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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6a46:

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

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

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 6a46

Go back to Calcium Binding Sites List in 6a46
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 6a46

Go back to Calcium Binding Sites List in 6a46
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 6a46

Go back to Calcium Binding Sites List in 6a46
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

Reference:

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
Page generated: Sat Dec 12 05:56:26 2020

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