.00
 O3P D:TMP1000 2.0 33.9 0.5
OE2 D:GLU20 2.0 26.7 1.0
OD2 D:ASP18 2.1 23.4 1.0
OD2 D:ASP200 2.2 23.0 1.0
CG D:ASP18 2.8 23.4 1.0
OD1 D:ASP18 2.9 25.8 1.0
MG D:MG801 3.0 13.7 1.0
CD D:GLU20 3.0 23.0 1.0
P D:TMP1000 3.1 34.4 0.5
CG D:ASP200 3.3 23.0 1.0
O2P D:TMP1000 3.3 33.3 0.5
OE1 D:GLU20 3.4 19.2 1.0
O D:LEU19 3.4 23.3 1.0
CB D:ASP200 3.7 21.8 1.0
O D:HOH1015 3.8 17.4 1.0
O1P D:TMP1000 3.9 35.6 0.5
O D:HOH1044 3.9 9.4 1.0
O D:HOH1055 4.2 33.1 1.0
O D:THR196 4.2 25.7 1.0
CA D:HIS195 4.3 27.2 1.0
CB D:ASP18 4.3 23.0 1.0
C D:LEU19 4.3 22.9 1.0
CG D:GLU20 4.3 23.1 1.0
O5' D:TMP1000 4.4 35.1 0.5
OD1 D:ASP200 4.4 22.4 1.0
O D:HOH1045 4.5 17.1 1.0
C D:THR196 4.7 25.1 1.0
C5' D:TMP1000 4.7 36.2 0.5
C D:HIS195 4.7 26.4 1.0
CA D:ALA197 4.7 24.0 1.0
N D:LEU19 4.8 22.9 1.0
ND1 D:HIS195 4.8 30.7 1.0
N D:HIS195 4.8 27.2 1.0
N D:ALA197 4.9 24.2 1.0
N D:THR196 4.9 26.0 1.0
O D:HOH1011 5.0 12.8 1.0
N D:GLU20 5.0 22.6 1.0

Magnesium binding site 8 out of 8 in 2o4g

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Magnesium binding site 8 out of 8 in the Structure of TREX1 in Complex with A Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of TREX1 in Complex with A Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg801

b:13.7
occ:1.00
 O D:HOH1045 2.0 17.1 1.0
O D:HOH1044 2.0 9.4 1.0
OD1 D:ASP18 2.1 25.8 1.0
O D:HOH1011 2.2 12.8 1.0
O3P D:TMP1000 2.3 33.9 0.5
O D:HOH1015 2.3 17.4 1.0
MG D:MG800 3.0 26.5 1.0
CG D:ASP18 3.2 23.4 1.0
O1P D:TMP1000 3.3 35.6 0.5
P D:TMP1000 3.3 34.4 0.5
OD2 D:ASP18 3.7 23.4 1.0
O D:HOH1055 3.8 33.1 1.0
O D:LEU19 3.9 23.3 1.0
OD2 D:ASP130 4.0 27.4 1.0
O5' D:TMP1000 4.2 35.1 0.5
O D:HOH1004 4.2 13.1 1.0
OD1 D:ASP130 4.3 24.9 1.0
O D:HIS124 4.4 22.7 1.0
O D:HOH1047 4.4 21.6 1.0
CB D:ASP18 4.5 23.0 1.0
OD2 D:ASP200 4.5 23.0 1.0
O2P D:TMP1000 4.6 33.3 0.5
CG D:ASP130 4.6 24.6 1.0
N D:LEU19 4.7 22.9 1.0
C5' D:TMP1000 4.7 36.2 0.5
OE2 D:GLU20 4.7 26.7 1.0
CA D:ASP18 4.9 22.8 1.0

Reference:

M.Brucet, J.Querol-Audi, M.Serra, X.Ramirez-Espain, K.Bertlik, L.Ruiz, J.Lloberas, M.J.Macias, I.Fita, A.Celada. Structure of the Dimeric Exonuclease TREX1 in Complex with Dna Displays A Proline-Rich Binding Site For Ww Domains. J.Biol.Chem. V. 282 14547 2007.
ISSN: ISSN 0021-9258
PubMed: 17355961
DOI: 10.1074/JBC.M700236200
Page generated: Wed Aug 14 01:04:10 2024

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