Atomistry » Calcium » PDB 2o8o-2ovu » 2oa8
Atomistry »
  Calcium »
    PDB 2o8o-2ovu »
      2oa8 »

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

Enzymatic activity of Crystal Structure of MTREX1 with Ssdna

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

Protein crystallography data

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

Calcium Binding Sites:

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 2oa8

Go back to Calcium Binding Sites List in 2oa8
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 2oa8

Go back to Calcium Binding Sites List in 2oa8
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 2oa8

Go back to Calcium Binding Sites List in 2oa8
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 2oa8

Go back to Calcium Binding Sites List in 2oa8
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

Reference:

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
Page generated: Sat Dec 12 03:48:27 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy