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Zinc in PDB 3b6p: Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc)

Enzymatic activity of Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc)

All present enzymatic activity of Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc):
3.1.11.2;

Protein crystallography data

The structure of Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc), PDB code: 3b6p was solved by M.Brucet, J.Querol-Audi, I.Fita, A.Celada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.18 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.772, 81.496, 92.539, 90.00, 103.11, 90.00
R / Rfree (%) 24.6 / 28.5

Other elements in 3b6p:

The structure of Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc) also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc) (pdb code 3b6p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc), PDB code: 3b6p:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3b6p

Go back to Zinc Binding Sites List in 3b6p
Zinc binding site 1 out of 4 in the Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn800

b:28.4
occ:1.00
 OD2 A:ASP200 2.0 27.5 1.0
O3P A:TMP1000 2.1 24.5 1.0
OE2 A:GLU20 2.1 27.7 1.0
OD2 A:ASP18 2.2 28.5 1.0
CG A:ASP18 2.9 28.6 1.0
OD1 A:ASP18 3.0 29.2 1.0
CG A:ASP200 3.0 27.5 1.0
CD A:GLU20 3.1 27.6 1.0
P A:TMP1000 3.3 24.4 1.0
OE1 A:GLU20 3.4 27.5 1.0
O2P A:TMP1000 3.4 24.3 1.0
NA A:NA801 3.4 22.4 1.0
CB A:ASP200 3.5 27.5 1.0
O A:HOH1119 3.7 29.2 1.0
O A:LEU19 3.9 28.0 1.0
O A:THR196 4.1 29.3 1.0
OD1 A:ASP200 4.1 27.2 1.0
CA A:HIS195 4.1 29.7 1.0
O1P A:TMP1000 4.2 24.8 1.0
C A:HIS195 4.3 29.6 1.0
O A:HOH1117 4.3 17.9 1.0
C A:THR196 4.3 29.2 1.0
CG A:GLU20 4.4 27.7 1.0
CB A:ASP18 4.4 28.5 1.0
O5' A:TMP1000 4.4 24.1 1.0
N A:THR196 4.4 29.5 1.0
C5' A:TMP1000 4.5 23.6 1.0
C A:LEU19 4.6 28.1 1.0
N A:ALA197 4.6 29.0 1.0
CA A:ALA197 4.6 28.9 1.0
O A:HOH1118 4.6 16.6 1.0
O A:HIS195 4.7 29.6 1.0
N A:HIS195 4.8 29.9 1.0
CA A:THR196 4.9 29.3 1.0
N A:LEU19 5.0 28.3 1.0
CA A:ASP200 5.0 27.5 1.0

Zinc binding site 2 out of 4 in 3b6p

Go back to Zinc Binding Sites List in 3b6p
Zinc binding site 2 out of 4 in the Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn800

b:25.6
occ:1.00
 OE2 B:GLU20 2.0 27.8 1.0
OD2 B:ASP18 2.0 28.0 1.0
OD2 B:ASP200 2.1 27.9 1.0
O3P B:TMP1000 2.2 24.4 1.0
CG B:ASP18 2.9 28.0 1.0
CD B:GLU20 3.0 28.0 1.0
CG B:ASP200 3.1 27.4 1.0
OD1 B:ASP18 3.1 27.8 1.0
P B:TMP1000 3.4 24.5 1.0
CB B:ASP200 3.5 27.3 1.0
O2P B:TMP1000 3.5 24.3 1.0
OE1 B:GLU20 3.5 27.5 1.0
O B:THR196 3.7 27.9 1.0
NA B:NA801 3.8 25.8 1.0
O B:LEU19 3.9 28.2 1.0
C B:THR196 4.0 27.9 1.0
CA B:HIS195 4.1 28.3 1.0
OD1 B:ASP200 4.2 27.6 1.0
C B:HIS195 4.2 28.2 1.0
O B:HOH1100 4.2 22.7 1.0
O1P B:TMP1000 4.2 24.6 1.0
CG B:GLU20 4.2 28.1 1.0
N B:THR196 4.3 28.1 1.0
CB B:ASP18 4.3 28.0 1.0
O B:HOH1099 4.4 24.8 1.0
N B:ALA197 4.4 27.9 1.0
O B:HOH1097 4.4 16.7 1.0
CA B:ALA197 4.5 27.9 1.0
O5' B:TMP1000 4.5 24.2 1.0
C B:LEU19 4.6 28.1 1.0
O B:HIS195 4.6 28.2 1.0
C5' B:TMP1000 4.6 24.1 1.0
CA B:THR196 4.7 27.9 1.0
N B:HIS195 4.8 28.3 1.0
CA B:ASP200 4.9 27.3 1.0

