Calcium in PDB 5hrt: Crystal Structure of Mouse Autotaxin in Complex with A Dna Aptamer

All present enzymatic activity of Crystal Structure of Mouse Autotaxin in Complex with A Dna Aptamer:
3.1.4.39;

The structure of Crystal Structure of Mouse Autotaxin in Complex with A Dna Aptamer, PDB code: 5hrt was solved by K.Kato, H.Nishimasu, J.Morita, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.15 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	120.062, 208.757, 90.036, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.2

The structure of Crystal Structure of Mouse Autotaxin in Complex with A Dna Aptamer also contains other interesting chemical elements:

Potassium	(K)	1 atom
Zinc	(Zn)	2 atoms
Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Mouse Autotaxin in Complex with A Dna Aptamer (pdb code 5hrt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Mouse Autotaxin in Complex with A Dna Aptamer, PDB code: 5hrt:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Mouse Autotaxin in Complex with A Dna Aptamer


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 Mouse Autotaxin in Complex with A Dna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca914 b:22.2 occ:1.00 O A:LEU741 2.3 22.9 1.0 OD1 A:ASP735 2.3 19.2 1.0 OD1 A:ASN737 2.4 23.6 1.0 OD1 A:ASN739 2.4 20.4 1.0 O A:HOH1155 2.4 26.2 1.0 CB A:ASP743 3.2 43.6 1.0 CG A:ASN739 3.4 23.7 1.0 CG A:ASN737 3.4 25.6 1.0 CG A:ASP735 3.4 22.6 1.0 C A:LEU741 3.5 22.4 1.0 CA A:ASP743 3.8 36.0 1.0 ND2 A:ASN737 3.9 28.1 1.0 ND2 A:ASN739 3.9 25.7 1.0 CA A:ASP735 3.9 20.4 1.0 N A:ASP743 4.0 28.6 1.0 N A:LEU741 4.0 22.9 1.0 C A:ARG742 4.1 25.4 1.0 CG A:ASP743 4.1 42.8 1.0 O A:ARG742 4.1 23.6 1.0 CB A:ASP735 4.2 17.8 1.0 N A:ASN739 4.2 21.8 1.0 CA A:LEU741 4.2 21.2 1.0 OD1 A:ASP743 4.3 35.0 1.0 OD2 A:ASP735 4.4 20.3 1.0 OE2 A:GLU747 4.4 35.4 1.0 O A:PHE734 4.5 21.3 1.0 C A:ASP735 4.5 21.3 1.0 CB A:LEU741 4.5 20.6 1.0 N A:ARG742 4.5 21.4 1.0 N A:ASN737 4.5 23.7 1.0 CB A:ASN739 4.6 23.0 1.0 N A:TYR738 4.7 23.0 1.0 CB A:ASN737 4.7 23.4 1.0 N A:GLY740 4.7 19.7 1.0 N A:TYR736 4.8 19.9 1.0 CA A:ASN739 4.8 21.1 1.0 CA A:ARG742 4.8 23.6 1.0 C A:ASN737 4.8 24.1 1.0 O2 A:GOL927 4.9 56.7 1.0 C A:ASN739 4.9 22.9 1.0 CA A:ASN737 4.9 23.0 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Mouse Autotaxin in Complex with A Dna Aptamer


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 Mouse Autotaxin in Complex with A Dna Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2101 b:49.8 occ:1.00 O B:HOH2213 2.3 44.2 1.0 OP2 B:DG2025 2.3 63.5 1.0 O B:HOH2207 2.4 45.3 1.0 O6 B:OMG2009 2.5 52.4 1.0 O B:HOH2215 2.5 43.3 1.0 O B:HOH2214 2.5 52.7 1.0 O B:HOH2218 2.7 43.0 1.0 C6 B:OMG2009 3.5 50.2 1.0 P B:DG2025 3.7 64.9 1.0 N7 B:OMG2009 4.1 49.5 1.0 C5 B:OMG2009 4.1 48.1 1.0 O5' B:DG2025 4.3 62.8 1.0 O B:HOH2201 4.3 48.6 1.0 N7 B:DG2008 4.3 53.0 1.0 C2' B:DT2024 4.4 54.3 1.0 C5 B:DG2008 4.4 54.5 1.0 C3' B:DT2024 4.5 61.1 1.0 C6 B:DG2008 4.6 50.1 1.0 N1 B:OMG2009 4.6 47.8 1.0 O3' B:DT2024 4.7 64.4 1.0 O6 B:DG2008 4.7 52.5 1.0 OP1 B:DG2025 4.7 69.8 1.0 CD1 A:LEU458 4.7 68.6 1.0 C8 B:DG2008 4.8 52.4 1.0 C8 B:DG2025 4.9 45.7 1.0 C4 B:DG2008 5.0 47.5 1.0

K.Kato, H.Ikeda, S.Miyakawa, S.Futakawa, Y.Nonaka, M.Fujiwara, S.Okudaira, K.Kano, J.Aoki, J.Morita, R.Ishitani, H.Nishimasu, Y.Nakamura, O.Nureki. Structural Basis For Specific Inhibition of Autotaxin By A Dna Aptamer Nat.Struct.Mol.Biol. V. 23 395 2016.
ISSN: ESSN 1545-9985
PubMed: 27043297
DOI: 10.1038/NSMB.3200