Calcium in PDB 2oa8: Crystal Structure of MTREX1 with Ssdna

All present enzymatic activity of Crystal Structure of MTREX1 with Ssdna:
3.1.11.2;

The structure of Crystal Structure of MTREX1 with Ssdna, PDB code: 2oa8 was solved by U.De Silva, T.Hollis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.90 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.850, 57.141, 68.470, 90.00, 107.47, 90.00
R / Rfree (%)	19.2 / 25.9

The binding sites of Calcium atom in the Crystal Structure of MTREX1 with Ssdna (pdb code 2oa8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of MTREX1 with Ssdna, PDB code: 2oa8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of MTREX1 with Ssdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of MTREX1 with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:40.3 occ:1.00 O B:HOH329 2.1 33.9 1.0 O B:HOH418 2.3 29.4 1.0 OD1 B:ASP18 2.4 48.2 1.0 O B:HOH330 2.5 38.7 1.0 OP1 C:DG4 2.6 28.3 1.0 O3' C:DC3 2.8 34.5 1.0 CA B:CA301 3.1 82.2 1.0 P C:DG4 3.2 30.8 1.0 CG B:ASP18 3.6 42.6 1.0 C3' C:DC3 4.0 36.1 1.0 O C:HOH128 4.0 48.0 1.0 O B:HOH332 4.1 22.2 1.0 O B:HOH302 4.1 25.3 1.0 C4' C:DC3 4.1 33.4 1.0 O B:LEU19 4.2 40.0 1.0 OP2 C:DG4 4.2 33.9 1.0 O5' C:DG4 4.3 31.8 1.0 OD2 B:ASP18 4.3 45.5 1.0 OD2 B:ASP130 4.3 47.2 1.0 C5' C:DG4 4.3 28.4 1.0 C5' C:DC3 4.3 30.4 1.0 OD1 B:ASP130 4.3 50.5 1.0 OD2 B:ASP200 4.4 43.2 1.0 O C:HOH97 4.4 30.0 1.0 O B:HIS124 4.6 38.4 1.0 CB B:ASP18 4.6 39.5 1.0 CG B:ASP130 4.8 45.2 1.0 OE1 B:GLU20 4.8 46.5 1.0 CB B:ASP200 4.9 39.1 1.0 C2' C:DC3 5.0 36.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of MTREX1 with Ssdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of MTREX1 with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca401 b:54.2 occ:1.00 OD1 A:ASP18 2.3 35.9 1.0 OP1 D:DG4 2.4 30.2 1.0 O A:HOH406 2.4 39.6 1.0 O A:HOH471 2.5 26.2 1.0 O A:HOH430 2.6 30.7 1.0 O3' D:DC3 2.8 31.2 1.0 P D:DG4 3.2 33.1 1.0 CG A:ASP18 3.6 35.8 1.0 CA A:CA402 3.6 56.4 1.0 C3' D:DC3 4.0 33.8 1.0 C4' D:DC3 4.1 31.1 1.0 O D:HOH59 4.2 40.8 1.0 OD2 A:ASP200 4.2 50.1 1.0 O A:HOH410 4.2 29.6 1.0 OD2 A:ASP130 4.3 32.2 1.0 OD2 A:ASP18 4.3 42.0 1.0 O A:LEU19 4.3 35.6 1.0 OP2 D:DG4 4.3 36.6 1.0 O A:HOH431 4.3 32.0 1.0 C5' D:DG4 4.3 30.7 1.0 O5' D:DG4 4.3 30.2 1.0 C5' D:DC3 4.4 30.1 1.0 OE1 A:GLU20 4.5 43.2 1.0 OD1 A:ASP130 4.5 33.8 1.0 O A:HIS124 4.6 36.0 1.0 CB A:ASP18 4.6 33.5 1.0 CG A:ASP130 4.8 36.6 1.0 N A:LEU19 4.9 34.4 1.0 C2' D:DC3 4.9 31.4 1.0 CA A:ASP18 4.9 33.7 1.0 CB A:ASP200 5.0 38.2 1.0 CG A:ASP200 5.0 41.