Zinc binding site 3 out of 4 in 3b6p

Go back to Zinc Binding Sites List in 3b6p
Zinc binding site 3 out of 4 in the Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn800

b:27.2
occ:1.00
 OE2 C:GLU20 2.0 27.9 1.0
OD2 C:ASP18 2.0 28.3 1.0
OD2 C:ASP200 2.1 26.9 1.0
O3P C:TMP1000 2.1 26.9 1.0
CG C:ASP18 2.9 28.2 1.0
CG C:ASP200 3.0 26.7 1.0
OD1 C:ASP18 3.0 28.1 1.0
CD C:GLU20 3.1 27.9 1.0
P C:TMP1000 3.3 26.7 1.0
CB C:ASP200 3.4 26.6 1.0
O2P C:TMP1000 3.4 26.7 1.0
OE1 C:GLU20 3.5 27.6 1.0
NA C:NA801 3.7 31.6 1.0
O C:LEU19 3.9 28.2 1.0
O C:THR196 4.0 27.6 1.0
OD1 C:ASP200 4.1 27.0 1.0
CA C:HIS195 4.1 28.0 1.0
O1P C:TMP1000 4.2 26.8 1.0
C C:HIS195 4.2 27.9 1.0
O C:HOH1103 4.2 21.8 1.0
C C:THR196 4.2 27.5 1.0
CG C:GLU20 4.3 28.1 1.0
CB C:ASP18 4.3 28.2 1.0
N C:THR196 4.4 27.7 1.0
O C:HOH1100 4.4 17.3 1.0
O5' C:TMP1000 4.5 26.9 1.0
C5' C:TMP1000 4.6 27.1 1.0
N C:ALA197 4.6 27.4 1.0
CA C:ALA197 4.6 27.4 1.0
C C:LEU19 4.6 28.2 1.0
O C:HIS195 4.7 27.9 1.0
N C:HIS195 4.8 28.1 1.0
CA C:ASP200 4.9 26.6 1.0
CA C:THR196 4.9 27.6 1.0

Zinc binding site 4 out of 4 in 3b6p

Go back to Zinc Binding Sites List in 3b6p
Zinc binding site 4 out of 4 in the Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of TREX1 in Complex with A Nucleotide and Inhibitor Ions (Sodium and Zinc) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn800

b:28.8
occ:1.00
 OE2 D:GLU20 2.0 26.5 1.0
OD2 D:ASP200 2.0 27.5 1.0
OD2 D:ASP18 2.1 27.7 1.0
O3P D:TMP1000 2.1 26.9 1.0
CG D:ASP18 2.9 28.0 1.0
CG D:ASP200 3.0 27.5 1.0
CD D:GLU20 3.0 26.6 1.0
OD1 D:ASP18 3.0 28.5 1.0
P D:TMP1000 3.4 26.9 1.0
CB D:ASP200 3.4 27.6 1.0
OE1 D:GLU20 3.5 26.5 1.0
NA D:NA801 3.6 25.8 1.0
O2P D:TMP1000 3.6 26.8 1.0
O D:LEU19 3.9 27.2 1.0
O D:THR196 3.9 29.6 1.0
O D:HOH1138 4.0 32.6 1.0
OD1 D:ASP200 4.1 27.1 1.0
CA D:HIS195 4.1 29.9 1.0
C D:THR196 4.2 29.5 1.0
O1P D:TMP1000 4.2 27.1 1.0
CG D:GLU20 4.3 26.7 1.0
C D:HIS195 4.3 29.8 1.0
CB D:ASP18 4.3 27.9 1.0
O D:HOH1132 4.3 26.6 1.0
N D:THR196 4.4 29.7 1.0
O5' D:TMP1000 4.5 26.7 1.0
CA D:ALA197 4.5 29.1 1.0
N D:ALA197 4.5 29.3 1.0
O D:HOH1134 4.5 24.4 1.0
C D:LEU19 4.6 27.3 1.0
C5' D:TMP1000 4.6 26.4 1.0
N D:HIS195 4.8 30.0 1.0
O D:HIS195 4.8 29.8 1.0
CA D:ASP200 4.9 27.7 1.0
CA D:THR196 4.9 29.6 1.0
N D:LEU19 5.0 27.6 1.0

Reference:

M.Brucet, J.Querol-Audi, K.Bertlik, J.Lloberas, I.Fita, A.Celada. Structural and Biochemical Studies of TREX1 Inhibition By Metals. Identification of A New Active Histidine Conserved in Deddh Exonucleases. Protein Sci. V. 17 2059 2008.
ISSN: ISSN 0961-8368
PubMed: 18780819
DOI: 10.1110/PS.036426.108
Page generated: Thu Oct 24 11:27:08 2024

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