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

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

The structure of Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-IP7, PDB code: 6pck 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)	27.38 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.411, 56.612, 62.556, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 17.3

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

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-IP7 (pdb code 6pck). 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 1-IP7, PDB code: 6pck:
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 1-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 1-IP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:15.8 occ:1.00 O A:HOH426 3.1 16.5 1.0 ND2 A:ASN86 3.1 15.0 1.0 O A:HOH322 3.1 14.4 1.0 NE2 A:GLN136 3.4 13.9 1.0 CE1 A:HIS91 3.7 12.2 1.0 CG A:GLN136 3.7 10.8 1.0 CB A:VAL135 3.9 11.6 1.0 CB A:ASN86 4.0 12.9 1.0 CD A:GLN136 4.0 11.9 1.0 CG A:ASN86 4.0 13.9 1.0 CD A:LYS133 4.2 15.4 1.0 O A:HOH405 4.3 37.4 1.0 NE2 A:HIS91 4.3 11.6 1.0 CG2 A:VAL135 4.5 13.9 1.0 N A:GLN136 4.5 10.2 1.0 CG1 A:VAL135 4.5 11.7 1.0 O A:HOH431 4.7 36.9 1.0 O A:HOH314 4.7 18.6 1.0 NZ A:LYS133 4.7 29.1 1.0 ND1 A:HIS91 4.7 11.8 1.0 O A:HOH343 4.8 11.3 1.0 OH A:TYR139 4.8 11.4 1.0 CA A:VAL135 4.8 11.3 1.0 O A:HOH469 4.9 16.8 1.0 CB A:GLN136 4.9 10.4 1.0 CE A:LYS133 5.0 22.1 1.0 N A:VAL135 5.0 10.8 1.0 C A:VAL135 5.0 10.2 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 in Complex with 1-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 1-IP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:21.5 occ:1.00 O A:HOH480 2.9 34.1 1.0 N A:GLU32 3.0 17.6 1.0 OG A:SER28 3.0 21.4 1.0 N A:SER28 3.2 14.9 1.0 N A:GLU33 3.2 14.8 1.0 OG A:SER30 3.4 25.8 0.4 N A:GLU31 3.5 18.1 1.0 CB A:ARG27 3.6 17.7 1.0 O A:SER28 3.7 17.3 1.0 CA A:GLU32 3.7 19.0 1.0 N A:ARG27 3.8 13.6 1.0 CB A:SER28 3.8 21.2 1.0 O A:GLU33 3.8 15.2 1.0 CA A:GLU31 3.8 18.8 1.0 C A:GLU31 3.8 18.3 1.0 CA A:SER28 3.9 17.4 1.0 C A:ARG27 3.9 16.2 1.0 CB A:GLU32 3.9 21.8 1.0 C A:GLU32 3.9 17.0 1.0 CA A:ARG27 4.0 15.4 1.0 C A:SER28 4.1 19.5 1.0 CA A:GLU33 4.2 13.9 1.0 CB A:GLU33 4.2 16.0 1.0 C A:SER30 4.3 22.0 1.0 CB A:SER30 4.4 26.0 0.6 C A:GLU33 4.5 14.3 1.0 CB A:SER30 4.6 25.5 0.4 CB A:PHE26 4.6 13.6 1.0 N A:SER30 4.7 21.6 1.0 CG A:GLU33 4.7 23.4 1.0 CA A:SER30 4.7 25.5 0.6 CG A:GLU32 4.7 26.4 1.0 O A:HOH483 4.7 41.0 1.0 C A:PHE26 4.7 13.4 1.0 CA A:SER30 4.7 24.9 0.4 CG A:ARG27 4.7 25.9 1.0 O A:ARG27 4.9 21.4 1.0 O A:GLU31 5.0 20.5 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