Cobalt in PDB 5ywt: Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang

All present enzymatic activity of Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang:
3.1.11.2;

The structure of Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang, PDB code: 5ywt was solved by Y.Y.Hsiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.79 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.170, 80.350, 85.220, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 21.9

The structure of Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Cobalt atom in the Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang (pdb code 5ywt). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang, PDB code: 5ywt:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:30.7 occ:1.00 H A:ALA214 2.5 17.1 1.0 H A:GLN213 2.6 13.2 1.0 HB2 A:GLN213 2.8 18.6 1.0 O A:HOH688 2.9 31.6 1.0 HG2 A:GLN213 3.0 25.1 1.0 HB3 A:LYS211 3.0 17.7 1.0 O A:HOH680 3.0 25.9 1.0 HD2 A:PRO212 3.1 17.9 1.0 HA A:LYS211 3.2 15.2 1.0 N A:GLN213 3.2 14.9 1.0 N A:ALA214 3.3 16.9 1.0 C A:LYS211 3.4 14.9 1.0 CB A:GLN213 3.5 17.9 1.0 HB2 A:ALA214 3.5 17.7 1.0 CA A:LYS211 3.6 15.4 1.0 N A:PRO212 3.6 16.0 1.0 CG A:GLN213 3.7 20.8 1.0 HB3 A:ALA214 3.7 17.7 1.0 CB A:LYS211 3.7 16.9 1.0 CA A:GLN213 3.7 15.8 1.0 O A:LYS211 3.8 14.4 1.0 CD A:PRO212 3.8 16.9 1.0 CB A:ALA214 4.0 17.5 1.0 C A:GLN213 4.0 16.8 1.0 HG3 A:GLN213 4.0 25.1 1.0 HG2 A:LYS211 4.1 25.0 1.0 HG2 A:PRO212 4.2 18.8 1.0 C A:PRO212 4.2 15.2 1.0 CA A:ALA214 4.2 17.1 1.0 HB3 A:GLN213 4.4 18.6 1.0 CG A:LYS211 4.5 20.4 1.0 HB2 A:LYS211 4.5 17.7 1.0 CA A:PRO212 4.5 16.1 1.0 O A:HOH524 4.5 25.2 1.0 HD3 A:PRO212 4.6 17.9 1.0 CG A:PRO212 4.6 17.2 1.0 HA A:GLN213 4.7 14.4 1.0 O A:HOH588 4.7 28.3 1.0 H A:LEU215 4.7 12.5 1.0 HA A:ALA214 4.8 17.0 1.0 HD3 A:LYS211 4.8 35.6 1.0 HB1 A:ALA214 4.9 17.7 1.0 CD A:GLN213 4.9 24.1 1.0

Cobalt binding site 2 out of 3 in the Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang within 5.0Å range: probe atom residue distance (Å) B Occ A:Co303 b:31.2 occ:1.00 HE21 A:GLN12 2.3 17.5 1.0 HE2 A:HIS40 2.6 22.3 1.0 HB3 A:PRO116 2.7 20.7 1.0 O A:HOH458 3.1 28.8 1.0 NE2 A:GLN12 3.2 15.7 1.0 HG3 A:GLN12 3.4 13.9 1.0 NE2 A:HIS40 3.5 18.6 1.0 CB A:PRO116 3.5 16.9 1.0 HB2 A:PRO116 3.6 20.7 1.0 HB3 A:GLN12 3.6 11.8 1.0 HE22 A:GLN12 3.6 17.5 1.0 CG A:GLN12 4.1 13.9 1.0 CD A:GLN12 4.1 15.6 1.0 HD2 A:HIS40 4.2 21.5 1.0 O A:HOH471 4.2 29.1 1.0 HG2 A:PRO116 4.2 19.9 1.0 HG3 A:PRO116 4.2 19.9 1.0 CD2 A:HIS40 4.2 17.9 1.0 CG A:PRO116 4.2 16.2 1.0 HA3 B:GLY96 4.3 20.6 1.0 CB A:GLN12 4.3 12.6 1.0 CE1 A:HIS40 4.5 18.7 1.0 HE1 A:HIS40 4.6 22.1 1.0 HB2 A:GLN12 4.7 11.8 1.0 HA2 B:GLY96 4.7 20.6 1.0 CA A:PRO116 4.8 16.2 1.0 HA A:PRO116 4.8 19.4 1.0 HG2 A:GLN12 4.9 13.9 1.0 CA B:GLY96 5.0 17.7 1.0

Cobalt binding site 3 out of 3 in the Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of TREX1 in Complex with A Duplex Dna with 3' Overhang within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:50.7 occ:1.00 H B:GLY80 2.4 21.5 1.0 HD2 B:PRO79 2.8 20.1 1.0 HB2 B:SER78 3.0 25.3 1.0 N B:GLY80 3.2 19.7 1.0 HA3 B:GLY80 3.3 22.6 1.0 HB2 B:PRO79 3.6 22.4 1.0 CD B:PRO79 3.7 21.5 1.0 CA B:GLY80 3.8 19.8 1.0 HG B:SER78 3.8 25.4 1.0 CB B:SER78 3.9 22.1 1.0 N B:PRO79 4.0 20.3 1.0 OG B:SER78 4.0 21.6 1.0 HG2 B:PRO79 4.2 21.8 1.0 O D:HOH401 4.2 19.9 1.0 CB B:PRO79 4.3 22.6 1.0 C B:PRO79 4.3 19.4 1.0 CG B:PRO79 4.3 22.7 1.0 HA2 B:GLY80 4.3 22.6 1.0 HD3 B:PRO79 4.4 20.1 1.0 CA B:PRO79 4.4 20.4 1.0 H B:ALA81 4.5 18.1 1.0 C B:SER78 4.5 19.2 1.0 HB3 B:SER78 4.5 25.3 1.0 CA B:SER78 4.7 21.0 1.0 HA B:SER78 4.9 23.2 1.0 C B:GLY80 5.0 17.9 1.0

K.W.Huang, T.C.Liu, R.Y.Liang, L.Y.Chu, H.L.Cheng, J.W.Chu, Y.Y.Hsiao. Structural Basis For Overhang Excision and Terminal Unwinding of Dna Duplexes By TREX1 Plos Biol. V. 16 05653 2018.
ISSN: ESSN 1545-7885
PubMed: 29734329
DOI: 10.1371/JOURNAL.PBIO.2005653