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Zinc 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
Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Mouse Autotaxin in Complex with A Dna Aptamer, PDB code: 5hrt:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5hrt

Go back to Zinc Binding Sites List in 5hrt
Zinc 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 Zinc with other atoms in the Zn 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:Zn912

b:27.6
occ:1.00
OD1 A:ASP171 1.9 32.6 1.0
OG1 A:THR209 2.0 31.9 1.0
OD2 A:ASP358 2.1 24.3 1.0
NE2 A:HIS359 2.1 22.4 1.0
CG A:ASP171 2.6 30.3 1.0
OD2 A:ASP171 2.9 34.5 1.0
CD2 A:HIS359 2.9 17.9 1.0
CB A:THR209 2.9 28.7 1.0
CG A:ASP358 3.0 22.8 1.0
CE1 A:HIS359 3.1 18.4 1.0
OD1 A:ASP358 3.2 21.7 1.0
CG2 A:THR209 3.3 29.8 1.0
CA A:THR209 3.3 23.8 1.0
O A:HOH1008 3.7 51.2 1.0
N A:THR209 3.9 23.9 1.0
CB A:ASP171 4.0 27.8 1.0
CG A:HIS359 4.1 20.5 1.0
ND1 A:HIS359 4.1 23.1 1.0
O A:HOH1042 4.1 33.1 1.0
N A:GLY172 4.2 23.6 1.0
CA A:ASP171 4.3 26.1 1.0
CB A:ASP358 4.3 20.3 1.0
CE1 A:HIS474 4.3 23.8 1.0
OD1 A:ASP311 4.4 25.1 1.0
C A:ASP171 4.5 27.0 1.0
CG A:ASP311 4.5 26.5 1.0
C A:LYS208 4.6 24.8 1.0
NE2 A:HIS474 4.6 20.8 1.0
C A:THR209 4.7 25.3 1.0
OD2 A:ASP311 4.7 26.4 1.0
O A:HOH1406 4.8 55.0 1.0
ZN A:ZN913 4.9 25.2 1.0

Zinc binding site 2 out of 2 in 5hrt

Go back to Zinc Binding Sites List in 5hrt
Zinc 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 Zinc with other atoms in the Zn 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
A:Zn913

b:25.2
occ:1.00
O B:HOH2206 2.0 27.9 1.0
NE2 A:HIS315 2.0 33.1 1.0
OD2 A:ASP311 2.0 26.4 1.0
NE2 A:HIS474 2.1 20.8 1.0
OD1 A:ASP311 2.6 25.1 1.0
CG A:ASP311 2.6 26.5 1.0
CD2 A:HIS315 2.9 21.8 1.0
CD2 A:HIS474 3.0 19.1 1.0
CE1 A:HIS315 3.0 27.5 1.0
CE1 A:HIS474 3.2 23.8 1.0
O A:HOH1008 3.9 51.2 1.0
OP1 B:DC2012 4.0 31.9 1.0
CG A:HIS315 4.1 26.5 1.0
ND1 A:HIS315 4.1 24.2 1.0
CB A:ASP311 4.1 25.5 1.0
O A:HOH1074 4.2 28.8 1.0
CG A:HIS474 4.2 20.3 1.0
O A:HOH1291 4.2 40.3 1.0
ND1 A:HIS474 4.2 21.9 1.0
O A:HOH1042 4.3 33.1 1.0
CE1 A:HIS359 4.4 18.4 1.0
CE A:MET361 4.4 25.2 1.0
C5' B:DC2012 4.5 27.7 1.0
NE2 A:HIS359 4.6 22.4 1.0
O A:ASP311 4.7 25.0 1.0
OD1 A:ASP171 4.8 32.6 1.0
O A:HOH1406 4.9 55.0 1.0
OG1 A:THR209 4.9 31.9 1.0
ZN A:ZN912 4.9 27.6 1.0
CA A:ASP311 5.0 25.4 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: Wed Dec 16 06:20:50 2020

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