Chlorine in PDB 6pcl: Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7

All present enzymatic activity of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7:
3.6.1.52;

The structure of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7, PDB code: 6pcl was solved by D.E.Dollins, J.Neubauer, J.Dong, J.D.York, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.60 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.560, 59.576, 62.358, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 16.1

The structure of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7 also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Chlorine atom in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7 (pdb code 6pcl). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7, PDB code: 6pcl:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7


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 Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl205 b:15.7 occ:1.00 O A:HOH310 3.1 14.4 1.0 O A:HOH397 3.2 15.6 1.0 ND2 A:ASN86 3.2 17.6 1.0 NE2 A:GLN136 3.6 15.4 1.0 CE1 A:HIS91 3.6 14.3 1.0 CG A:GLN136 3.7 11.1 1.0 CB A:VAL135 4.0 10.7 1.0 CD A:GLN136 4.2 12.3 1.0 CD A:LYS133 4.2 15.4 1.0 CB A:ASN86 4.2 13.7 1.0 CG A:ASN86 4.2 16.8 1.0 NE2 A:HIS91 4.2 13.7 1.0 O A:HOH437 4.3 50.0 1.0 O A:HOH412 4.3 45.5 1.0 N A:GLN136 4.5 9.4 1.0 CG1 A:VAL135 4.6 12.0 1.0 CG2 A:VAL135 4.7 12.6 1.0 O A:HOH325 4.7 23.8 1.0 CE A:LYS133 4.7 19.2 1.0 O A:HOH321 4.7 11.2 1.0 ND1 A:HIS91 4.7 12.7 1.0 OH A:TYR139 4.7 11.7 1.0 CA A:VAL135 4.9 10.6 1.0 CB A:GLN136 4.9 10.3 1.0 C A:VAL135 5.0 9.8 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7


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 Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 5-IP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl206 b:21.4 occ:1.00 O A:HOH443 2.9 37.2 1.0 OG A:SER28 3.1 21.3 1.0 N A:GLU32 3.1 18.7 1.0 N A:SER28 3.3 16.0 1.0 OG A:SER30 3.3 31.9 0.4 N A:GLU33 3.3 15.1 1.0 N A:GLU31 3.7 20.0 1.0 O A:SER28 3.7 18.0 1.0 CB A:ARG27 3.8 16.3 1.0 N A:ARG27 3.8 13.5 1.0 CB A:SER28 3.8 20.6 1.0 O A:GLU33 3.8 14.8 1.0 CA A:GLU32 3.9 19.9 1.0 CA A:SER28 3.9 18.1 1.0 CB A:GLU32 4.0 21.5 1.0 C A:ARG27 4.0 16.1 1.0 C A:GLU31 4.0 18.8 1.0 CA A:GLU31 4.0 18.3 1.0 C A:GLU32 4.0 18.4 1.0 CA A:ARG27 4.1 14.4 1.0 C A:SER28 4.1 19.7 1.0 CA A:GLU33 4.2 14.2 1.0 CB A:GLU33 4.2 16.0 1.0 C A:SER30 4.4 23.9 1.0 CB A:SER30 4.5 28.3 0.6 C A:GLU33 4.5 13.7 1.0 CB A:SER30 4.5 27.9 0.4 N A:SER30 4.7 21.6 1.0 CB A:PHE26 4.7 14.7 1.0 CA A:SER30 4.7 23.8 0.6 CG A:GLU33 4.7 21.0 1.0 CA A:SER30 4.7 24.5 0.4 C A:PHE26 4.7 13.0 1.0 CG A:GLU32 4.9 25.8 1.0 CG A:ARG27 5.0 22.2 1.0

D.E.Dollins, W.Bai, P.C.Fridy, J.C.Otto, J.L.Neubauer, S.G.Gattis, K.P.M.Mehta, J.D.York. VIP1 Is A Kinase and Pyrophosphatase Switch That Regulates Inositol Diphosphate Signaling. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
PubMed: 32303658
DOI: 10.1073/PNAS.1908875117