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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5hrt:

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
Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Mouse Autotaxin in Complex with A Dna Aptamer, PDB code: 5hrt:

Sodium binding site 1 out of 1 in 5hrt

Go back to Sodium Binding Sites List in 5hrt
Sodium binding site 1 out of 1 in the Crystal Structure of Mouse Autotaxin in Complex with A Dna Aptamer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na915

b:30.6
occ:1.00
 O A:HOH1298 2.3 27.2 1.0
O A:SER800 2.3 24.4 1.0
O A:ASN797 2.4 23.9 1.0
OG A:SER803 2.5 27.6 1.0
O A:HOH1392 2.6 40.4 1.0
O A:HOH1193 2.7 36.5 1.0
C A:ASN797 3.2 24.9 1.0
C A:SER800 3.4 27.3 1.0
CB A:SER803 3.5 27.0 1.0
CA A:ASP798 3.7 26.7 1.0
N A:ASP798 3.8 25.8 1.0
C A:ASP798 4.0 27.4 1.0
N A:SER803 4.0 30.1 1.0
N A:SER800 4.1 26.4 1.0
O A:ASP798 4.1 26.8 1.0
CA A:CYS801 4.2 31.3 1.0
CA A:SER800 4.3 26.6 1.0
N A:CYS801 4.3 25.3 1.0
CB A:ASN797 4.3 21.8 1.0
CA A:ASN797 4.3 23.3 1.0
C A:CYS801 4.4 31.0 1.0
CA A:SER803 4.4 31.3 1.0
O A:HOH1191 4.5 30.2 1.0
O A:HOH1277 4.5 36.3 1.0
OD1 A:ASP798 4.5 32.2 1.0
O A:CYS801 4.6 28.1 1.0
CB A:SER800 4.7 22.5 1.0
N A:GLU799 4.7 24.4 1.0
N A:ASN802 4.9 27.6 1.0

Reference:

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
Page generated: Tue Dec 15 11:03:44 2020

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