Chlorine in PDB 6bnm: Crystal Structure of the P-REX2 pH Domain

The structure of Crystal Structure of the P-REX2 pH Domain, PDB code: 6bnm was solved by J.N.Cash, P.V.Sharma, J.J.G.Tesmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.05 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	60.105, 60.105, 86.238, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 23.2

The binding sites of Chlorine atom in the Crystal Structure of the P-REX2 pH Domain (pdb code 6bnm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the P-REX2 pH Domain, PDB code: 6bnm:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the P-REX2 pH Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the P-REX2 pH Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:27.5 occ:1.00 N A:GLY-2 3.3 34.5 1.0 C A:GLY-2 3.4 31.4 1.0 N A:GLU219 3.4 27.4 1.0 CA A:GLY-2 3.4 31.4 1.0 N A:PHE0 3.4 28.8 1.0 CB A:PHE0 3.6 27.5 1.0 O A:GLY-2 3.7 32.2 1.0 N A:GLU-1 3.7 31.7 1.0 CG A:GLU219 3.8 47.4 1.0 CA A:PHE0 3.9 27.9 1.0 C A:PHE0 4.1 25.9 1.0 CB A:GLU219 4.2 37.7 1.0 CD A:GLU219 4.3 52.6 1.0 CA A:GLU219 4.4 31.0 1.0 C A:GLU-1 4.4 32.4 1.0 OE1 A:GLU219 4.5 58.1 1.0 CA A:GLU-1 4.7 33.9 1.0 CG A:PHE0 4.7 26.3 1.0 CD2 A:PHE0 4.8 25.9 1.0 OE2 A:GLU219 5.0 59.1 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the P-REX2 pH Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the P-REX2 pH Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:35.6 occ:1.00 NH2 A:ARG360 3.2 38.3 1.0 N A:VAL307 3.2 25.1 1.0 NH1 A:ARG360 3.3 39.8 1.0 CA A:GLU306 3.6 28.4 1.0 CZ A:ARG360 3.7 40.2 1.0 CB A:GLU306 3.7 32.0 1.0 O A:VAL307 3.7 27.2 1.0 C A:GLU306 3.9 25.2 1.0 CG A:GLU306 3.9 36.8 1.0 CA A:VAL307 4.2 25.5 1.0 C A:VAL307 4.4 26.6 1.0 CB A:VAL307 4.5 25.6 1.0 O A:MET305 4.6 28.9 1.0 CD A:GLU306 4.7 43.2 1.0 O A:HOH509 4.7 50.5 1.0 N A:GLU306 4.9 26.0 1.0 CG2 A:VAL307 5.0 26.2 1.0 NE A:ARG360 5.0 42.0 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the P-REX2 pH Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the P-REX2 pH Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:37.1 occ:1.00 O A:HOH554 3.1 57.2 1.0 NZ A:LYS254 3.1 39.4 1.0 NE A:ARG263 3.3 38.1 1.0 CE2 A:TYR274 3.7 32.3 1.0 CB A:ARG297 3.7 36.5 1.0 CD A:ARG297 3.8 44.1 1.0 CE A:LYS254 3.9 36.3 1.0 NH2 A:ARG263 3.9 40.5 1.0 CG A:ARG297 4.0 38.7 1.0 CZ A:ARG263 4.1 39.3 1.0 CD A:LYS254 4.1 31.9 1.0 CD2 A:TYR274 4.1 32.0 1.0 CD A:ARG263 4.1 35.4 1.0 CG A:ARG263 4.7 35.6 1.0 NE A:ARG297 4.8 49.1 1.0 CZ A:TYR274 4.8 33.0 1.0 OG A:SER256 4.8 65.3 1.0 CA A:ARG297 4.9 34.5 1.0 O A:ARG297 4.9 34.7 1.0 NE2 A:GLN261 5.0 66.7 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the P-REX2 pH Domain


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the P-REX2 pH Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:38.3 occ:1.00 NH2 A:ARG363 3.1 31.4 1.0 O A:HOH516 3.2 33.3 1.0 NH1 A:ARG363 3.2 29.1 1.0 CZ A:ARG363 3.6 32.5 1.0 CG A:ARG360 3.9 39.3 1.0 NE A:ARG360 4.0 42.0 1.0 O A:THR302 4.0 24.8 1.0 O A:HOH527 4.1 34.1 1.0 CA A:GLU303 4.1 33.7 1.0 CD A:ARG360 4.2 41.9 1.0 O A:GLU303 4.4 34.1 1.0 CE A:LYS364 4.4 71.8 1.0 C A:GLU303 4.6 31.7 1.0 C A:THR302 4.7 27.4 1.0 N A:GLU303 4.7 29.6 1.0 CZ A:ARG360 4.8 40.2 1.0 CB A:ARG360 4.8 34.1 1.0 NE A:ARG363 4.9 32.1 1.0 NZ A:LYS364 5.0 74.8 1.0

J.N.Cash, P.V.Sharma, J.J.G.Tesmer. Structural and Biochemical Characterization of the Pleckstrin Homology Domain of the Rhogef P-REX2 and Its Regulation By PIP3. J.Struct.Biol. V. 1 2019.
ISSN: ESSN 1095-8657
DOI: 10.1016/J.YJSBX.2018.100001