Calcium in PDB 6a46: Structure of TREX2 in Complex with A Nucleotide (Dcmp)

All present enzymatic activity of Structure of TREX2 in Complex with A Nucleotide (Dcmp):
3.1.11.2;

The structure of Structure of TREX2 in Complex with A Nucleotide (Dcmp), PDB code: 6a46 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)	28.86 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.808, 54.773, 88.716, 90.00, 100.76, 90.00
R / Rfree (%)	19.3 / 22.8

The structure of Structure of TREX2 in Complex with A Nucleotide (Dcmp) also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Structure of TREX2 in Complex with A Nucleotide (Dcmp) (pdb code 6a46). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of TREX2 in Complex with A Nucleotide (Dcmp), PDB code: 6a46:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of TREX2 in Complex with A Nucleotide (Dcmp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of TREX2 in Complex with A Nucleotide (Dcmp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:58.2 occ:1.00 H A:LEU172 2.5 37.5 1.0 HD2 A:HIS117 3.0 31.9 1.0 HB2 A:SER171 3.1 43.6 1.0 HA A:SER171 3.2 39.9 1.0 N A:LEU172 3.3 31.3 1.0 HB2 A:LEU172 3.5 36.8 1.0 O A:HOH460 3.5 36.4 1.0 O A:HOH414 3.6 48.2 1.0 CA A:SER171 3.8 33.2 1.0 CB A:SER171 3.8 36.4 1.0 CD2 A:HIS117 3.9 26.6 1.0 HB3 A:LEU172 3.9 36.8 1.0 CB A:LEU172 4.1 30.6 1.0 C A:SER171 4.1 32.8 1.0 HB3 A:SER171 4.2 43.6 1.0 HE2 A:HIS117 4.3 32.9 1.0 CA A:LEU172 4.3 31.7 1.0 NE2 A:HIS117 4.5 27.4 1.0 H A:ALA173 4.5 39.5 1.0 HB2 A:ASN118 4.8 35.7 1.0 O A:HOH457 4.9 37.8 1.0 HA A:LEU172 4.9 38.0 1.0 OG A:SER171 4.9 38.4 1.0 O A:HOH430 5.0 38.3 1.0

Calcium binding site 2 out of 3 in the Structure of TREX2 in Complex with A Nucleotide (Dcmp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of TREX2 in Complex with A Nucleotide (Dcmp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:80.6 occ:1.00 H B:ALA96 2.7 48.7 1.0 HB2 B:ASN94 2.9 53.5 1.0 H B:GLY95 3.0 49.5 1.0 HH22 B:ARG99 3.0 62.4 1.0 N B:ALA96 3.4 40.6 1.0 HB2 B:ALA96 3.4 49.3 1.0 HH21 B:ARG99 3.5 62.4 1.0 CG B:ASN94 3.5 42.8 1.0 N B:GLY95 3.5 41.2 1.0 ND2 B:ASN94 3.5 44.7 1.0 NH2 B:ARG99 3.5 52.0 1.0 HD22 B:ASN94 3.6 53.6 1.0 HA3 B:GLY95 3.6 48.9 1.0 CB B:ASN94 3.6 44.6 1.0 HD21 B:ASN94 3.9 53.6 1.0 CA B:GLY95 3.9 40.7 1.0 OD1 B:ASN94 4.0 40.8 1.0 HB3 B:ALA96 4.0 49.3 1.0 C B:GLY95 4.1 37.7 1.0 CB B:ALA96 4.1 41.1 1.0 HB3 B:ASN94 4.3 53.5 1.0 CA B:ALA96 4.3 38.8 1.0 C B:ASN94 4.3 42.3 1.0 HA B:ALA96 4.6 46.5 1.0 CA B:ASN94 4.6 44.3 1.0 CZ B:ARG99 4.8 50.9 1.0 HA2 B:GLY95 4.8 48.9 1.0 O B:HOH429 4.9 42.4 1.0 HB1 B:ALA96 5.0 49.3 1.0 HH12 B:ARG99 5.0 65.2 1.0

Calcium binding site 3 out of 3 in the Structure of TREX2 in Complex with A Nucleotide (Dcmp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of TREX2 in Complex with A Nucleotide (Dcmp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:73.6 occ:1.00 NE2 B:HIS177 2.4 81.5 1.0 HE1 B:HIS177 3.0 98.4 1.0 CE1 B:HIS177 3.0 82.0 1.0 CD2 B:HIS177 3.5 77.6 1.0 HD2 B:HIS177 3.9 93.1 1.0 ND1 B:HIS177 4.2 79.0 1.0 CG B:HIS177 4.5 75.1 1.0 HA B:GLN181 4.6 95.5 1.0 HD1 B:HIS177 4.8 94.8 1.0 HB3 B:GLN181 4.9 0.8 1.0

H.L.Cheng, C.T.Lin, K.W.Huang, S.Wang, Y.T.Lin, S.I.Toh, Y.Y.Hsiao. Structural Insights Into the Duplex Dna Processing of TREX2 Nucleic Acids Res. V. 46 12166 2018.
ISSN: ESSN 1362-4962
PubMed: 30357414
DOI: 10.1093/NAR/GKY970