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of MTREX1 with Ssdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of MTREX1 with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:56.4 occ:1.00 OD2 A:ASP200 2.0 50.1 1.0 OE1 A:GLU20 2.0 43.2 1.0 OP1 D:DG4 2.2 30.2 1.0 OE2 A:GLU20 2.7 35.9 1.0 CD A:GLU20 2.7 36.0 1.0 CG A:ASP200 3.2 41.8 1.0 CA A:HIS195 3.4 59.3 1.0 OD1 A:ASP18 3.5 35.9 1.0 P D:DG4 3.5 33.1 1.0 OD2 A:ASP18 3.5 42.0 1.0 CA D:CA401 3.6 54.2 1.0 CG A:ASP18 3.9 35.8 1.0 ND1 A:HIS195 3.9 63.7 1.0 CB A:ASP200 4.0 38.2 1.0 OD1 A:ASP200 4.1 45.5 1.0 N A:HIS195 4.1 61.4 1.0 OP2 D:DG4 4.1 36.6 1.0 CB A:HIS195 4.1 60.2 1.0 CG A:HIS195 4.2 62.8 1.0 CG A:GLU20 4.2 37.6 1.0 O5' D:DG4 4.2 30.2 1.0 C A:HIS195 4.3 56.7 1.0 C5' D:DG4 4.3 30.7 1.0 O A:LEU19 4.5 35.6 1.0 O A:THR196 4.6 45.4 1.0 O3' D:DC3 4.6 31.2 1.0 O A:HOH471 4.7 26.2 1.0 CE1 A:HIS195 4.8 63.9 1.0 O A:HIS195 4.8 56.9 1.0 O A:HOH430 4.9 30.7 1.0 C A:THR196 5.0 46.8 1.0 N A:THR196 5.0 53.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of MTREX1 with Ssdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of MTREX1 with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:82.2 occ:1.00 O C:HOH97 1.9 30.0 1.0 OE1 B:GLU20 2.2 46.5 1.0 OD2 B:ASP200 2.2 43.2 1.0 OP1 C:DG4 2.3 28.3 1.0 OD1 B:ASP18 2.7 48.2 1.0 OD2 B:ASP18 2.9 45.5 1.0 CD B:GLU20 3.1 42.7 1.0 CA C:CA302 3.1 40.3 1.0 CG B:ASP18 3.2 42.6 1.0 OE2 B:GLU20 3.2 43.4 1.0 CG B:ASP200 3.3 41.7 1.0 O B:HOH313 3.4 51.3 1.0 CB B:ASP200 3.7 39.1 1.0 O B:HOH418 3.7 29.4 1.0 P C:DG4 3.7 30.8 1.0 O B:LEU19 4.2 40.0 1.0 O B:HOH330 4.4 38.7 1.0 OD1 B:ASP200 4.4 44.8 1.0 O5' C:DG4 4.4 31.8 1.0 CG B:GLU20 4.5 37.3 1.0 OP2 C:DG4 4.5 33.9 1.0 O3' C:DC3 4.6 34.5 1.0 C5' C:DG4 4.6 28.4 1.0 CB B:ASP18 4.7 39.5 1.0 O B:THR196 4.7 39.1 1.0 C B:LEU19 4.8 38.4 1.0 O C:HOH128 4.9 48.0 1.0 CA B:ALA197 5.0 37.9 1.0

U.De Silva, S.Choudhury, S.L.Bailey, S.Harvey, F.W.Perrino, T.Hollis. The Crystal Structure of TREX1 Explains the 3' Nucleotide Specificity and Reveals A Polyproline II Helix For Protein Partnering. J.Biol.Chem. V. 282 10537 2007.
ISSN: ISSN 0021-9258
PubMed: 17293595
DOI: 10.1074/JBC.M700039200