Bromine in PDB 5awx: Crystal Structure of Human Ptprz D1 Domain

All present enzymatic activity of Crystal Structure of Human Ptprz D1 Domain:
3.1.3.48;

The structure of Crystal Structure of Human Ptprz D1 Domain, PDB code: 5awx was solved by H.Sugawara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.40 / 1.86
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.641, 72.245, 90.557, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.1

The binding sites of Bromine atom in the Crystal Structure of Human Ptprz D1 Domain (pdb code 5awx). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of Human Ptprz D1 Domain, PDB code: 5awx:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of Human Ptprz D1 Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Human Ptprz D1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3001 b:33.8 occ:1.00 O A:HOH3273 2.6 34.9 1.0 O A:HOH3285 3.2 16.3 1.0 NZ A:LYS1836 3.3 36.3 1.0 N A:SER1934 3.4 10.7 1.0 CB A:SER1934 3.5 13.4 1.0 O A:HOH3241 3.7 11.4 1.0 SG A:CYS1933 3.8 11.9 1.0 CB A:CYS1933 3.9 11.4 1.0 NE A:ARG1939 3.9 13.7 1.0 CA A:SER1934 4.0 12.8 1.0 CD A:ARG1939 4.0 14.1 1.0 CZ A:ARG1939 4.1 14.5 1.0 N A:ALA1935 4.2 11.1 1.0 O A:HOH3161 4.3 16.8 1.0 CE A:LYS1836 4.4 31.5 1.0 NH1 A:ARG1939 4.4 14.9 1.0 C A:CYS1933 4.5 10.8 1.0 O A:HOH3267 4.5 17.1 1.0 CG A:ARG1939 4.5 13.0 1.0 C A:SER1934 4.6 11.8 1.0 NH2 A:ARG1939 4.7 15.0 1.0 CA A:CYS1933 4.7 9.8 1.0 OG A:SER1934 4.8 15.5 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of Human Ptprz D1 Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Human Ptprz D1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3002 b:46.4 occ:1.00 O A:HOH3131 3.3 33.4 1.0 O A:HOH3306 3.3 32.8 1.0 NE2 A:GLN1971 3.7 27.9 1.0 CB A:SER1765 3.8 15.9 1.0 CA A:SER1765 4.0 14.7 1.0 CB A:TYR1787 4.2 13.9 1.0 CE A:LYS1795 4.2 36.5 1.0 O A:TYR1787 4.4 13.4 1.0 CG A:LYS1795 4.5 24.2 1.0 O A:HIS1764 4.5 16.5 1.0 CD A:GLN1971 4.8 20.8 1.0 O A:SER1765 4.9 14.7 1.0 C A:TYR1787 4.9 12.3 1.0 CD A:LYS1795 4.9 27.0 1.0 O A:HOH3294 4.9 35.8 1.0 CG A:GLN1971 5.0 19.5 1.0 N A:SER1765 5.0 13.8 1.0 C A:SER1765 5.0 13.4 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of Human Ptprz D1 Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Human Ptprz D1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3003 b:60.4 occ:1.00 ND2 A:ASN1851 3.3 51.0 1.0 O A:HOH3303 3.5 32.9 1.0 O A:HOH3126 3.6 21.9 1.0 CD A:ARG1813 3.9 13.7 1.0 CE2 A:PHE1852 4.2 19.7 1.0 CZ A:PHE1852 4.2 18.6 1.0 CG A:ASN1851 4.3 43.0 1.0 CB A:ASN1851 4.3 32.9 1.0 ND2 A:ASN1874 4.6 29.8 1.0 CD2 A:LEU1772 4.8 19.4 1.0 NE A:ARG1813 4.8 14.5 1.0 CG A:ARG1813 4.9 12.9 1.0 CD A:LYS1876 4.9 65.9 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of Human Ptprz D1 Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Human Ptprz D1 Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3004 b:51.1 occ:1.00 O A:HOH3240 2.9 28.7 1.0 NH2 A:ARG1755 3.2 14.8 1.0 NH1 A:ARG1755 3.5 15.6 1.0 CB A:ASP1838 3.5 22.8 1.0 N A:ASP1838 3.5 15.8 1.0 CZ A:ARG1755 3.8 13.9 1.0 CA A:ASP1838 3.8 19.6 1.0 CD A:ARG1835 3.8 22.0 1.0 CG A:ARG1835 3.9 21.4 1.0 C A:CYS1837 4.0 15.5 1.0 CA A:LEU1804 4.0 13.0 1.0 CD2 A:LEU1804 4.1 16.1 1.0 O A:PRO1803 4.3 12.9 1.0 O A:CYS1837 4.5 15.1 1.0 CG A:ASP1838 4.5 29.8 1.0 NE A:ARG1835 4.5 21.9 1.0 N A:LYS1805 4.5 17.5 1.0 CA A:CYS1837 4.6 14.3 1.0 CB A:LEU1804 4.7 13.7 1.0 OD1 A:ASP1838 4.7 41.2 1.0 C A:LEU1804 4.7 14.8 1.0 CG A:LEU1804 4.8 15.2 1.0 N A:CYS1837 4.8 13.6 1.0 N A:LEU1804 5.0 12.5 1.0

A.Fujikawa, A.Nagahira, H.Sugawara, K.Ishii, S.Imajo, M.Matsumoto, K.Kuboyama, R.Suzuki, N.Tanga, M.Noda, S.Uchiyama, T.Tomoo, A.Ogata, M.Masumura, M.Noda. Small-Molecule Inhibition of Ptprz Reduces Tumor Growth in A Rat Model of Glioblastoma Sci Rep V. 6 20473 2016.
ISSN: ESSN 2045-2322
PubMed: 26857455
DOI: 10.1038/SREP20473