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Calcium in PDB 3mxm: TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant

Enzymatic activity of TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant

All present enzymatic activity of TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant:
3.1.11.2;

Protein crystallography data

The structure of TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant, PDB code: 3mxm was solved by S.L.Bailey, T.Hollis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.71 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.468, 86.026, 92.790, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.3

Other elements in 3mxm:

The structure of TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant also contains other interesting chemical elements:

Iodine (I) 12 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant (pdb code 3mxm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant, PDB code: 3mxm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3mxm

Go back to Calcium Binding Sites List in 3mxm
Calcium binding site 1 out of 4 in the TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca243

b:16.3
occ:0.44
 OP1 D:DG4 2.5 16.4 1.0
OE1 B:GLU20 2.6 13.2 1.0
OD2 B:ASP18 2.6 11.8 1.0
OD2 B:ASP200 2.6 12.2 1.0
CB B:ASP200 3.4 12.3 1.0
CD B:GLU20 3.4 15.0 1.0
CG B:ASP200 3.4 13.3 1.0
CG B:ASP18 3.5 15.2 1.0
OE2 B:GLU20 3.5 15.4 1.0
OD1 B:ASP18 3.6 10.7 1.0
CA D:CA5 3.7 15.4 0.6
CA B:HIS195 3.8 16.0 1.0
P D:DG4 3.9 14.7 1.0
CD2 B:HIS195 3.9 17.5 1.0
O B:LEU19 4.1 13.8 1.0
O B:THR196 4.1 12.7 1.0
O D:HOH37 4.2 14.4 1.0
N B:HIS195 4.2 13.6 1.0
C B:HIS195 4.4 17.9 1.0
CG B:HIS195 4.5 20.3 1.0
O5' D:DG4 4.5 11.6 1.0
OP2 D:DG4 4.6 16.7 1.0
O B:HOH282 4.6 22.7 1.0
OD1 B:ASP200 4.6 15.8 1.0
C B:THR196 4.6 12.4 1.0
CB B:HIS195 4.7 17.9 1.0
N B:THR196 4.7 12.7 1.0
NE2 B:HIS195 4.7 17.7 1.0
CG B:GLU20 4.8 15.9 1.0
CA B:ASP200 4.8 12.9 1.0
C5' D:DG4 4.8 12.3 1.0
O B:HOH276 4.9 14.1 1.0
O D:HOH50 4.9 16.6 1.0
CB B:ASP18 4.9 10.4 1.0
O B:HOH252 4.9 14.4 1.0
O3' D:DC3 4.9 13.0 1.0
CA B:ALA197 4.9 9.9 1.0

Calcium binding site 2 out of 4 in 3mxm

Go back to Calcium Binding Sites List in 3mxm
Calcium binding site 2 out of 4 in the TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca243

b:19.1
occ:0.54
 OD2 A:ASP200 2.5 13.6 1.0
OP1 C:DG4 2.5 12.4 1.0
OE1 A:GLU20 2.6 10.5 1.0
OD2 A:ASP18 2.6 11.4 1.0
CG A:ASP200 3.3 13.2 1.0
CB A:ASP200 3.3 9.0 1.0
CD A:GLU20 3.4 15.0 1.0
OE2 A:GLU20 3.5 12.3 1.0
CG A:ASP18 3.5 11.3 1.0
OD1 A:ASP18 3.6 9.5 1.0
CA C:CA5 3.8 12.9 0.6
CA A:HIS195 3.9 19.3 1.0
P C:DG4 3.9 10.7 1.0
CD2 A:HIS195 3.9 29.6 1.0
O A:THR196 4.1 11.4 1.0
O C:HOH45 4.2 13.0 1.0
O A:LEU19 4.3 11.8 1.0
N A:HIS195 4.3 19.0 1.0
C A:HIS195 4.4 15.3 1.0
OD1 A:ASP200 4.5 18.2 1.0
CG A:HIS195 4.5 28.0 1.0
OP2 C:DG4 4.5 12.8 1.0
C A:THR196 4.6 10.8 1.0
O5' C:DG4 4.7 11.1 1.0
CB A:HIS195 4.7 20.3 1.0
O A:HOH464 4.7 27.5 1.0
N A:THR196 4.7 13.2 1.0
NE2 A:HIS195 4.8 30.6 1.0
CA A:ASP200 4.8 9.0 1.0
CG A:GLU20 4.8 12.9 1.0
O A:HOH257 4.9 10.2 1.0
O A:HOH260 4.9 13.3 1.0
C5' C:DG4 4.9 11.9 1.0
O3' C:DC3 4.9 9.5 1.0
CB A:ASP18 4.9 8.9 1.0
CA A:ALA197 5.0 7.7 1.0
O C:HOH32 5.0 14.2 1.0

