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Sodium 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:

Zinc (Zn) 4 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 3b6p

Go back to Sodium Binding Sites List in 3b6p
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:22.4
occ:1.00
 O A:HOH1122 2.3 27.2 1.0
O A:HOH1117 2.4 17.9 1.0
O A:HOH1119 2.4 29.2 1.0
O3P A:TMP1000 2.4 24.5 1.0
OD1 A:ASP18 2.5 29.2 1.0
O A:HOH1124 3.4 53.0 1.0
ZN A:ZN800 3.4 28.4 1.0
P A:TMP1000 3.5 24.4 1.0
CG A:ASP18 3.6 28.6 1.0
O1P A:TMP1000 3.7 24.8 1.0
O5' A:TMP1000 3.8 24.1 1.0
O A:HOH1118 4.0 16.6 1.0
OD2 A:ASP18 4.1 28.5 1.0
C5' A:TMP1000 4.1 23.6 1.0
OD2 A:ASP130 4.2 28.4 1.0
O A:HOH1121 4.2 22.0 1.0
OD1 A:ASP130 4.2 28.3 1.0
O A:HIS124 4.3 27.3 1.0
O A:LEU19 4.3 28.0 1.0
OD2 A:ASP200 4.4 27.5 1.0
O A:HOH1120 4.5 35.3 1.0
CG A:ASP130 4.7 28.0 1.0
O2P A:TMP1000 4.8 24.3 1.0
O A:HOH1123 4.8 34.1 1.0
CB A:ASP18 4.8 28.5 1.0
N A:LEU19 5.0 28.3 1.0

Sodium binding site 2 out of 4 in 3b6p

Go back to Sodium Binding Sites List in 3b6p
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:25.8
occ:1.00
 O B:HOH1101 2.3 27.5 1.0
O B:HOH1097 2.4 16.7 1.0
OD1 B:ASP18 2.6 27.8 1.0
O B:HOH1100 2.6 22.7 1.0
O3P B:TMP1000 2.6 24.4 1.0
P B:TMP1000 3.6 24.5 1.0
CG B:ASP18 3.7 28.0 1.0
O1P B:TMP1000 3.8 24.6 1.0
ZN B:ZN800 3.8 25.6 1.0
O5' B:TMP1000 3.9 24.2 1.0
O B:HOH1099 4.0 24.8 1.0
OD2 B:ASP130 4.0 28.3 1.0
O B:HIS124 4.1 27.2 1.0
C5' B:TMP1000 4.1 24.1 1.0
OD2 B:ASP18 4.2 28.0 1.0
OD1 B:ASP130 4.3 28.2 1.0
O B:LEU19 4.4 28.2 1.0
O B:HOH1079 4.4 23.1 1.0
O B:HOH1102 4.4 33.4 1.0
CG B:ASP130 4.6 28.1 1.0
O B:HOH1098 4.6 24.1 1.0
OD2 B:ASP200 4.7 27.9 1.0
CB B:ASP18 5.0 28.0 1.0
O2P B:TMP1000 5.0 24.3 1.0

Sodium binding site 3 out of 4 in 3b6p

Go back to Sodium Binding Sites List in 3b6p
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:31.6
occ:1.00
 O C:HOH1102 2.2 27.9 1.0
O C:HOH1100 2.4 17.3 1.0
O C:HOH1103 2.5 21.8 1.0
OD1 C:ASP18 2.6 28.1 1.0
O3P C:TMP1000 2.6 26.9 1.0
P C:TMP1000 3.6 26.7 1.0
ZN C:ZN800 3.7 27.2 1.0
CG C:ASP18 3.8 28.2 1.0
O1P C:TMP1000 3.8 26.8 1.0
O5' C:TMP1000 3.9 26.9 1.0
O C:HIS124 4.0 27.6 1.0
OD2 C:ASP130 4.1 29.1 1.0
C5' C:TMP1000 4.2 27.1 1.0
OD1 C:ASP130 4.2 28.9 1.0
OD2 C:ASP18 4.3 28.3 1.0
O C:HOH1101 4.3 36.5 1.0
O C:HOH1104 4.4 14.5 1.0
O C:LEU19 4.4 28.2 1.0
O C:HOH1099 4.5 25.4 1.0
CG C:ASP130 4.6 28.7 1.0
OD2 C:ASP200 4.6 26.9 1.0
O2P C:TMP1000 4.9 26.7 1.0
CB C:ASP18 5.0 28.2 1.0

Sodium binding site 4 out of 4 in 3b6p

Go back to Sodium Binding Sites List in 3b6p
Sodium 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 Sodium with other atoms in the Na 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:Na801

b:25.8
occ:1.00
 O D:HOH1136 2.3 20.1 1.0
O D:HOH1132 2.3 26.6 1.0
O D:HOH1138 2.5 32.6 1.0
O3P D:TMP1000 2.5 26.9 1.0
OD1 D:ASP18 2.6 28.5 1.0
P D:TMP1000 3.4 26.9 1.0
O D:HOH1137 3.4 58.8 1.0
O1P D:TMP1000 3.5 27.1 1.0
ZN D:ZN800 3.6 28.8 1.0
CG D:ASP18 3.7 28.0 1.0
O5' D:TMP1000 3.7 26.7 1.0
O D:HOH1134 3.8 24.4 1.0
C5' D:TMP1000 4.1 26.4 1.0
O D:HIS124 4.1 26.9 1.0
OD2 D:ASP18 4.2 27.7 1.0
O D:HOH1133 4.3 19.4 1.0
OD1 D:ASP130 4.3 27.4 1.0
OD2 D:ASP130 4.4 27.4 1.0
O D:LEU19 4.4 27.2 1.0
OD2 D:ASP200 4.6 27.5 1.0
O D:HOH1135 4.6 34.1 1.0
O2P D:TMP1000 4.8 26.8 1.0
CG D:ASP130 4.8 27.2 1.0
CB D:ASP18 5.0 27.9 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: Mon Oct 7 06:00:04 2024

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