Calcium binding site 3 out of 4 in 3mxm

Go back to Calcium Binding Sites List in 3mxm
Calcium binding site 3 out of 4 in the TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca5

b:12.9
occ:0.64
 O A:HOH255 2.4 9.1 1.0
O C:HOH45 2.4 13.0 1.0
OD1 A:ASP18 2.4 9.5 1.0
O A:HOH257 2.4 10.2 1.0
OP1 C:DG4 2.5 12.4 1.0
O3' C:DC3 2.7 9.5 1.0
P C:DG4 3.2 10.7 1.0
CG A:ASP18 3.5 11.3 1.0
CA A:CA243 3.8 19.1 0.5
C3' C:DC3 4.0 10.7 1.0
O A:HOH259 4.0 9.3 1.0
OD2 A:ASP18 4.0 11.4 1.0
O A:LEU19 4.1 11.8 1.0
O A:HOH260 4.1 13.3 1.0
OD2 A:ASP130 4.2 9.9 1.0
C4' C:DC3 4.2 11.5 1.0
C5' C:DG4 4.2 11.9 1.0
OD1 A:ASP130 4.3 11.6 1.0
O5' C:DG4 4.3 11.1 1.0
OP2 C:DG4 4.3 12.8 1.0
O C:HOH32 4.4 14.2 1.0
O A:HIS124 4.5 12.4 1.0
C5' C:DC3 4.5 10.0 1.0
CG A:ASP130 4.6 8.2 1.0
N A:LEU19 4.7 8.5 1.0
CB A:ASP18 4.7 8.9 1.0
C2' C:DC3 4.8 10.1 1.0
CA A:ASP18 5.0 9.2 1.0

Calcium binding site 4 out of 4 in 3mxm

Go back to Calcium Binding Sites List in 3mxm
Calcium binding site 4 out of 4 in the TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of TREX1 3' Exonuclease V201D Aicardi-Goutieres Syndrome Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca5

b:15.4
occ:0.61
 O D:HOH37 2.4 14.4 1.0
OD1 B:ASP18 2.4 10.7 1.0
O B:HOH256 2.4 11.8 1.0
OP1 D:DG4 2.4 16.4 1.0
O B:HOH252 2.5 14.4 1.0
O3' D:DC3 2.7 13.0 1.0
P D:DG4 3.2 14.7 1.0
CG B:ASP18 3.5 15.2 1.0
CA B:CA243 3.7 16.3 0.4
O B:HOH251 4.0 11.8 1.0
OD2 B:ASP18 4.0 11.8 1.0
C3' D:DC3 4.0 11.1 1.0
O B:HOH276 4.1 14.1 1.0
O B:LEU19 4.1 13.8 1.0
C4' D:DC3 4.2 11.0 1.0
OD2 B:ASP130 4.2 12.7 1.0
OP2 D:DG4 4.2 16.7 1.0
O D:HOH50 4.2 16.6 1.0
O5' D:DG4 4.3 11.6 1.0
OD1 B:ASP130 4.3 13.9 1.0
C5' D:DG4 4.3 12.3 1.0
C5' D:DC3 4.4 13.5 1.0
O B:HIS124 4.5 14.2 1.0
CG B:ASP130 4.7 14.1 1.0
N B:LEU19 4.7 10.2 1.0
CB B:ASP18 4.7 10.4 1.0
C2' D:DC3 4.9 12.7 1.0
CA B:ASP18 5.0 8.2 1.0

Reference:

S.L.Bailey, S.Harvey, F.W.Perrino, T.Hollis. X-Ray Crystal Structures of TREX1 3' Exonuclease Autoimmune Disease Mutants To Be Published.
Page generated: Sat Jul 13 13:47:24 2024

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